Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002294.1 Hibiscus syriacus cultivar Beakdansim tig00004665_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: 108458
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6217 original size:29 final size:28
Alignment explanation
Indices: 6160--6217 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
6150 AATTAAAATC
* **
6160 AAAATCAAAATTCAATGCTATAATTGAT
1 AAAATCAAAATTCAATGATATAAACGAT
*
6188 AAAATTAAAAGTTCAATGATATAAACGAT
1 AAAATCAAAA-TTCAATGATATAAACGAT
6217 A
1 A
6218 TAAAACCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAATCAAAATTCAATGATATAAACGAT
Found at i:16479 original size:89 final size:91
Alignment explanation
Indices: 16377--16542 Score: 291
Period size: 91 Copynumber: 1.8 Consensus size: 91
16367 TAATAGTTAA
*
16377 ATTTATTAAATTA-T-TATATTGAAAATCTATAAAATTTATATATTTAAAAGATTAAAATTGATA
1 ATTTATTAAATTATTATATATTGAAAATCTATAAAATCTATATATTTAAAAGATTAAAATTGATA
*
16440 CTATACCAAGTGAAGCCACTTTTTTC
66 CTACACCAAGTGAAGCCACTTTTTTC
16466 ATTTATTAAATTATTATATATTGAAAATCTATAAAATCTATATATTTAAAAGATTAAAATTGATA
1 ATTTATTAAATTATTATATATTGAAAATCTATAAAATCTATATATTTAAAAGATTAAAATTGATA
*
16531 CTACGCCAAGTG
66 CTACACCAAGTG
16543 GTCACTTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
89 13 0.18
90 1 0.01
91 58 0.81
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (91 bp):
ATTTATTAAATTATTATATATTGAAAATCTATAAAATCTATATATTTAAAAGATTAAAATTGATA
CTACACCAAGTGAAGCCACTTTTTTC
Found at i:29090 original size:2 final size:2
Alignment explanation
Indices: 29083--29122 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
29073 ATGGATTGCT
29083 TA TA TA TA -A TA TA -A 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
29123 ATTTACGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37298 original size:19 final size:20
Alignment explanation
Indices: 37257--37298 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
37247 CGGTAAAAAA
*
37257 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATCA-TATTT
37278 TTACCTAAAACATCA-ATTT
1 TTACCTAAAACATCATATTT
37297 TT
1 TT
37299 CTAACATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
21 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (20 bp):
TTACCTAAAACATCATATTT
Found at i:42264 original size:29 final size:30
Alignment explanation
Indices: 42221--42277 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
42211 ACTCCGTCCC
42221 TGTATATTGTGATATAT-AAATTTTAATTT
1 TGTATATTGTGATATATAAAATTTTAATTT
42250 TGTATATT-TGTATATATAAAATTTTAAT
1 TGTATATTGTG-ATATATAAAATTTTAAT
42278 ATAATCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 2 0.08
29 14 0.54
30 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (30 bp):
TGTATATTGTGATATATAAAATTTTAATTT
Found at i:43324 original size:53 final size:54
Alignment explanation
Indices: 43208--43431 Score: 230
Period size: 53 Copynumber: 4.3 Consensus size: 54
43198 GGCGTTCGCA
* *
43208 TAAGGCGTGGGCACGGCTT-TTCATCCAGAGCGA-GGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTCAGT
*
43260 TAAGGCTTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTCAGT
* * * * *
43314 TAAGG-GTGGGCACGGCTTATCCATCCCGAGCTACTGCAAAAGAA-TC-TCTACT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTC-AGT
* * * * ** * *
43366 TAAGGCGTGGG-A--ACTTATTCACCCACATCTTTCGCAGAAGAAATATTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTCAGT
*
43417 TATGGCGTGGGCACG
1 TAAGGCGTGGGCACG
43432 CCATCTATCG
Statistics
Matches: 141, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
50 20 0.14
51 15 0.11
52 31 0.22
53 52 0.37
54 23 0.16
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTACCGCAGAAGAAGTCTTCAGT
Found at i:48847 original size:34 final size:32
Alignment explanation
Indices: 48785--48847 Score: 74
Period size: 34 Copynumber: 1.9 Consensus size: 32
48775 TTGGTATACT
*
48785 TTTTAAATATAAAATACTAAAATTTTAATTTA
1 TTTTAAATATAAAATACTAAAATATTAATTTA
*
48817 TTTTAAATTATGAAAATATTAATAA-ATTAAT
1 TTTTAAA-TAT-AAAATACTAA-AATATTAAT
48848 ATAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 7 0.27
33 3 0.12
34 14 0.54
35 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (32 bp):
TTTTAAATATAAAATACTAAAATATTAATTTA
Found at i:53728 original size:54 final size:54
Alignment explanation
Indices: 53669--53777 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
53659 TGACAACTAT
53669 ATTCAAAAGAACAAAATATATATTAATCATTACTTTTTTTATATGAACTTTGTA
1 ATTCAAAAGAACAAAATATATATTAATCATTACTTTTTTTATATGAACTTTGTA
* *
53723 ATTCAAAAGAACAAAATATATATTAATCATTACTTTTTTTATTTGAATTTTGTA
1 ATTCAAAAGAACAAAATATATATTAATCATTACTTTTTTTATATGAACTTTGTA
53777 A
1 A
53778 GGGAAATGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (54 bp):
ATTCAAAAGAACAAAATATATATTAATCATTACTTTTTTTATATGAACTTTGTA
Found at i:54352 original size:30 final size:31
Alignment explanation
Indices: 54317--54436 Score: 129
Period size: 32 Copynumber: 3.9 Consensus size: 31
54307 GAATGACCTA
* *
54317 TCCATATGTTCCGAAGAACATATGTAAT-TG
1 TCCATATGTCCCGAAGAACATAGGTAATATG
54347 TCCATATGTCCCGAA-ATACATAGGTAATCATG
1 TCCATATGTCCCGAAGA-ACATAGGTAAT-ATG
* *
54379 TCCATATGTCCCGAAGGACATAGGTAA-ACTA
1 TCCATATGTCCCGAAGAACATAGGTAATA-TG
* * *
54410 TCCATATATCTCGAAAAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
54437 CTCTCGACTC
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
29 1 0.01
30 25 0.32
31 24 0.31
32 27 0.35
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAATATG
Found at i:54387 original size:62 final size:63
Alignment explanation
Indices: 54317--54436 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
54307 GAATGACCTA
* * * * * *
54317 TCCATATGTTCCGAAGAACATATGT-AATTGTCCATATGTCCCGAAATACATAGGTAATCATG
1 TCCATATGTCCCGAAGAACATAGGTAAACTATCCATATATCCCGAAAAACATAGGTAATCATG
* *
54379 TCCATATGTCCCGAAGGACATAGGTAAACTATCCATATATCTCGAAAAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAAACTATCCATATATCCCGAAAAACATAGGTAA
54437 CTCTCGACTC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 22 0.45
63 27 0.55
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (63 bp):
TCCATATGTCCCGAAGAACATAGGTAAACTATCCATATATCCCGAAAAACATAGGTAATCATG
Found at i:59223 original size:2 final size:2
Alignment explanation
Indices: 59216--59268 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
59206 TGTTCAGTGC
59216 AT 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 AT
59258 AT AT AT AT AT A
1 AT AT AT AT AT A
59269 GGAAACATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60905 original size:135 final size:135
Alignment explanation
Indices: 60661--61150 Score: 813
Period size: 135 Copynumber: 3.6 Consensus size: 135
60651 TTGTTAGATT
* * * * *
60661 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
60725 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
60789 TAGGTC
130 TAGGTC
60795 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
60860 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
60925 AGGTC
131 AGGTC
60930 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
60995 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
61060 AGGTC
131 AGGTC
* *
61065 GAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCATTATGAACT
* *
61130 CTCCATTAAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
61151 ACCTCTTTTT
Statistics
Matches: 338, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
134 32 0.09
135 259 0.77
136 47 0.14
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:62124 original size:1 final size:1
Alignment explanation
Indices: 62109--62167 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
62099 TCCTTCTTCA
* * * * * * *
62109 TTTTTTCTTTCTTTTTTTTTTTCTTTTTTTTTCTTCTTTTTATTTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62168 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:62132 original size:27 final size:26
Alignment explanation
Indices: 62102--62170 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 26
62092 CGAACCCTCC
*
62102 TTCTTCATTTTTTCTTTCTTTTTTTTT
1 TTCTT-ATTTTTTCTTTCTTTTTATTT
*
62129 TTCTTTTTTTTTC-TTCTTTTTATTT
1 TTCTTATTTTTTCTTTCTTTTTATTT
62154 TT-TTATTTTTT-TTTCTT
1 TTCTTATTTTTTCTTTCTT
62171 CAAGCATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 13 0.34
25 13 0.34
26 7 0.18
27 5 0.13
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (26 bp):
TTCTTATTTTTTCTTTCTTTTTATTT
Found at i:62149 original size:26 final size:28
Alignment explanation
Indices: 62109--62171 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
62099 TCCTTCTTCA
*
62109 TTTTTTCTT-TCTTTT-TTTTTTTCTTT
1 TTTTTTCTTCTCTTTTATTTTTTTATTT
62135 TTTTTTCTTCT-TTTTATTTTTTTATTT
1 TTTTTTCTTCTCTTTTATTTTTTTATTT
62162 TTTTTTCTTC
1 TTTTTTCTTC
62172 AAGCATAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (28 bp):
TTTTTTCTTCTCTTTTATTTTTTTATTT
Found at i:62167 original size:13 final size:13
Alignment explanation
Indices: 62109--62167 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
62099 TCCTTCTTCA
*
62109 TTTTTTCTTTC-T
1 TTTTTTTTTTCTT
62121 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
*
62134 TTTTTTTCTTCTT
1 TTTTTTTTTTCTT
*
62147 TTTATTTTTTTATT
1 TTT-TTTTTTTCTT
62161 TTTTTTT
1 TTTTTTT
62168 CTTCAAGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
12 10 0.24
13 20 0.49
14 11 0.27
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:74288 original size:2 final size:2
Alignment explanation
Indices: 74281--74319 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
74271 TGTTCAGTGC
74281 AT AT AT AT 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 AT AT AT AT A
74320 GGAAACATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77584 original size:23 final size:23
Alignment explanation
Indices: 77558--77603 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
77548 AAAGTAATAT
77558 ATTATTTTTTTAAAAAAAATTAA
1 ATTATTTTTTTAAAAAAAATTAA
* *
77581 ATTATTTTTTTAATAAATATTAA
1 ATTATTTTTTTAAAAAAAATTAA
77604 CATTTATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATTTTTTTAAAAAAAATTAA
Found at i:77701 original size:28 final size:28
Alignment explanation
Indices: 77669--77723 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
77659 AAGTTCAAAC
*
77669 TCGAA-TTTAACTTGAATCAAACATGAGT
1 TCGAATTTTAA-TAGAATCAAACATGAGT
*
77697 TCGAATTTTAATAGAATTAAACATGAG
1 TCGAATTTTAATAGAATCAAACATGAG
77724 AATATTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (28 bp):
TCGAATTTTAATAGAATCAAACATGAGT
Found at i:78011 original size:33 final size:33
Alignment explanation
Indices: 77974--78050 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
77964 AAAAATTAAT
*
77974 ATTTTAGGTAGCGATTTACCGAAAATGTTAAAC
1 ATTTTAGGTAGCGATTTACCAAAAATGTTAAAC
*
78007 ATTTTAGGTAACGATTTACCAAAAATGTTAAAC
1 ATTTTAGGTAGCGATTTACCAAAAATGTTAAAC
78040 ATTTTAGGTAG
1 ATTTTAGGTAG
78051 AACCCAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (33 bp):
ATTTTAGGTAGCGATTTACCAAAAATGTTAAAC
Found at i:80148 original size:21 final size:20
Alignment explanation
Indices: 80124--80162 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
80114 GACTCAACGA
*
80124 TTAATTCTAAAATCTAAGGAT
1 TTAATGCTAAAAT-TAAGGAT
*
80145 TTAATGCTCAAATTAAGG
1 TTAATGCTAAAATTAAGG
80163 CATTAGACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTAATGCTAAAATTAAGGAT
Found at i:80511 original size:21 final size:22
Alignment explanation
Indices: 80469--80516 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
80459 ACATAAACTA
* * *
80469 TTTAAAATTTAGATTCTGTAAT
1 TTTAAAACTTAAAATCTGTAAT
80491 TTTAAAACTTAAAATCT-TAAT
1 TTTAAAACTTAAAATCTGTAAT
80512 TTTAA
1 TTTAA
80517 GCCATAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTAAAACTTAAAATCTGTAAT
Found at i:81487 original size:34 final size:34
Alignment explanation
Indices: 81449--81515 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
81439 AGTACTGGTA
* *
81449 TATGATTGTCACCTCAAGCAATACTCCAGTACCT
1 TATGATTGTCACCGCAAGCAAAACTCCAGTACCT
*
81483 TATGATTGTCACCGCAAGCAAAATTCCAGTACC
1 TATGATTGTCACCGCAAGCAAAACTCCAGTACC
81516 CGAACTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (34 bp):
TATGATTGTCACCGCAAGCAAAACTCCAGTACCT
Found at i:83420 original size:22 final size:22
Alignment explanation
Indices: 83392--83441 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
83382 GAACTTGATG
83392 TAAAACTTGATATTAAGGTTAA
1 TAAAACTTGATATTAAGGTTAA
*
83414 TAAAACTTGATATTGAGGTTAA
1 TAAAACTTGATATTAAGGTTAA
83436 TAAAAC
1 TAAAAC
83442 GTGTGTGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (22 bp):
TAAAACTTGATATTAAGGTTAA
Found at i:106441 original size:24 final size:24
Alignment explanation
Indices: 106387--106481 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
106377 ATTTCCGACT
* *
106387 TGAATTCTGTTATGA-TACATGACC
1 TGAATTCTGTTATGATTTC-TGATC
*
106411 TAAATTCTGTTATGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
* * * *
106435 TGGATTCTGTTATGATATATGTTC
1 TGAATTCTGTTATGATTTCTGATC
* *
106459 TGAATTCTGTTTTGGTTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
106482 ATCTCCGTTT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 54 0.96
25 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:106442 original size:48 final size:48
Alignment explanation
Indices: 106390--106481 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
106380 TCCGACTTGA
106390 ATTCTGTTATGATACATGACCTAAATTCTGTTATGATTTCTGATCTGG
1 ATTCTGTTATGATACATGACCTAAATTCTGTTATGATTTCTGATCTGG
* ** * * *
106438 ATTCTGTTATGATATATGTTCTGAATTCTGTTTTGGTTTCTGAT
1 ATTCTGTTATGATACATGACCTAAATTCTGTTATGATTTCTGAT
106482 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTCTGTTATGATACATGACCTAAATTCTGTTATGATTTCTGATCTGG
Done.