Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005421.1 Hibiscus syriacus cultivar Beakdansim tig00012435_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: 109268
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5454 original size:11 final size:11
Alignment explanation
Indices: 5438--5467 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5428 CTTTAAAATG
5438 AAAAAAATATA
1 AAAAAAATATA
5449 AAAAAAATATA
1 AAAAAAATATA
5460 AAAAAAAT
1 AAAAAAAT
5468 TACGAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATATA
Found at i:5601 original size:18 final size:19
Alignment explanation
Indices: 5559--5598 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5549 TTTGGTTCAC
*
5559 GGAATGTAAAATTATCAGTG
1 GGAATGTAAAATTACCAG-G
*
5579 GGAATGTAAGATTACCAGG
1 GGAATGTAAAATTACCAGG
5598 G
1 G
5599 AATAAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.38, C:0.07, G:0.30, T:0.25
Consensus pattern (19 bp):
GGAATGTAAAATTACCAGG
Found at i:17626 original size:2 final size:2
Alignment explanation
Indices: 17619--17652 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17609 AAGATGTTAT
17619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17653 AAGTAGAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21637 original size:28 final size:28
Alignment explanation
Indices: 21542--21629 Score: 142
Period size: 28 Copynumber: 3.1 Consensus size: 28
21532 ATATTTTTTA
*
21542 TTAAAAAAACCCAAAAATTTTGAAAATC
1 TTAAAAAAACCCAAAAACTTTGAAAATC
21570 TTAAAAAAACCCAAAAACTTTGAAAATC
1 TTAAAAAAACCCAAAAACTTTGAAAATC
*
21598 TTTAAAAAAACCCAAAAA-ATTGAAAATC
1 -TTAAAAAAACCCAAAAACTTTGAAAATC
21626 TTAA
1 TTAA
21630 TTTCAACCTA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
27 4 0.07
28 36 0.63
29 17 0.30
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (28 bp):
TTAAAAAAACCCAAAAACTTTGAAAATC
Found at i:28285 original size:17 final size:17
Alignment explanation
Indices: 28263--28297 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28253 ACCTGTTGCT
28263 CTTCCTGCTCATATATC
1 CTTCCTGCTCATATATC
28280 CTTCCTGCTCATATATC
1 CTTCCTGCTCATATATC
28297 C
1 C
28298 ATCTAGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (17 bp):
CTTCCTGCTCATATATC
Found at i:28746 original size:35 final size:35
Alignment explanation
Indices: 28695--28806 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
28685 AAAACATTCC
* *
28695 TCAATTTCATTATAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
28730 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
28765 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
28800 TCAATTT
1 TCAATTT
28807 AAGGAGGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:29911 original size:35 final size:34
Alignment explanation
Indices: 29856--29967 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
29846 AAAAAGACAG
* * *
29856 AAATTAAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGG-TTTAGAATA
*
29891 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTT-GGGTTTAGAATA
* *
29926 AAATTGAATTACTTTGGAATTTGTGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTTG-GGTTTAGAATA
29961 AAATTGA
1 AAATTGA
29968 GGATTGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.94
36 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTAGAATTTGGGTTTAGAATA
Found at i:30140 original size:29 final size:29
Alignment explanation
Indices: 30087--30142 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
30077 TGCAAATGGA
* *
30087 TTAAATGTTAGGGGACTATATTGTAAGTT
1 TTAAAAGTTAGGGGACTATAATGTAAGTT
30116 TTAAAAGTTAGGGGACCTA-AATGTAAG
1 TTAAAAGTTAGGGGA-CTATAATGTAAG
30143 CTTCAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
TTAAAAGTTAGGGGACTATAATGTAAGTT
Found at i:35230 original size:35 final size:34
Alignment explanation
Indices: 35145--35231 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
35135 AAAATAATTT
*
35145 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
35179 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
35217 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
35232 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:37500 original size:17 final size:18
Alignment explanation
Indices: 37460--37497 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
37450 TTATATAAGA
*
37460 AAAATA-TTAAATAACTT
1 AAAATACTTAAATAAATT
37477 AAAATACTTAAATAAATT
1 AAAATACTTAAATAAATT
37495 AAA
1 AAA
37498 TACACAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATACTTAAATAAATT
Found at i:37831 original size:17 final size:18
Alignment explanation
Indices: 37790--37828 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
37780 ATTATATAAG
*
37790 TAAAATA-TTAAATAACT
1 TAAAATACTTAAATAAAT
37807 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
37825 TAAA
1 TAAA
37829 TACACAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:37876 original size:331 final size:331
Alignment explanation
Indices: 37274--37938 Score: 1267
Period size: 331 Copynumber: 2.0 Consensus size: 331
37264 AAAATAAATA
37274 ATTACAAAAATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATA
1 ATTACAAAAATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATA
*
37339 ATTTAAATTAAATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATATGATTTCT
66 ATTTAAATTAAATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATATAATTTCT
*
37404 ATCCAAGCGAAGTAGACCGTCTTCCATTATATTTCTGCAAAAAAAATTATATAAGAAAAATATTA
131 ATCCAAGCGAAGTAGACCGTCTTCCATTACATTTCTGCAAAAAAAATTATATAAGAAAAATATTA
37469 AATAACTTAAAATACTTAAATAAATTAAATACACAATATTAAAAATATAATAAAATATACCTTAA
196 AATAACTTAAAATACTTAAATAAATTAAATACACAATATTAAAAATATAATAAAATATACCTTAA
*
37534 ACAGAGAATATAAGAGTATTTGAGAGAAATTGAGAGAATTTGGTGTGATGAAAGTGATTGAGGAT
261 ACAGAGAATATAAGAGTATTTGAGAGAAATTGAGAGAATTTGGTGTGATGAAAGTGATTGAGCAT
37599 GAGGGT
326 GAGGGT
37605 ATTACAAAAATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATA
1 ATTACAAAAATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATA
* *
37670 ATTTAAATTAAATTAAAACATTAAAATGTTACTGTATCAGTAAAGTGTCGAGATATATAATTTCT
66 ATTTAAATTAAATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATATAATTTCT
*
37735 ATCCAAGCGAAGTAGACCGTCTTCCATTACATTTCTGCAAAAAAAATTATATAAGTAAAATATTA
131 ATCCAAGCGAAGTAGACCGTCTTCCATTACATTTCTGCAAAAAAAATTATATAAGAAAAATATTA
37800 AATAACTTAAAATACTTAAATAAATTAAATACACAATATTAAAAATATAATAAAATATACCTTAA
196 AATAACTTAAAATACTTAAATAAATTAAATACACAATATTAAAAATATAATAAAATATACCTTAA
*
37865 ACGGAGAATATAAGAGTATTTGAGAGAAATTGAGAGAATTTGGTGTGATGAAAGTGATTGAGCAT
261 ACAGAGAATATAAGAGTATTTGAGAGAAATTGAGAGAATTTGGTGTGATGAAAGTGATTGAGCAT
37930 GAGGGT
326 GAGGGT
37936 ATT
1 ATT
37939 TATAGAAAGG
Statistics
Matches: 327, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
331 327 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (331 bp):
ATTACAAAAATTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACAAATTATTACTAATA
ATTTAAATTAAATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATATAATTTCT
ATCCAAGCGAAGTAGACCGTCTTCCATTACATTTCTGCAAAAAAAATTATATAAGAAAAATATTA
AATAACTTAAAATACTTAAATAAATTAAATACACAATATTAAAAATATAATAAAATATACCTTAA
ACAGAGAATATAAGAGTATTTGAGAGAAATTGAGAGAATTTGGTGTGATGAAAGTGATTGAGCAT
GAGGGT
Found at i:52834 original size:12 final size:12
Alignment explanation
Indices: 52794--52836 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 12
52784 TCTCTTTTTC
52794 TCTTCTTTCTATTT
1 TCTTCTTTC--TTT
52808 TCTCTCTTATCTTT
1 TCT-TCTT-TCTTT
52822 TCTTCTTTCTTT
1 TCTTCTTTCTTT
52834 TCT
1 TCT
52837 CCCAACCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.30
13 4 0.15
14 9 0.33
15 4 0.15
16 2 0.07
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTTCTTT
Found at i:59514 original size:23 final size:24
Alignment explanation
Indices: 59488--59534 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
59478 AATTGAACAG
*
59488 AATAT-ATA-TAATAAATTTTAGTT
1 AATATGATATTAA-AAATTTGAGTT
59511 AATATGATATTAAAAATTTGAGTT
1 AATATGATATTAAAAATTTGAGTT
59535 TAAGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 13 0.62
25 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (24 bp):
AATATGATATTAAAAATTTGAGTT
Found at i:71299 original size:31 final size:31
Alignment explanation
Indices: 71250--71319 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
71240 TAAGGGAAAA
* **
71250 TAGTCACTAACGTTATCGATCTGTTTGAATTT
1 TAGTCCCTAACGTTATCGATCCATTTG-ATTT
*
71282 T-GTCCCTAATGTTATCGATCCATTTGATTT
1 TAGTCCCTAACGTTATCGATCCATTTGATTT
71312 TAGTCCCT
1 TAGTCCCT
71320 TAGCCGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.15
31 27 0.82
32 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.44
Consensus pattern (31 bp):
TAGTCCCTAACGTTATCGATCCATTTGATTT
Found at i:71400 original size:30 final size:31
Alignment explanation
Indices: 71348--71423 Score: 145
Period size: 30 Copynumber: 2.5 Consensus size: 31
71338 CAATTCTAGT
71348 CCCTCAACCATGTTATTTTTTTTGAATGAAA
1 CCCTCAACCATGTTATTTTTTTTGAATGAAA
71379 CCCTCAACCATGTTA-TTTTTTTGAATGAAA
1 CCCTCAACCATGTTATTTTTTTTGAATGAAA
71409 CCCTCAACCATGTTA
1 CCCTCAACCATGTTA
71424 GGGACTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 30 0.67
31 15 0.33
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (31 bp):
CCCTCAACCATGTTATTTTTTTTGAATGAAA
Found at i:71627 original size:30 final size:30
Alignment explanation
Indices: 71593--71665 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
71583 AGAATACTAA
* *
71593 TTTGACCTTGAACTTCAGATAAAATATCAT
1 TTTGACCCTAAACTTCAGATAAAATATCAT
* * *
71623 TTTGACCCTAAACTTTATATAAAATATCAA
1 TTTGACCCTAAACTTCAGATAAAATATCAT
*
71653 TTTAATCCCTAAA
1 TTTGA-CCCTAAA
71666 TTCGATCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 29 0.81
31 7 0.19
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTGACCCTAAACTTCAGATAAAATATCAT
Found at i:73174 original size:31 final size:31
Alignment explanation
Indices: 73103--73183 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
73093 AATTAACAGT
* **
73103 TAAGTGATTAAAATATAAT-AATCAATAATG
1 TAAGTGATTAAAATATAATAAATCAACAAAA
* * *
73133 TAAATAATTAAAATTTAATAAATCAACAAAA
1 TAAGTGATTAAAATATAATAAATCAACAAAA
73164 TAAGTGATTAAAATATAATA
1 TAAGTGATTAAAATATAATA
73184 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 16 0.39
31 25 0.61
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (31 bp):
TAAGTGATTAAAATATAATAAATCAACAAAA
Found at i:73659 original size:35 final size:35
Alignment explanation
Indices: 73612--73725 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 35
73602 AAAACATTCC
* * *
73612 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
73647 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * *
73682 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
73717 TCAATTTAA
1 TCAATTTAA
73726 GGTTTAGAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:75104 original size:35 final size:35
Alignment explanation
Indices: 75056--75167 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
75046 TCTAACCCTT
* * * *
75056 AAATTAAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
75091 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
75126 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
75161 AAATTGA
1 AAATTGA
75168 GGACTGTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:75399 original size:2 final size:2
Alignment explanation
Indices: 75392--75442 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
75382 ACTTTACCCT
75392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75434 TA TA TA TA T
1 TA TA TA TA T
75443 CTTTAAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89759 original size:20 final size:20
Alignment explanation
Indices: 89734--89773 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
89724 ATGTGATAAT
89734 TTGCATTATATAAAATTTAG
1 TTGCATTATATAAAATTTAG
89754 TTGCATTATATAAAATTTAG
1 TTGCATTATATAAAATTTAG
89774 GGTAAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGCATTATATAAAATTTAG
Found at i:91109 original size:31 final size:30
Alignment explanation
Indices: 91074--91131 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
91064 TTATTTTTTA
* *
91074 TTTAGTTACTCATTTATTATTTAGTTTTCGT
1 TTTAGTCACTCATCTATTATTTA-TTTTCGT
*
91105 TTTAGTCATTCATCTATTATTTATTTT
1 TTTAGTCACTCATCTATTATTTATTTT
91132 AAATCACACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (30 bp):
TTTAGTCACTCATCTATTATTTATTTTCGT
Found at i:91470 original size:2 final size:2
Alignment explanation
Indices: 91465--91489 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91455 TCTAGATTTA
91465 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 A
91490 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91907 original size:17 final size:19
Alignment explanation
Indices: 91880--91919 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
91870 TTTTTAGTAT
91880 TTTTTTAATGTTATAAT-A
1 TTTTTTAATGTTATAATAA
*
91898 TTTTTT-ATGTTTTAATAA
1 TTTTTTAATGTTATAATAA
91916 TTTT
1 TTTT
91920 AATTTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTAATGTTATAATAA
Found at i:91945 original size:19 final size:16
Alignment explanation
Indices: 91882--91938 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
91872 TTTAGTATTT
* *
91882 TTTTAATGTTATAATAT
1 TTTTAAT-TTCTAATAA
* *
91899 TTTTTATGTTTTAATAA
1 TTTTAAT-TTCTAATAA
91916 TTTTAATTTCTAATAA
1 TTTTAATTTCTAATAA
91932 TTCTTAA
1 TT-TTAA
91939 ATTTTCTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTAATTTCTAATAA
Found at i:92260 original size:20 final size:19
Alignment explanation
Indices: 92235--92287 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
92225 CATTTATATA
92235 AATTTATAATATTTTTTAT
1 AATTTATAATATTTTTTAT
* *
92254 AATTT-TAAAATTTTTAAT
1 AATTTATAATATTTTTTAT
*
92272 GAAATTATAATATTTT
1 -AATTTATAATATTTT
92288 ATGATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.39
19 9 0.32
20 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTTATAATATTTTTTAT
Found at i:94546 original size:23 final size:23
Alignment explanation
Indices: 94510--94573 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
94500 CAGCTCGTAT
94510 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
94533 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
94556 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
94574 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:94856 original size:30 final size:29
Alignment explanation
Indices: 94803--94861 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
94793 TGTAAACATA
* *
94803 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
94833 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
94862 GTATCACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:96054 original size:20 final size:20
Alignment explanation
Indices: 96022--96075 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
96012 GAAATATTGA
*
96022 TGCATCAATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
*
96042 TGTATCGATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
96062 TGCATCGATGCACC
1 TGCATCGATGCACC
96076 TTCAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACCCCTTAC
Found at i:96116 original size:21 final size:21
Alignment explanation
Indices: 96092--96146 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
96082 ATTTGTCTTG
* *
96092 GTGCATCGGTGCACACTCATA
1 GTGCATCGATACACACTCATA
96113 GTGCATCGATACACACTCATA
1 GTGCATCGATACACACTCATA
96134 GTGCATCGATACA
1 GTGCATCGATACA
96147 TTCATGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
GTGCATCGATACACACTCATA
Found at i:98410 original size:64 final size:64
Alignment explanation
Indices: 98334--98558 Score: 217
Period size: 64 Copynumber: 3.5 Consensus size: 64
98324 TTGTTTGAAT
* * * **
98334 GTGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-T
98397 C-
63 CG
* * *
98398 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
* ** * * * **
98462 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
*
98526 ATGCATCGATGCATCA-GTAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCAT
98559 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.02
64 125 0.93
65 7 0.05
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
Found at i:99253 original size:31 final size:31
Alignment explanation
Indices: 99215--99401 Score: 324
Period size: 31 Copynumber: 6.0 Consensus size: 31
99205 AGGGTCGAGG
99215 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
99246 GTTTACCTATGTTCTTCGGGATATATGGACG
1 GTTTACCTATGTTCTTCGGGACATATGGACT
99277 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
99308 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
99339 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
99370 GTTTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
99401 G
1 G
99402 GTCATTCGGG
Statistics
Matches: 150, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
30 1 0.01
31 148 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:101946 original size:25 final size:25
Alignment explanation
Indices: 101912--101961 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
101902 ACGAGTCTAC
101912 AATAAGAAGGTCCCGATATAGCCCT
1 AATAAGAAGGTCCCGATATAGCCCT
*
101937 AATAAGAAGGTCCCGATATATCCCT
1 AATAAGAAGGTCCCGATATAGCCCT
101962 TCAACAAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (25 bp):
AATAAGAAGGTCCCGATATAGCCCT
Found at i:102415 original size:5 final size:6
Alignment explanation
Indices: 102380--102413 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
102370 ATAATATTAA
102380 TAAATT TAAATT TAAATT TAAA-T TAAA-T TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
102414 AATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:102422 original size:2 final size:2
Alignment explanation
Indices: 102415--102505 Score: 57
Period size: 2 Copynumber: 48.0 Consensus size: 2
102405 AATTAAATTA
* * * * * *
102415 AT AT AT AT AT A- AT AT TT AT AT AT TT AA AT -T AA AT -T AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
102454 AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA 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
102494 AT AT AT AT AT AT
1 AT AT AT AT AT AT
102506 CCGACCCGAT
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
1 5 0.08
2 61 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102467 original size:37 final size:37
Alignment explanation
Indices: 102402--102505 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
102392 TAAATTTAAA
102402 TTAAATTAAATT-AATATATATATAATATTTATATAT
1 TTAAATTAAATTAAATATATATATAATATTTATATAT
*
102438 TTAAATTAAATTAAAAATATATATAATATTTATATAT
1 TTAAATTAAATTAAATATATATATAATATTTATATAT
* *
102475 TTAATTTAAATATATATATATATATATATAT
1 TTAAATTAAAT-TAAATATATATATA-ATAT
102506 CCGACCCGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 12 0.20
37 33 0.54
38 12 0.20
39 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTAAATTAAATTAAATATATATATAATATTTATATAT
Found at i:102888 original size:11 final size:11
Alignment explanation
Indices: 102872--102930 Score: 90
Period size: 11 Copynumber: 5.7 Consensus size: 11
102862 GTCCTCCTCT
102872 TGATAATTGTA
1 TGATAATTGTA
102883 TGATAATT-T-
1 TGATAATTGTA
102892 TGATAATTGTA
1 TGATAATTGTA
102903 TGATAATT-T-
1 TGATAATTGTA
102912 TGATAATTGTA
1 TGATAATTGTA
102923 TGATAATT
1 TGATAATT
102931 TTAAATAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
9 16 0.36
10 4 0.09
11 24 0.55
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (11 bp):
TGATAATTGTA
Found at i:102896 original size:20 final size:20
Alignment explanation
Indices: 102871--102932 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
102861 TGTCCTCCTC
102871 TTGATAATTGTATGATAATT
1 TTGATAATTGTATGATAATT
102891 TTGATAATTGTATGATAATT
1 TTGATAATTGTATGATAATT
102911 TTGATAATTGTATGATAATT
1 TTGATAATTGTATGATAATT
102931 TT
1 TT
102933 AAATAAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGATAATTGTATGATAATT
Found at i:103318 original size:24 final size:24
Alignment explanation
Indices: 103278--103323 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
103268 AATTGATATA
*
103278 ATTTTAAATATTAATTT-TTTTAT
1 ATTTTAAATAATAATTTGTTTTAT
*
103301 ATTTGTAAATAATGATTTGTTTT
1 ATTT-TAAATAATAATTTGTTTT
103324 CAACGTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
ATTTTAAATAATAATTTGTTTTAT
Done.