Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003316.1 Hibiscus syriacus cultivar Beakdansim tig00006982_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: 69388
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12953 original size:22 final size:23
Alignment explanation
Indices: 12928--13019 Score: 61
Period size: 23 Copynumber: 4.2 Consensus size: 23
12918 CACCATAGCT
*
12928 CATAATTTGCACCGAAGTG-TCA
1 CATAATTTGCACCGAAGTGACCA
12950 CATAATTAT-C-CCGAA-TGACCA
1 CATAATT-TGCACCGAAGTGACCA
* * *
12971 CATAGTTTGCACTGAAGTG-CAA
1 CATAATTTGCACCGAAGTGACCA
** *
12993 CATAGGGTTGCACCTAAGTG-CCA
1 CATA-ATTTGCACCGAAGTGACCA
13016 CATA
1 CATA
13020 TTTATCCCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
20 3 0.05
21 14 0.25
22 18 0.32
23 21 0.38
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (23 bp):
CATAATTTGCACCGAAGTGACCA
Found at i:14457 original size:29 final size:30
Alignment explanation
Indices: 14375--14463 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
14365 AATTTAAGGC
* *
14375 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTATTTGGACTTGAATTGAATTTAA
*
14406 AAAACGTATTTGGACTTGAATTGAATTTAA
1 AAAATGTATTTGGACTTGAATTGAATTTAA
14436 AAAATGTATTTGGACTT-AATTGAATTTA
1 AAAATGTATTTGGACTTGAATTGAATTTA
14464 TTCAAAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.20
30 39 0.72
31 4 0.07
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (30 bp):
AAAATGTATTTGGACTTGAATTGAATTTAA
Found at i:14667 original size:21 final size:21
Alignment explanation
Indices: 14641--14682 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14631 ATTTGAATAT
*
14641 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
14662 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
14683 CCCATTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:15005 original size:34 final size:32
Alignment explanation
Indices: 14966--15035 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
14956 TTTTGTAAAG
*
14966 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
15000 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
15032 GGGA
1 GGGA
15036 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:33923 original size:34 final size:34
Alignment explanation
Indices: 33885--34011 Score: 123
Period size: 34 Copynumber: 3.7 Consensus size: 34
33875 AAAAAAAAAC
*
33885 ATATAATCAATCTACATAAACAAATCAACTAGGA
1 ATATAATCAATCGACATAAACAAATCAACTAGGA
* ** *
33919 ATATAATCAATGGACATAAACAAAGAAAC-A-AA
1 ATATAATCAATCGACATAAACAAATCAACTAGGA
* * * *
33951 ACCGTATACTCAATCTACATAAACAGATCGACTAGGA
1 A---TATAATCAATCGACATAAACAAATCAACTAGGA
*
33988 ATATAATCAATGGACATAAACAAA
1 ATATAATCAATCGACATAAACAAA
34012 GAAAGTACAA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
32 2 0.03
33 1 0.01
34 44 0.62
35 21 0.30
36 1 0.01
37 2 0.03
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.20
Consensus pattern (34 bp):
ATATAATCAATCGACATAAACAAATCAACTAGGA
Found at i:33985 original size:69 final size:69
Alignment explanation
Indices: 33886--34015 Score: 233
Period size: 69 Copynumber: 1.9 Consensus size: 69
33876 AAAAAAAACA
33886 TATAATCAATCTACATAAACAAATCAACTAGGAATATAATCAATGGACATAAACAAAGAAACAAA
1 TATAATCAATCTACATAAACAAATCAACTAGGAATATAATCAATGGACATAAACAAAGAAACAAA
33951 ACCG
66 ACCG
* * *
33955 TATACTCAATCTACATAAACAGATCGACTAGGAATATAATCAATGGACATAAACAAAGAAA
1 TATAATCAATCTACATAAACAAATCAACTAGGAATATAATCAATGGACATAAACAAAGAAA
34016 GTACAAAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (69 bp):
TATAATCAATCTACATAAACAAATCAACTAGGAATATAATCAATGGACATAAACAAAGAAACAAA
ACCG
Found at i:44765 original size:21 final size:21
Alignment explanation
Indices: 44739--44778 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44729 CAGAACCCTA
*
44739 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
44760 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
44779 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:44813 original size:20 final size:21
Alignment explanation
Indices: 44759--44821 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
44749 GATTCCCCTG
44759 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
44783 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
44803 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
44822 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:54434 original size:3 final size:3
Alignment explanation
Indices: 54426--54454 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54416 ATTAATTAAT
54426 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54455 GTGGGACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:59247 original size:16 final size:16
Alignment explanation
Indices: 59223--59274 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
59213 AATCAAGGTG
*
59223 AGAACAAAGAAAAGAA
1 AGAAGAAAGAAAAGAA
**
59239 AGATTAAAG-AAAGAAA
1 AGAAGAAAGAAAAG-AA
*
59255 AAAAGAAAGAAAAGAA
1 AGAAGAAAGAAAAGAA
59271 AGAA
1 AGAA
59275 AACCGATCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AGAAGAAAGAAAAGAA
Found at i:59268 original size:21 final size:22
Alignment explanation
Indices: 59232--59276 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 22
59222 GAGAACAAAG
59232 AAAAGAAAGATTAAAGAAAGAAA
1 AAAAGAAAGA-TAAAGAAAGAAA
59255 AAAAGAAAGA-AAAGAAAGAAA
1 AAAAGAAAGATAAAGAAAGAAA
59276 A
1 A
59277 CCGATCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
23 10 0.45
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAGAAAGATAAAGAAAGAAA
Found at i:59269 original size:9 final size:9
Alignment explanation
Indices: 59228--59276 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 9
59218 AGGTGAGAAC
59228 AAAGAAAAG
1 AAAGAAAAG
59237 AAAGATTAAAG
1 AAAGA--AAAG
59248 AAAGAAAAAAAG
1 AAAG---AAAAG
59260 AAAGAAAAG
1 AAAGAAAAG
59269 AAAGAAAA
1 AAAGAAAA
59277 CCGATCAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 18 0.51
11 8 0.23
12 8 0.23
14 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:61417 original size:54 final size:54
Alignment explanation
Indices: 61344--61635 Score: 413
Period size: 54 Copynumber: 5.4 Consensus size: 54
61334 ATTTTTAAAG
* * * * * *
61344 ATTTTCAGAGGTTTTTTGATGTTTACAAATGAATGTTGAAAGAACCTAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
* * *
61398 ATTTTTATGGGTTTCTTGATGTTTTCAAATGAATTATGAAAGAAGCTAAGCCTG
1 ATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
* * * *
61452 ATTTTTAGGGATTTCTTAATATTTTCAAATGAATTTTGAAAGAAGCTAAGCCTG
1 ATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
* *
61506 ATTTTCAGGGGGTTTCTTGATGTTTTCAAATGAATATTGAAAGAAGCTAAGCCTA
1 ATTTTTA-GGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
* * *
61561 ATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATTTTTAAAGAAGCTAAGCTTA
1 ATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
61615 ATTTTTAGGGGTTTCTTGATG
1 ATTTTTAGGGGTTTCTTGATG
61636 ATAGATGTAA
Statistics
Matches: 212, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 164 0.77
55 48 0.23
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
ATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTA
Found at i:61553 original size:109 final size:108
Alignment explanation
Indices: 61369--61635 Score: 401
Period size: 109 Copynumber: 2.5 Consensus size: 108
61359 TTGATGTTTA
* * *
61369 CAAATGAATGTTGAAAGAACCTAAGCCTAATTTTTATGGGTTTCTTGATGTTTTCAAATGAATTA
1 CAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTA
* *
61434 TGAAAGAAGCTAAGCCTGATTTTTAGGGATTTCTTAATATTTT
66 TGAAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTAATATCTT
* *
61477 CAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGGTTTCTTGATGTTTTCAAATGAA-T
1 CAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTA-GGGGTTTCTTGATGTTTTCAAATGAATT
* * *
61541 ATTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTCTT
65 A-TGAAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTAATATCTT
* *
61586 CAAATGAATTTTTAAAGAAGCTAAGCTTAATTTTTAGGGGTTTCTTGATG
1 CAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
61636 ATAGATGTAA
Statistics
Matches: 143, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
108 48 0.34
109 95 0.66
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (108 bp):
CAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTA
TGAAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTAATATCTT
Found at i:63330 original size:118 final size:118
Alignment explanation
Indices: 63117--63368 Score: 346
Period size: 118 Copynumber: 2.1 Consensus size: 118
63107 CAATGGTTAG
* * * *
63117 TAATTGGAAGAACTCGTCTGATGAGGGAGAAGAAGTTCATAACGAGAAGAACTTGTTCAACCTTG
1 TAATTAGAAGAACTTGTCTGATGAGGGAGAAGAAGTTCATAACAAGAAGAACTTATTCAACCTTG
* * *
63182 GTTCGATTCCATCACAGAATAAGGTGGATCAAAATTTCCAATGGAAG-AGTTCA
66 GTTCGAATCCATCACAGAAGAAGGTAGATCAAAATTTCCAAT-GAAGAAGTTCA
* *
63235 TAATTAGAAGAACTTGTAC-GATGAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAAGCTT
1 TAATTAGAAGAACTTGT-CTGATGAGGGAGAAGAAGTTCATAACAAGAAGAACTTATTCAACCTT
* * * *
63299 TGTTCGAATCCATCACATAAGGAGGTAGATCAACATTTCCAATGAAGAAGTTCA
65 GGTTCGAATCCATCACAGAAGAAGGTAGATCAAAATTTCCAATGAAGAAGTTCA
*
63353 TAATGAGAAGAACTTG
1 TAATTAGAAGAACTTG
63369 CTCAACCTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
117 4 0.03
118 113 0.96
119 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (118 bp):
TAATTAGAAGAACTTGTCTGATGAGGGAGAAGAAGTTCATAACAAGAAGAACTTATTCAACCTTG
GTTCGAATCCATCACAGAAGAAGGTAGATCAAAATTTCCAATGAAGAAGTTCA
Found at i:63353 original size:79 final size:79
Alignment explanation
Indices: 63263--63445 Score: 287
Period size: 79 Copynumber: 2.3 Consensus size: 79
63253 CGATGAGGGA
* * * *
63263 GAAGAAGTTCATAATAAGAAGAACTTATTCAAGCTTTGTTCGAATCCATCACATAAGGAGGTAGA
1 GAAGAAGTTCATAATGAGAAGAACTTACTCAACCTTTGTTCGAATCCATCACAGAAGGAGGTAGA
63328 TCAACATTTCCAAT
66 TCAACATTTCCAAT
* *
63342 GAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTTGTTCGAATCCATCACAGAAGGAGGTGGA
1 GAAGAAGTTCATAATGAGAAGAACTTACTCAACCTTTGTTCGAATCCATCACAGAAGGAGGTAGA
63407 TCAACATTTCCAAT
66 TCAACATTTCCAAT
*
63421 G-GGAGAGTTCATAATGAGAAGAACT
1 GAAGA-AGTTCATAATGAGAAGAACT
63446 CATCTGATAA
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 2 0.02
79 94 0.98
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (79 bp):
GAAGAAGTTCATAATGAGAAGAACTTACTCAACCTTTGTTCGAATCCATCACAGAAGGAGGTAGA
TCAACATTTCCAAT
Found at i:63482 original size:197 final size:197
Alignment explanation
Indices: 63145--63519 Score: 554
Period size: 197 Copynumber: 1.9 Consensus size: 197
63135 TGATGAGGGA
* * *
63145 GAAGAAGTTCATAACGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATAAGGTGGA
1 GAAGAAGTTCATAACGAGAAGAACTTGCTCAACCTTGGTTCGAATCCATCACAGAAGAAGGTGGA
* ** *
63210 TCAAAATTTCCAATGGAAGAGTTCATAATTAGAAGAACTTGTACGATGAGGGAGAAGAAGTTCAT
66 TCAAAATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATACGATAAGGGAGAAGAAGTTCAT
* * *
63275 AATAAGAAGAACTTATTCAAGCTTTGTTCGAATCCATCACATAAGGAGGTAGATCAACATTTCCA
131 AATAAGAAGAACTTATTCAACCTTAGCTCGAATCCATCACATAAGGAGGTAGATCAACATTTCCA
63340 AT
196 AT
* * *
63342 GAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTTGTTCGAATCCATCACAGAAGGAGGTGGA
1 GAAGAAGTTCATAACGAGAAGAACTTGCTCAACCTTGGTTCGAATCCATCACAGAAGAAGGTGGA
* * *
63407 TCAACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCAT-CTGATAAGGGAGAAGAAGTTTA
66 TCAAAATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATAC-GATAAGGGAGAAGAAGTTCA
* * **
63471 TAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAG
130 TAATAAGAAGAACTTATTCAACCTTAGCTCGAATCCATCACATAAGGAG
63520 TTGGAATAGC
Statistics
Matches: 157, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
196 1 0.01
197 156 0.99
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (197 bp):
GAAGAAGTTCATAACGAGAAGAACTTGCTCAACCTTGGTTCGAATCCATCACAGAAGAAGGTGGA
TCAAAATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCATACGATAAGGGAGAAGAAGTTCAT
AATAAGAAGAACTTATTCAACCTTAGCTCGAATCCATCACATAAGGAGGTAGATCAACATTTCCA
AT
Found at i:63667 original size:22 final size:22
Alignment explanation
Indices: 63642--63710 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
63632 GGTTCATAAT
63642 GAGAAGAACTCGTTCGATGAGG
1 GAGAAGAACTCGTTCGATGAGG
* **
63664 GAGAATAA---GTTC-AT-AAT
1 GAGAAGAACTCGTTCGATGAGG
63681 GAGAAGAACTCGTTCGATGAGG
1 GAGAAGAACTCGTTCGATGAGG
63703 GAGAAGAA
1 GAGAAGAA
63711 GTTCATAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 8 0.22
18 2 0.06
19 4 0.11
20 4 0.11
21 2 0.06
22 16 0.44
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (22 bp):
GAGAAGAACTCGTTCGATGAGG
Found at i:63668 original size:19 final size:19
Alignment explanation
Indices: 63646--63707 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
63636 CATAATGAGA
63646 AGAACTCGTTCGATGAGGG
1 AGAACTCGTTCGATGAGGG
* * *
63665 AGAA-TAAGTTC-ATAATGAGA
1 AGAACT-CGTTCGATGA-G-GG
63685 AGAACTCGTTCGATGAGGG
1 AGAACTCGTTCGATGAGGG
63704 AGAA
1 AGAA
63708 GAAGTTCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 4 0.12
19 14 0.44
20 10 0.31
21 4 0.12
ACGTcount: A:0.37, C:0.11, G:0.31, T:0.21
Consensus pattern (19 bp):
AGAACTCGTTCGATGAGGG
Found at i:63677 original size:39 final size:39
Alignment explanation
Indices: 63633--63734 Score: 186
Period size: 39 Copynumber: 2.6 Consensus size: 39
63623 CAATAGAAGG
*
63633 GTTCATAATGAGAAGAACTCGTTCGATGAGGGAGAATAA
1 GTTCATAATGAGAAGAACTCGTTCGATGAGGGAGAAGAA
63672 GTTCATAATGAGAAGAACTCGTTCGATGAGGGAGAAGAA
1 GTTCATAATGAGAAGAACTCGTTCGATGAGGGAGAAGAA
*
63711 GTTCATAATGAGAAGAACTTGTTC
1 GTTCATAATGAGAAGAACTCGTTC
63735 AACCTTAGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (39 bp):
GTTCATAATGAGAAGAACTCGTTCGATGAGGGAGAAGAA
Found at i:63725 original size:17 final size:17
Alignment explanation
Indices: 63664--63727 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
63654 TTCGATGAGG
*
63664 GAGAATAAGTTCATAAT
1 GAGAAGAAGTTCATAAT
**
63681 GAGAAGAACTCGTTCGATGAGG
1 GAGAAGAA---GTTC-AT-AAT
63703 GAGAAGAAGTTCATAAT
1 GAGAAGAAGTTCATAAT
63720 GAGAAGAA
1 GAGAAGAA
63728 CTTGTTCAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 16 0.43
18 2 0.05
19 4 0.11
20 4 0.11
21 2 0.05
22 9 0.24
ACGTcount: A:0.44, C:0.08, G:0.28, T:0.20
Consensus pattern (17 bp):
GAGAAGAAGTTCATAAT
Found at i:64006 original size:42 final size:42
Alignment explanation
Indices: 63953--64091 Score: 185
Period size: 42 Copynumber: 3.4 Consensus size: 42
63943 GATTTCATAG
*
63953 CATAAAGAGTTGGATCAACATCATCATTTTGCTCGTCCATCA
1 CATAAGGAGTTGGATCAACATCATCATTTTGCTCGTCCATCA
* * *
63995 TAAAAGGAGTTGGATCATCATCATCATTTTGCTCGTCCATCA
1 CATAAGGAGTTGGATCAACATCATCATTTTGCTCGTCCATCA
* * *
64037 CATAAGGAGTTGGAGCAGA-ATCA-C-CTTGGCTCGTCCATCA
1 CATAAGGAGTTGGATCA-ACATCATCATTTTGCTCGTCCATCA
64077 CATAAGGAGTTGGAT
1 CATAAGGAGTTGGAT
64092 TAGCATCACC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 28 0.33
41 1 0.01
42 56 0.66
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
CATAAGGAGTTGGATCAACATCATCATTTTGCTCGTCCATCA
Found at i:64115 original size:40 final size:40
Alignment explanation
Indices: 64031--64115 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
64021 TTTTGCTCGT
**
64031 CCATCACATAAGGAGTTGGAGCAGAATCACCTTGGCTCGT
1 CCATCACATAAGGAGTTGGAGCAGAATCACCTTGGCTCAA
** * *
64071 CCATCACATAAGGAGTTGGATTAGCATCACCTTGGGTCAA
1 CCATCACATAAGGAGTTGGAGCAGAATCACCTTGGCTCAA
64111 CCATC
1 CCATC
64116 GCAGTGTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCATCACATAAGGAGTTGGAGCAGAATCACCTTGGCTCAA
Done.