Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006852.1 Hibiscus syriacus cultivar Beakdansim tig00017432_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: 80401
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9 original size:4 final size:4
Alignment explanation
Indices: 1--957 Score: 1795
Period size: 4 Copynumber: 243.5 Consensus size: 4
1 TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGT- TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
94 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
140 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
188 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
236 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
284 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
332 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
380 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
428 TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
475 -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
522 TGTA --TA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
567 TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
613 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
661 -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
708 TGTA TGTA TG-A TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA -GTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
752 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
800 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
848 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
896 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
944 TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TG
958 AATGAGTCAT
Statistics
Matches: 936, Mismatches: 0, Indels: 34
0.96 0.00 0.04
Matches are distributed among these distances:
2 10 0.01
3 21 0.02
4 905 0.97
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:1681 original size:35 final size:36
Alignment explanation
Indices: 1642--1718 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
1632 TTTTCAATTT
*
1642 TTTTAAAATCC-TATTTAAAC-TTAGTTTTTATTTCA
1 TTTTAAAA-CCGTATTAAAACTTTAGTTTTTATTTCA
* * *
1677 TTTTAATACCGTCTTAAAACTTTAGTTTTTGTTTCA
1 TTTTAAAACCGTATTAAAACTTTAGTTTTTATTTCA
1713 TTTTAA
1 TTTTAA
1719 TACTCTCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 2 0.06
35 14 0.39
36 20 0.56
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (36 bp):
TTTTAAAACCGTATTAAAACTTTAGTTTTTATTTCA
Found at i:15581 original size:19 final size:19
Alignment explanation
Indices: 15557--15608 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
15547 ATTTATTTTT
* *
15557 AGATTCGTAGCTTACTGTC
1 AGATTCATAACTTACTGTC
15576 AGATTCATAACTTACTGTC
1 AGATTCATAACTTACTGTC
15595 AGATTCATAACTTA
1 AGATTCATAACTTA
15609 TTTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (19 bp):
AGATTCATAACTTACTGTC
Found at i:15619 original size:19 final size:19
Alignment explanation
Indices: 15578--15641 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
15568 TTACTGTCAG
* * *
15578 ATTCATAACTTACTGTCAG
1 ATTCATAACTTATTTTCAA
*
15597 ATTCATAACTTATTTTTAA
1 ATTCATAACTTATTTTCAA
**
15616 ATTCATAGTTTATTTTCAA
1 ATTCATAACTTATTTTCAA
15635 ATTCATA
1 ATTCATA
15642 GTCCAATACA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTCATAACTTATTTTCAA
Found at i:15917 original size:18 final size:19
Alignment explanation
Indices: 15896--15935 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
15886 TAATTATTAT
15896 ATATTATTCAAT-TATCAA-
1 ATATTA-TCAATATATCAAC
15914 ATA-TATCAATATATCAAC
1 ATATTATCAATATATCAAC
15932 ATAT
1 ATAT
15936 CCAACTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATTATCAATATATCAAC
Found at i:19992 original size:60 final size:59
Alignment explanation
Indices: 19928--20060 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 59
19918 TTTGGGGTTC
* * *
19928 AATTTAGAAAGAGGGTAATT-GTCTAG-GGATGAAATTAGAGTGTTCAAAAGTTTGAGGACT
1 AATTTAGAAAGAGAGT-ATTAGT-TAGAGGATGAAATTAGAATGTTCAAAAG-TTAAGGACT
* * * *
19988 AATTTAGAATGTGAGTCTTAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTAAGGACT
1 AATTTAGAAAGAGAGTATTAGTTAGAGGATGAAATTAGAATGTTCAAAAGTTAAGGACT
*
20047 AATTTAGAATGAGA
1 AATTTAGAAAGAGA
20061 AATTAAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 25 0.40
60 38 0.60
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
AATTTAGAAAGAGAGTATTAGTTAGAGGATGAAATTAGAATGTTCAAAAGTTAAGGACT
Found at i:20078 original size:41 final size:42
Alignment explanation
Indices: 20018--20099 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
20008 GTTTGAGGAT
* * * *
20018 GAAATTAGAATGTTCAAAAG-TTAAGGACTAATTTAGAATGA
1 GAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATGA
*
20059 GAAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAATG
1 GAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATG
20100 TGTATTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 17 0.49
42 18 0.51
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (42 bp):
GAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATGA
Found at i:22349 original size:13 final size:13
Alignment explanation
Indices: 22333--22362 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22323 TTTAATATTT
*
22333 ATCGGGTCGGGTA
1 ATCGGGCCGGGTA
22346 ATCGGGCCGGGTA
1 ATCGGGCCGGGTA
22359 ATCG
1 ATCG
22363 AGTAATCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
ATCGGGCCGGGTA
Found at i:22399 original size:6 final size:6
Alignment explanation
Indices: 22388--22416 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22378 GAGTACCAAA
22388 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
22417 TTAACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:24824 original size:20 final size:20
Alignment explanation
Indices: 24799--24839 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24789 AGTCCAGTAC
24799 TTGGTTGGTTGGATGTATAA
1 TTGGTTGGTTGGATGTATAA
24819 TTGGTTGGTTGGATGTATAA
1 TTGGTTGGTTGGATGTATAA
24839 T
1 T
24840 GCCTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (20 bp):
TTGGTTGGTTGGATGTATAA
Found at i:25395 original size:66 final size:66
Alignment explanation
Indices: 25289--25421 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
25279 AGGGCATCTC
* * *
25289 CACCTAGGGATGAAAGTCCTGATAGACGGAGCCGCGGTGGAAGGTCTCCAAGTCCTCGAAGTGTT
1 CACCTAGGGATGAAAGTCCTGATAGACAGAGCCGCGGTGGAAGGTCCCCAAGTCCTCAAAGTGTT
25354 T
66 T
* * *
25355 CACCTAGGGGTGAAAGTCCTGTTAGACAGAGCCGCGGTGGACGGTCCCCAAGTCCTCAAAGTGTT
1 CACCTAGGGATGAAAGTCCTGATAGACAGAGCCGCGGTGGAAGGTCCCCAAGTCCTCAAAGTGTT
25420 T
66 T
25421 C
1 C
25422 CCCGCGAGGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (66 bp):
CACCTAGGGATGAAAGTCCTGATAGACAGAGCCGCGGTGGAAGGTCCCCAAGTCCTCAAAGTGTT
T
Found at i:27089 original size:32 final size:31
Alignment explanation
Indices: 27038--27115 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
27028 TATTGAATGG
* * *
27038 AATGATTATT-AAATTTATTATATTGCTATAA
1 AATGATCATTAAAATTTATTAAATTG-TACAA
27069 AATGATCATTAAAATTTATTAAATTGTACAA
1 AATGATCATTAAAATTTATTAAATTGTACAA
*
27100 AATGGTCATTGAAAAT
1 AATGATCATT-AAAAT
27116 GATTGAACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 22 0.54
32 19 0.46
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (31 bp):
AATGATCATTAAAATTTATTAAATTGTACAA
Found at i:34289 original size:85 final size:84
Alignment explanation
Indices: 34177--34346 Score: 227
Period size: 87 Copynumber: 2.0 Consensus size: 84
34167 GACTAAACAT
**
34177 ACACAAAGTAATAATAAGTAAAGATAAAGCGCACATAGA-TT-TGTGTAAAAACCCTAAAAATGA
1 ACACAAAGTAATAATAAGTAAAGATAAAGAACACATAGATTTATGTGTAAAAACCCTAAAAATGA
34240 AAAATCACAGCCACAACCA
66 AAAATCACAGCCACAACCA
* * * *
34259 ACACAAAGTAATACTAATAGATAAAGATAAAGAATACATAGATTTATGTGTAAAATCCCTAAAGA
1 ACACAAAGTAATAAT-A-AG-TAAAGATAAAGAACACATAGATTTATGTGTAAAAACCCTAAAAA
* *
34324 TGAAAAATCACATCTACAACCA
63 TGAAAAATCACAGCCACAACCA
34346 A
1 A
34347 GGGAGTAGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
82 14 0.19
83 1 0.01
84 2 0.03
85 18 0.24
86 2 0.03
87 38 0.51
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.20
Consensus pattern (84 bp):
ACACAAAGTAATAATAAGTAAAGATAAAGAACACATAGATTTATGTGTAAAAACCCTAAAAATGA
AAAATCACAGCCACAACCA
Found at i:39633 original size:23 final size:24
Alignment explanation
Indices: 39567--39633 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 24
39557 TACAAACGTG
*
39567 TAAATTTTTAAAA-AGTTATA-T-
1 TAAATTTTTAAAAGACTTATATTA
* *
39588 TAAA-TTTTAAGAGTACGTA-ATTA
1 TAAATTTTTAAAAG-ACTTATATTA
39611 TAAATTTTTAAAAGA-TTATATTA
1 TAAATTTTTAAAAGACTTATATTA
39634 ATTTATCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.20
21 5 0.14
22 6 0.17
23 9 0.26
24 8 0.23
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (24 bp):
TAAATTTTTAAAAGACTTATATTA
Found at i:51002 original size:216 final size:213
Alignment explanation
Indices: 50625--51372 Score: 831
Period size: 216 Copynumber: 3.5 Consensus size: 213
50615 CTGCTACTGA
* * * * * * **
50625 AACTGAATTAGCTTCTTTAGAGTCCAGTTTCAAAAGTGATGTTCCCCGCAGGGTTAAGTTGGAAA
1 AACTGAATTAGCTTCTTTAGAGTCTAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGCTGGAGG
* * *
50690 AGGAAGAAAATACTGGTGCTGATA-AAAATGGCGAGAGGATTGGCAAAATTGAGGGTACTACTTC
66 AGGAAGAAAATACTGGTGCTGA-AGAAAATGGGGAGAGGATAGGTAAAATTGAGGGTACTACTTC
* ** ** * * *
50754 AAGA-ATGGAAACCCAGATGAATTTAGTTCCTGATATAGAAAAGGCTTCTCCTCCATTGGCAGTT
130 AA-ATACGGAGTCTAAGATG-A-TTAGTTCCTGATCTAGAAAA-GCTTCTCCTCCAATGGCAGCT
* *
50818 CCCGGTATTGAAAGTGAAATTAG
191 CCTGCTATTGAAAGTGAAATTAG
* *
50841 AACTGAATTAGCTT-TCCTAGAGTCTAGTTCCAAAAGTGAAGTTTCCCACAGTGTTAAGCTGGAG
1 AACTGAATTAGCTTCT-TTAGAGTCTAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGCTGGAG
* * * *
50905 GAGGACGAAAATACTGGTGCTGAAGAAAATGGGGAGAGGATAGGTGAAATTGAGGGTACCAATTC
65 GAGGAAGAAAATACTGGTGCTGAAGAAAATGGGGAGAGGATAGGTAAAATTGAGGGTACTACTTC
* * * * *
50970 AAATACGGAGTTTAAGATAGATTCAATTCCTGATCTAGAACATGCTTCTCCTGCAAGGGCAGCTC
130 AAATACGGAGTCTAAGAT-GATT-AGTTCCTGATCTAGAA-AAGCTTCTCCTCCAATGGCAGCTC
* * *
51035 CTGCCATTGAAACTGCAATTAG
192 CTGCTATTGAAAGTGAAATTAG
* * * * * * *
51057 AACTGAATTAACTTCTGTGGAGGCTAGTTCCAAAAGTGAACTTCCCCACAATGTTAAGCTGAAGG
1 AACTGAATTAGCTTCTTTAGAGTCTAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGCTGGAGG
* * * * * * * * **
51122 AGAAAGCAAATACTAGTGCTGAGGAAAATCGGGAGAGAATGGGTAAAATTGAGGGTACTGCTTTG
66 AGGAAGAAAATACTGGTGCTGAAGAAAATGGGGAGAGGATAGGTAAAATTGAGGGTACTACTTCA
* *
51187 ATTACGGAGTCTAAGAT--TTAGTTCCTGATCTAGAACAATCTTCTCCTCCAATGGCAGCTCCTG
131 AATACGGAGTCTAAGATGATTAGTTCCTGATCTAGAA-AAGCTTCTCCTCCAATGGCAGCTCCTG
*
51250 CTATCGAAAGTGAAATTAG
195 CTATTGAAAGTGAAATTAG
* *
51269 AACTGAATTAGCTTCTTTAGAGTCTAGTTCCAAAAGCGAAGTTCCCCACGGTGTTAAGCTGGAGG
1 AACTGAATTAGCTTCTTTAGAGTCTAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGCTGGAGG
* * *
51334 AGGAAGAAAATACTGGTGCTGAGGAAAAAGGTGAGAGGA
66 AGGAAGAAAATACTGGTGCTGAAGAAAATGGGGAGAGGA
51373 CTGCTAAAAT
Statistics
Matches: 441, Mismatches: 84, Indels: 18
0.81 0.15 0.03
Matches are distributed among these distances:
212 142 0.32
213 2 0.00
215 5 0.01
216 289 0.66
217 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (213 bp):
AACTGAATTAGCTTCTTTAGAGTCTAGTTCCAAAAGTGAAGTTCCCCACAGTGTTAAGCTGGAGG
AGGAAGAAAATACTGGTGCTGAAGAAAATGGGGAGAGGATAGGTAAAATTGAGGGTACTACTTCA
AATACGGAGTCTAAGATGATTAGTTCCTGATCTAGAAAAGCTTCTCCTCCAATGGCAGCTCCTGC
TATTGAAAGTGAAATTAG
Found at i:56349 original size:48 final size:48
Alignment explanation
Indices: 56297--56392 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
56287 AGTTTGTAAA
56297 TTTAAATTTTAACGTGTAAGTAAAATAAATTAAATTAAAATAATCATT
1 TTTAAATTTTAACGTGTAAGTAAAATAAATTAAATTAAAATAATCATT
56345 TTTAAATTTTAACGTGTAAGTAAAATAAATTAAATTAAAATAATCATT
1 TTTAAATTTTAACGTGTAAGTAAAATAAATTAAATTAAAATAATCATT
56393 CTTATCGTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (48 bp):
TTTAAATTTTAACGTGTAAGTAAAATAAATTAAATTAAAATAATCATT
Found at i:60342 original size:19 final size:19
Alignment explanation
Indices: 60318--60356 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
60308 TTATATTATA
60318 TTTATACAACTTTAATTTC
1 TTTATACAACTTTAATTTC
* *
60337 TTTATATAATTTTAATTTC
1 TTTATACAACTTTAATTTC
60356 T
1 T
60357 ATTTTACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATACAACTTTAATTTC
Found at i:60398 original size:13 final size:13
Alignment explanation
Indices: 60382--60439 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
60372 TTTTCAATTT
60382 TTATTTCTTTGAA
1 TTATTTCTTTGAA
60395 TTATTT-TATT--A
1 TTATTTCT-TTGAA
* *
60406 TTATTTTCATATGAT
1 TTA-TTTC-TTTGAA
60421 TTATTTCTTTGAA
1 TTATTTCTTTGAA
60434 TTATTT
1 TTATTT
60440 TATTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
11 4 0.11
12 4 0.11
13 19 0.54
14 5 0.14
15 3 0.09
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (13 bp):
TTATTTCTTTGAA
Found at i:60403 original size:18 final size:18
Alignment explanation
Indices: 60380--60443 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
60370 TATTTTCAAT
60380 TTTTATTTCTTTGAATTA
1 TTTTATTTCTTTGAATTA
* **
60398 TTTTATTATTATTTTCA-TA
1 TTTTA-T-TTCTTTGAATTA
60417 TGATTTATTTCTTTGAATTA
1 T--TTTATTTCTTTGAATTA
60437 TTTTATT
1 TTTTATT
60444 ATTTTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 11 0.31
19 10 0.29
20 10 0.29
21 4 0.11
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTATTTCTTTGAATTA
Found at i:60427 original size:39 final size:37
Alignment explanation
Indices: 60381--60457 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 37
60371 ATTTTCAATT
60381 TTTATTTCTTTGAATTATTTTATTATTATTTTCATATGA
1 TTTATTTCTTTGAATTATTTTATTATT-TTTT-ATATGA
60420 TTTATTTCTTTGAATTATTTTATTATTTTTTATATGA
1 TTTATTTCTTTGAATTATTTTATTATTTTTTATATGA
60457 T
1 T
60458 GTGTTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 7 0.18
38 4 0.11
39 27 0.71
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (37 bp):
TTTATTTCTTTGAATTATTTTATTATTTTTTATATGA
Found at i:63172 original size:2 final size:2
Alignment explanation
Indices: 63165--63223 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
63155 ATTTATTTTC
63165 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
63207 AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT
63224 TATTATTCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64682 original size:21 final size:22
Alignment explanation
Indices: 64641--64683 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
64631 AGTGATCCTT
*
64641 TAAATTCAATCTGTTTTTTATTA
1 TAAATTCAATC-GTATTTTATTA
64664 TAAATTCAATC-TATTTTATT
1 TAAATTCAATCGTATTTTATT
64684 TACAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (22 bp):
TAAATTCAATCGTATTTTATTA
Found at i:64796 original size:2 final size:2
Alignment explanation
Indices: 64789--64824 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
64779 ATACACTTAA
64789 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
64825 GGATTATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72038 original size:18 final size:18
Alignment explanation
Indices: 72015--72052 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
72005 TAAAATGACT
*
72015 TAGTTTCACGTGTAGTGA
1 TAGTTTCACATGTAGTGA
72033 TAGTTTCACATGTAGTGA
1 TAGTTTCACATGTAGTGA
72051 TA
1 TA
72053 TTTTTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (18 bp):
TAGTTTCACATGTAGTGA
Done.