Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007755.1 Hibiscus syriacus cultivar Beakdansim tig00110021_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: 350557
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:318841 original size:99 final size:97
Alignment explanation
Indices: 318716--318904 Score: 272
Period size: 99 Copynumber: 1.9 Consensus size: 97
318706 AACATACAAA
* * * **
318716 AAAGAAAAAGAGTGACGGTGGTGCAAAGGCTAAGAAA-GAAAAGCGTCGTGGCAATGTCAAGGCT
1 AAAGAAAAAGAGTGACGGTGGTGCAAAGGATAAGAAAGGAAAA-CGTCGTGACAACGGAAAGGCT
318780 AAAGAAAAAGAGAGTGATGACGGTGCCAAGGCT
65 AAAGAAAAAGAGAGTGATGACGGTGCCAAGGCT
* *
318813 AAAGAAAAAGAGAGTGATGGTGGTGCAAAGGATAAGAAAGGAAAACGTCGTGATAACGGAAAGGC
1 AAAG-AAAA-AGAGTGACGGTGGTGCAAAGGATAAGAAAGGAAAACGTCGTGACAACGGAAAGGC
*
318878 TAAAGATAAAGAGAGTGATGACGGTGC
64 TAAAGAAAAAGAGAGTGATGACGGTGC
318905 AAAGATCAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 4 0.05
98 4 0.05
99 68 0.84
100 5 0.06
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.14
Consensus pattern (97 bp):
AAAGAAAAAGAGTGACGGTGGTGCAAAGGATAAGAAAGGAAAACGTCGTGACAACGGAAAGGCTA
AAGAAAAAGAGAGTGATGACGGTGCCAAGGCT
Found at i:330268 original size:15 final size:16
Alignment explanation
Indices: 330245--330274 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
330235 TTTTATCAAA
330245 AAATATTTTAAATTTT
1 AAATATTTTAAATTTT
330261 AAAT-TTTTAAATTT
1 AAATATTTTAAATTT
330275 GACCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTAAATTTT
Found at i:335853 original size:14 final size:14
Alignment explanation
Indices: 335834--335868 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
335824 ACAATGATAA
335834 ATGTACCAGGTACC
1 ATGTACCAGGTACC
335848 ATGTACCAGGTACC
1 ATGTACCAGGTACC
335862 ATGTACC
1 ATGTACC
335869 GATGCCCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (14 bp):
ATGTACCAGGTACC
Found at i:342267 original size:32 final size:32
Alignment explanation
Indices: 342186--342387 Score: 173
Period size: 32 Copynumber: 7.0 Consensus size: 32
342176 ACAATTACAA
342186 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
342218 -AACTACA--A--T--AATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATAC
*
342244 TAATAAATTATTTAAAATAAATCAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
342276 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
*
342308 -AACTACA--A--T--AATAAATCAATCC--A-
1 TAA-TAAATTATTTAAAATAAATCAATCCATAC
* *
342331 T-AT------TTTAAAATTAATAAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
342356 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAC
342388 AACTACAATA
Statistics
Matches: 137, Mismatches: 9, Indels: 48
0.71 0.05 0.25
Matches are distributed among these distances:
20 1 0.01
22 12 0.09
23 1 0.01
24 2 0.01
25 1 0.01
26 35 0.26
27 2 0.01
28 3 0.02
30 3 0.02
31 4 0.03
32 73 0.53
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:342282 original size:18 final size:17
Alignment explanation
Indices: 342226--342283 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
342216 ACAACTACAA
342226 TAATAAATCAATCCATAC
1 TAATAAATCAAT-CATAC
* *
342244 TAATAAAT-TAT-TTA-
1 TAATAAATCAATCATAC
*
342258 AAATAAATCAATCAATAC
1 TAATAAATCAATC-ATAC
342276 TAATAAAT
1 TAATAAAT
342284 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 4 0.13
18 15 0.50
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAATCAATCATAC
Found at i:342323 original size:26 final size:26
Alignment explanation
Indices: 342291--342489 Score: 105
Period size: 26 Copynumber: 7.6 Consensus size: 26
342281 AATTATTTAA
342291 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
*** *
342317 AATAAATCAATCCATA-TTTTAAAATT
1 AATAAATCAATCCATACAACTACAA-T
* * * *
342343 AATAAATCCATACTAATA-AATTATTTAA-
1 AATAAATCAAT-C-CATACAACTA--CAAT
342371 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* **
342397 AATAAATCAATACAT---A-TTTAA-
1 AATAAATCAATCCATACAACTACAAT
342418 AATAAATC-ATCCATACTAA-TA-ATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
*
342446 AAAATAAATCAATCTATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
342474 AATAAATCAATCCATA
1 AATAAATCAATCCATA
342490 TTTTAAAATA
Statistics
Matches: 132, Mismatches: 20, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
20 5 0.04
21 8 0.06
22 3 0.02
23 2 0.02
24 2 0.02
25 7 0.05
26 59 0.45
27 6 0.05
28 17 0.13
30 13 0.10
31 9 0.07
32 1 0.01
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:342358 original size:80 final size:81
Alignment explanation
Indices: 342254--343038 Score: 687
Period size: 80 Copynumber: 9.7 Consensus size: 81
342244 TAATAAATTA
* *
342254 TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA-A-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAA-TAAATATT
342317 AATAAATCAATCCATAT
65 AATAAATCAATCCATAT
* * *
342334 TTTAAAATTAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA-A-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAA-TAAATATT
*
342397 AATAAATCAATACATA-
65 AATAAATCAATCCATAT
* *
342413 TTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAATCTATACAACTACA-A-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAA-TAAATATT
342474 AATAAATCAATCCATAT
65 AATAAATCAATCCATAT
* *
342491 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAA-TA-
342556 TTAAAATAAATCAATCCATA-
63 TT--AATAAATCAATCCATAT
* * * ** * * *
342576 -CT--AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAA
1 TTTAAAATAAATCAATCCATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC-AATAA
* *
342638 ATTATTTA-AAATAAAT-CA-AT
60 A-TATTAATAAATCAATCCATAT
* * ** ** *
342658 CTATACAACTACAAT-AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATTCATACTAATAAA
1 -TTTA-AAATA-AATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATAC-AATAAA
**
342719 TTATTTAAAATAAATCAATTTATAT
61 -TA-TT--AATAAATCAATCCATAT
* *
342744 TTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA-A-T
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAA-TAAATATT
342807 AATAAATCAATCCATAT
65 AATAAATCAATCCATAT
*
342824 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAATA-T
* *
342889 TAAAATAATCAATCCATACA
64 TAATA-AATCAATCCATA-T
** * * *
342909 ACTACAAT-AAT-AATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAA-TA-
*
342966 TTAAAATAAATCAATCTATA-
63 TT--AATAAATCAATCCATAT
342986 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
343039 TTTTAAAACA
Statistics
Matches: 593, Mismatches: 62, Indels: 95
0.79 0.08 0.13
Matches are distributed among these distances:
77 82 0.14
78 33 0.06
79 40 0.07
80 212 0.36
81 12 0.02
82 19 0.03
83 28 0.05
84 41 0.07
85 33 0.06
86 50 0.08
87 40 0.07
88 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (81 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAATAAATATTA
ATAAATCAATCCATAT
Found at i:342379 original size:54 final size:54
Alignment explanation
Indices: 342186--343083 Score: 495
Period size: 54 Copynumber: 16.4 Consensus size: 54
342176 ACAATTACAA
* ** *
342186 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATAAATCCATAC
* ** *
342244 TAATAAATTATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATAAATCCATAC
* * * *
342303 -CATACAACTA--CAATAATAAATCAATCCATATTTTAAAATTAATAAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
* * **
342356 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-AATAAATCCATAC
* ** * *
342405 -AATACA-TATTTAAAATAAATC-ATCCATACTAATAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAA--A-AT-AAATAAATCCATAC
* * * *
342460 T-ATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATTAATTCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
*
342513 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATAAATCCATAC
*
342577 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
* *** * *
342632 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATAAATCCATAC
* * ** * ** **
342685 -CAT--A-T-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-AAATCCATAC
** * ** *
342735 -AATTTA-TATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATAAATCCATAC
* * * *
342793 -CATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
** * *
342846 TAATAAATTATTTAAAATAAATCAATCCATACTAATAATTATTTAAA-ATAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAA--A-ATAAATA-AATCCATAC
* * * *
342903 -CATACAACTA--CAATAAT-AATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
* * *
342955 AAATAAATTATTTAAAATAAATCAATCTATA-TTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
* *
343008 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
343062 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
343084 TATTTAAAAA
Statistics
Matches: 670, Mismatches: 94, Indels: 156
0.73 0.10 0.17
Matches are distributed among these distances:
46 7 0.01
47 15 0.02
48 30 0.04
49 3 0.00
50 19 0.03
51 14 0.02
52 39 0.06
53 78 0.12
54 173 0.26
55 79 0.12
56 23 0.03
57 31 0.05
58 84 0.13
59 11 0.02
60 14 0.02
61 1 0.00
62 1 0.00
63 1 0.00
64 31 0.05
65 16 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATAC
Found at i:342465 original size:157 final size:159
Alignment explanation
Indices: 342252--343038 Score: 656
Period size: 157 Copynumber: 4.8 Consensus size: 159
342242 ACTAATAAAT
342252 TATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
1 TATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
*
342317 AATAAATCAATCCATATTTTAAAATTAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
66 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
342382 CCATACAACTACAATAATAAATCAATACA
131 CCATACAACTACAATAATAAATCAATACA
* *
342411 TATTTAAAATAAATC-ATCCATACTAAT-AATTATTTAAAATAAATCAATCTATACAACTACAAT
1 TATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* *
342474 AATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAAT
66 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
342539 CCATACTAA-TAAATTATTTAAAATAAATCAATCCA
131 CCATAC-AACTACA--A--T--AATAAATCAATACA
* * * * * *
342574 TA-CT--AATAAATTATTTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA
1 TATTTAAAATAAATCA-ATCAATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC-AA
* * * * ** **
342635 -TA-AATTATTTAAAATAAAT-CA-ATCTATACAACTACAAT-AATAAAT-C-AATCCA-TATTT
59 CTACAA-TA-AT-AAATCAATCCATAT-TTTA-AAATA-AATAAATCCATACTAATAAATTA-TT
* * **
342692 TAAAATAAATCAATTCATACTAA-TAAATTATTTAAAATAAATCAATTTA
117 TAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATACA
* *
342741 TATTTTAAAATAAATCAACCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TA-TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
*
342806 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
65 TAATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAA
* *
342871 TCCATACTAA-TA-ATTATTTAAAATAATCAATCCA
130 TCCATAC-AACTACA--A--TAATA-AATCAATACA
* * ** * *
342905 TA---CAACTACAAT-AAT-AAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACAAATAAA
1 TATTTAAAATA-AATCAATCAATACTAATAAATTA-TTTAAAATAAATCAATCCATACAACTACA
* *
342962 TTATTTAAAATAAATCAATCTATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT
64 --A--T--AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAAT
343026 AAATCAATCCATA
123 AAATCAATCCATA
343039 TTTTAAAACA
Statistics
Matches: 529, Mismatches: 54, Indels: 87
0.79 0.08 0.13
Matches are distributed among these distances:
156 2 0.00
157 137 0.26
158 14 0.03
159 19 0.04
160 13 0.02
161 7 0.01
162 59 0.11
163 39 0.07
164 26 0.05
165 16 0.03
166 64 0.12
167 87 0.16
168 9 0.02
169 17 0.03
170 10 0.02
171 10 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (159 bp):
TATTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAATAATAAATCAATACA
Found at i:342517 original size:18 final size:18
Alignment explanation
Indices: 342496--342586 Score: 72
Period size: 18 Copynumber: 5.5 Consensus size: 18
342486 CATATTTTAA
342496 AATAAATTAATTCATACT
1 AATAAATTAATTCATACT
*
342514 AATAAATT-ATT--TA-A
1 AATAAATTAATTCATACT
* *
342528 AATAAATCAATCCATACT
1 AATAAATTAATTCATACT
*
342546 AATAAATT-ATT--TA-A
1 AATAAATTAATTCATACT
* *
342560 AATAAATCAATCCATACT
1 AATAAATTAATTCATACT
342578 AATAAATTA
1 AATAAATTA
342587 TTTTAAAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 16
0.67 0.14 0.20
Matches are distributed among these distances:
14 14 0.26
15 8 0.15
17 9 0.17
18 23 0.43
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATTAATTCATACT
Found at i:342530 original size:32 final size:32
Alignment explanation
Indices: 342491--342907 Score: 352
Period size: 32 Copynumber: 14.7 Consensus size: 32
342481 CAATCCATAT
* *
342491 TTTAAAATAAATTAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342523 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342555 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342587 TTTTAAAATAAATCAAT-C---C--AT--A-T-
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
342610 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
342642 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
342672 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
342690 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342722 TTTAAAATAAATCAAT---T--T-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
342744 TTTAAAATAAATCAACCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
342776 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
342806 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342824 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342856 TTTAAAATAAATCAATCCATACTAAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
342887 TTTAAAAT-AATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
342908 AACTACAATA
Statistics
Matches: 323, Mismatches: 9, Indels: 108
0.73 0.02 0.25
Matches are distributed among these distances:
20 2 0.01
22 58 0.18
23 4 0.01
24 6 0.02
25 4 0.01
26 32 0.10
27 4 0.01
28 6 0.02
29 2 0.01
30 17 0.05
31 19 0.06
32 153 0.47
33 16 0.05
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:342613 original size:22 final size:22
Alignment explanation
Indices: 342585--342630 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
342575 ACTAATAAAT
342585 TATTTTAAAATAAATCAATCCA
1 TATTTTAAAATAAATCAATCCA
342607 TATTTTAAAATAAATCAATCCA
1 TATTTTAAAATAAATCAATCCA
342629 TA
1 TA
342631 CTAATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (22 bp):
TATTTTAAAATAAATCAATCCA
Found at i:342639 original size:22 final size:22
Alignment explanation
Indices: 342590--342638 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
342580 TAAATTATTT
**
342590 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
342612 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
342635 TAAA
1 TAAA
342639 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:342853 original size:22 final size:23
Alignment explanation
Indices: 342778--342852 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
342768 ATAAATTATT
342778 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
342800 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
342826 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
342849 TAAA
1 TAAA
342853 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:342962 original size:22 final size:22
Alignment explanation
Indices: 342891--342962 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
342881 TAATTATTTA
*
342891 AAAT-AATCAATCCATACAACT
1 AAATAAATCAATCCATACAAAT
***
342912 ACAATAATAATCAATCCATA-TTTT
1 A-AAT-A-AATCAATCCATACAAAT
342936 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
342959 AAAT
1 AAAT
342963 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
21 1 0.03
22 19 0.49
23 2 0.05
24 4 0.10
25 13 0.33
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:342987 original size:21 final size:21
Alignment explanation
Indices: 342963--343002 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
342953 ACAAATAAAT
342963 TATTTAAAATAAATCAATCTA
1 TATTTAAAATAAATCAATCTA
342984 TATTTAAAATAAATCAATC
1 TATTTAAAATAAATCAATC
343003 CATACTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCTA
Found at i:343023 original size:32 final size:32
Alignment explanation
Indices: 342984--343083 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
342974 AATCAATCTA
342984 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
343016 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
343039 T-TTTAAAACAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
343070 TATTTAAAATAAAT
1 TATTTAAAATAAAT
343084 TATTTAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
22 15 0.27
23 2 0.04
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.04
32 29 0.52
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TATTTAAAATAAATCAATCCATACTAATAAAT
Found at i:343044 original size:22 final size:22
Alignment explanation
Indices: 343018--343060 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
343008 TAATAAATTA
*
343018 TTTAAAATAAATCAATCCATAT
1 TTTAAAACAAATCAATCCATAT
343040 TTTAAAACAAATCAATCCATA
1 TTTAAAACAAATCAATCCATA
343061 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAACAAATCAATCCATAT
Found at i:343082 original size:14 final size:15
Alignment explanation
Indices: 343063--343098 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
343053 AATCCATACT
343063 AATAAATTATTT-AA
1 AATAAATTATTTAAA
343077 AATAAATTATTTAAA
1 AATAAATTATTTAAA
343092 AATAAAT
1 AATAAAT
343099 CAATCCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATTATTTAAA
Found at i:343208 original size:10 final size:10
Alignment explanation
Indices: 343193--343229 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
343183 ATAATTGTTC
343193 TTGAAGAGGT
1 TTGAAGAGGT
343203 TTGAAGAGGT
1 TTGAAGAGGT
**
343213 TTGAAGACCT
1 TTGAAGAGGT
343223 TTGAAGA
1 TTGAAGA
343230 CATAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (10 bp):
TTGAAGAGGT
Found at i:343698 original size:2 final size:2
Alignment explanation
Indices: 343691--343730 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
343681 AATAAAAATA
343691 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
343731 GTTATATCGA
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
Done.