Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002005.1 Hibiscus syriacus cultivar Beakdansim tig00004100_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: 96017
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9814 original size:38 final size:38
Alignment explanation
Indices: 9772--9844 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
9762 TGTTGCTAAC
* * *
9772 CGAAAATATTATGAAGAATATAATATCTTAGATTACAA
1 CGAAAATATTATAAAAAATATAACATCTTAGATTACAA
* *
9810 CGAAAATATTATAAAAAATATCACATTTTAGATTA
1 CGAAAATATTATAAAAAATATAACATCTTAGATTA
9845 TGTCTAACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (38 bp):
CGAAAATATTATAAAAAATATAACATCTTAGATTACAA
Found at i:21266 original size:10 final size:12
Alignment explanation
Indices: 21239--21266 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21229 ATGATGCTTT
21239 GTGTGTGGTTAG
1 GTGTGTGGTTAG
21251 GTGTGTGGTTAG
1 GTGTGTGGTTAG
21263 GTGT
1 GTGT
21267 TTGGCTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (12 bp):
GTGTGTGGTTAG
Found at i:27104 original size:93 final size:93
Alignment explanation
Indices: 26938--27125 Score: 331
Period size: 93 Copynumber: 2.0 Consensus size: 93
26928 GCACTTCACT
*
26938 AGAATGACAATCAATGTTAGCAGATTGACTTAAATGCAACATGTTTTGAAAGGGATACTAGATGT
1 AGAACGACAATCAATGTTAGCAGATTGACTTAAATGCAACATGTTTTGAAAGGGATACTAGATGT
*
27003 GATGGTTTAATAAGTTTTTAGTTATGCA
66 GATAGTTTAATAAGTTTTTAGTTATGCA
* *
27031 AGAACGACAATCAATGTTAGCAGATTGACTTAAATGCAACATGTTTTGATAGGGATGCTAGATGT
1 AGAACGACAATCAATGTTAGCAGATTGACTTAAATGCAACATGTTTTGAAAGGGATACTAGATGT
*
27096 GATAGTTTAATAAGTTTTTAGTTGTGCA
66 GATAGTTTAATAAGTTTTTAGTTATGCA
27124 AG
1 AG
27126 TTATAATAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (93 bp):
AGAACGACAATCAATGTTAGCAGATTGACTTAAATGCAACATGTTTTGAAAGGGATACTAGATGT
GATAGTTTAATAAGTTTTTAGTTATGCA
Found at i:38172 original size:19 final size:19
Alignment explanation
Indices: 38120--38172 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
38110 TTGGACTCTC
*
38120 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCATTAAG
38139 AGTGCATCGGTGCATTAAG
1 AGTGCATCGGTGCATTAAG
*
38158 AGTGCATCGATGCAT
1 AGTGCATCGGTGCAT
38173 GAAATGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (19 bp):
AGTGCATCGGTGCATTAAG
Found at i:38339 original size:19 final size:20
Alignment explanation
Indices: 38312--38366 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
38302 ATTAATTTCG
*
38312 TGGTACATCGATGCATGGA-
1 TGGTGCATCGATGCATGGAT
38331 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
38351 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
38367 CACTTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:39280 original size:18 final size:18
Alignment explanation
Indices: 39254--39291 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
39244 TATTCTCCAG
*
39254 CTCAGACTATCATTATTT
1 CTCAAACTATCATTATTT
39272 CTCAAACTATCATTATTT
1 CTCAAACTATCATTATTT
39290 CT
1 CT
39292 TTAATGGAAA
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:0.29, C:0.24, G:0.03, T:0.45
Consensus pattern (18 bp):
CTCAAACTATCATTATTT
Found at i:47994 original size:25 final size:25
Alignment explanation
Indices: 47961--48008 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
47951 TAGTATGTTG
*
47961 CTCTCTGTTTTCGGTCTCTCTCTGT
1 CTCTCTGTTCTCGGTCTCTCTCTGT
* *
47986 CTCTGTGTTCTCTGTCTCTCTCT
1 CTCTCTGTTCTCGGTCTCTCTCT
48009 CTGTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (25 bp):
CTCTCTGTTCTCGGTCTCTCTCTGT
Found at i:47997 original size:19 final size:19
Alignment explanation
Indices: 47975--48013 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
47965 CTGTTTTCGG
* *
47975 TCTCTCTCTGTCTCTGTGT
1 TCTCTCTCTCTCTCTCTGT
*
47994 TCTCTGTCTCTCTCTCTGT
1 TCTCTCTCTCTCTCTCTGT
48013 T
1 T
48014 TTTTTTTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.13, T:0.54
Consensus pattern (19 bp):
TCTCTCTCTCTCTCTCTGT
Found at i:48493 original size:3 final size:3
Alignment explanation
Indices: 48485--48546 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
48475 AATATATATT
*
48485 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48533 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
48547 TGGGTAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49144 original size:113 final size:113
Alignment explanation
Indices: 48864--49526 Score: 1051
Period size: 113 Copynumber: 5.9 Consensus size: 113
48854 GATAGAATTA
* * *
48864 TTGAACAAGTTCTTCTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
48929 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAA-GTGATGAATTCAGGTAAAAGG
*
48978 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
49043 CTTTCTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGG
*
49091 TTGAACAAATTCTTCTCATTATGAACTT-TCTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
49155 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
65 ACTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGG
*
49204 TTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
49269 CTTTCTCTGGAAAAAATAATCCATCAAGTGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGG
49317 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* **
49382 CTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGG
*
49430 TTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
49495 CCTTCTCTGGAAATG-TAAATCCATCAAATGAT
66 CTTTCTCTGGAAAAGAT-AATCCATCAAGTGAT
49527 AGATTTGAAT
Statistics
Matches: 513, Mismatches: 33, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
112 2 0.00
113 424 0.83
114 87 0.17
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGG
Found at i:50397 original size:83 final size:83
Alignment explanation
Indices: 50258--50910 Score: 1218
Period size: 83 Copynumber: 7.9 Consensus size: 83
50248 GTAGTTCCTA
*
50258 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50323 ATTCAAAT-ATTGGTTCTG
66 ATTC-AATGATTGGTTCTG
50341 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50406 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
50424 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50489 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
50507 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50572 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
50590 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50655 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
50673 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50738 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
50756 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50821 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
50839 CTAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
50904 ATTCAAT
66 ATTCAAT
50911 TAATTGTTTG
Statistics
Matches: 560, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
82 3 0.01
83 557 0.99
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:52070 original size:21 final size:20
Alignment explanation
Indices: 52044--52095 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
52034 TTAACCCTCC
52044 TTTTTCTTTTTTTCCTCTCTT
1 TTTTTCTTTTTTTCCTCT-TT
**
52065 TTTTTCTTTTTTTTTTCTTT
1 TTTTTCTTTTTTTCCTCTTT
52085 TTCTTTCTTTT
1 TT-TTTCTTTT
52096 CTTCAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTTTTCCTCTTT
Found at i:52076 original size:10 final size:10
Alignment explanation
Indices: 52044--52095 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
52034 TTAACCCTCC
52044 TTTTTCTTTT
1 TTTTTCTTTT
* *
52054 TTTCCTCTCTT
1 TTT-TTCTTTT
52065 TTTTTCTTTTT
1 TTTTTC-TTTT
52076 TTTTTCTTTT
1 TTTTTCTTTT
*
52086 TCTTTCTTTT
1 TTTTTCTTTT
52096 CTTCAAGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:62725 original size:17 final size:17
Alignment explanation
Indices: 62703--62737 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62693 AAAATAAAAC
*
62703 ATATAAATATTATGAAA
1 ATATAAAAATTATGAAA
*
62720 ATATAAAAATTTTGAAA
1 ATATAAAAATTATGAAA
62737 A
1 A
62738 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATAAAAATTATGAAA
Found at i:62784 original size:6 final size:7
Alignment explanation
Indices: 62772--62796 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62762 TAAATATATA
62772 AATTTTT
1 AATTTTT
62779 AATTTTT
1 AATTTTT
62786 AATTTTT
1 AATTTTT
62793 AATT
1 AATT
62797 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:64397 original size:25 final size:25
Alignment explanation
Indices: 64364--64411 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
64354 TAGTATGTTG
*
64364 CTCTCTGTTTTCGGTCTCTCTCTGT
1 CTCTCTGTTCTCGGTCTCTCTCTGT
* *
64389 CTCTGTGTTCTCTGTCTCTCTCT
1 CTCTCTGTTCTCGGTCTCTCTCT
64412 CTGTTATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (25 bp):
CTCTCTGTTCTCGGTCTCTCTCTGT
Found at i:64400 original size:19 final size:19
Alignment explanation
Indices: 64378--64416 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
64368 CTGTTTTCGG
* *
64378 TCTCTCTCTGTCTCTGTGT
1 TCTCTCTCTCTCTCTCTGT
*
64397 TCTCTGTCTCTCTCTCTGT
1 TCTCTCTCTCTCTCTCTGT
64416 T
1 T
64417 ATCTTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.13, T:0.54
Consensus pattern (19 bp):
TCTCTCTCTCTCTCTCTGT
Found at i:64904 original size:3 final size:3
Alignment explanation
Indices: 64896--64957 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
64886 AATATATATT
*
64896 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64944 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
64958 TGGGTAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:65348 original size:38 final size:39
Alignment explanation
Indices: 65298--65380 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
65288 TAACCTATTG
65298 TTATTTGATCCATTGAAAGTTTGTAGGAAAATACTTAAT
1 TTATTTGATCCATTGAAAGTTTGTAGGAAAATACTTAAT
65337 TTATTT-ATCCATTGAAAGTTTGTAGGAAAATACTTAAT
1 TTATTTGATCCATTGAAAGTTTGTAGGAAAATACTTAAT
65375 TTATTT
1 TTATTT
65381 TAAATAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 38 0.86
39 6 0.14
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (39 bp):
TTATTTGATCCATTGAAAGTTTGTAGGAAAATACTTAAT
Found at i:66768 original size:2 final size:2
Alignment explanation
Indices: 66763--66789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66753 GAAATTTAAT
66763 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
66790 CAATATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81932 original size:2 final size:2
Alignment explanation
Indices: 81925--81949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81915 ACTCACGCGC
81925 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
81950 AAAGTAGTAT
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:82280 original size:20 final size:19
Alignment explanation
Indices: 82246--82283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
82236 ATTATTCTAC
*
82246 TATTGTAATTATAATTAAT
1 TATTATAATTATAATTAAT
82265 TATTATAATATATAATTAA
1 TATTATAAT-TATAATTAA
82284 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATTATAATTATAATTAAT
Found at i:82291 original size:12 final size:13
Alignment explanation
Indices: 82251--82299 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
82241 TCTACTATTG
*
82251 TAATTATAATTAA
1 TAATTATAATAAA
* *
82264 TTATTATAATATA
1 TAATTATAATAAA
82277 TAATTA-AATAAA
1 TAATTATAATAAA
*
82289 TAATTAAAATA
1 TAATTATAATA
82300 TATTTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATTATAATAAA
Found at i:82300 original size:25 final size:26
Alignment explanation
Indices: 82251--82302 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
82241 TCTACTATTG
* * *
82251 TAATTATAATTAATTATTATAATATA
1 TAATTATAATAAATAATTAAAATATA
82277 TAATTA-AATAAATAATTAAAATATA
1 TAATTATAATAAATAATTAAAATATA
82302 T
1 T
82303 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATTATAATAAATAATTAAAATATA
Found at i:82878 original size:28 final size:28
Alignment explanation
Indices: 82825--82881 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
82815 CCGTCATTCC
* * *
82825 TTTTAAGCACTAACTCGATGACATAATG
1 TTTTAAGAACTAACTCAATAACATAATG
*
82853 TTTTAAGAACTAACTCAATAATATAATG
1 TTTTAAGAACTAACTCAATAACATAATG
82881 T
1 T
82882 AACAGAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (28 bp):
TTTTAAGAACTAACTCAATAACATAATG
Done.