Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001440.1 Hibiscus syriacus cultivar Beakdansim tig00002789_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: 78581
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5801 original size:55 final size:56
Alignment explanation
Indices: 5712--5818 Score: 180
Period size: 55 Copynumber: 1.9 Consensus size: 56
5702 TGAGAAACGA
*
5712 TGTAATTTACCCTAAAAATATCCCTCCAATTGTAAATAATAAAAAGGAGAAAACAG
1 TGTAATTTACCCTAAAAATATCCCTCCAACTGTAAATAATAAAAAGGAGAAAACAG
* *
5768 TGTAATTTATCCTAAAAA-ATCCCTCCAACTGTAAATAATAAAAAGGGGAAA
1 TGTAATTTACCCTAAAAATATCCCTCCAACTGTAAATAATAAAAAGGAGAAA
5819 CTAGTTACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 31 0.65
56 17 0.35
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (56 bp):
TGTAATTTACCCTAAAAATATCCCTCCAACTGTAAATAATAAAAAGGAGAAAACAG
Found at i:11233 original size:27 final size:29
Alignment explanation
Indices: 11174--11230 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
11164 AATATATATA
*
11174 TTAACTTATATAACAATTAATAACTTAAT
1 TTAACTTATATAACAATTAATAACTCAAT
*
11203 TTAACTTAT-TAA-AATTTATAA-TCAAT
1 TTAACTTATATAACAATTAATAACTCAAT
11229 TT
1 TT
11231 TAATAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 8 0.31
28 3 0.12
29 9 0.35
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAACTTATATAACAATTAATAACTCAAT
Found at i:12040 original size:15 final size:15
Alignment explanation
Indices: 12022--12068 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
12012 TAACCGGTTT
12022 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
12037 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
12054 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
12069 TGATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:12050 original size:17 final size:17
Alignment explanation
Indices: 12025--12058 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12015 CCGGTTTCGG
12025 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
12042 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
12059 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:12493 original size:13 final size:13
Alignment explanation
Indices: 12472--12526 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
12462 AAGTTCGATA
*
12472 AATTCAAATACTT
1 AATTGAAATACTT
12485 AATTGAAATACTT
1 AATTGAAATACTT
* *
12498 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
12512 AATTGAAATACTT
1 AATTGAAATACTT
12525 AA
1 AA
12527 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:12608 original size:32 final size:33
Alignment explanation
Indices: 12512--12610 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
12502 AACTCAACAT
* * *
12512 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12545 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12578 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
12610 A
1 A
12611 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:12629 original size:21 final size:21
Alignment explanation
Indices: 12605--12644 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12595 ACTTCAAGTT
12605 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
12626 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
12645 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:13096 original size:13 final size:13
Alignment explanation
Indices: 13078--13144 Score: 91
Period size: 15 Copynumber: 4.9 Consensus size: 13
13068 ATAAAATCGG
13078 TTTTTTAACCGGT
1 TTTTTTAACCGGT
13091 TTTTTTCAAACCGGT
1 TTTTTT--AACCGGT
13106 TTTTTTAACCGGT
1 TTTTTTAACCGGT
13119 TTTTTTCAAACCGGT
1 TTTTTT--AACCGGT
13134 TTTTTT-ACCGG
1 TTTTTTAACCGG
13145 ATAAAAACCG
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.10
13 19 0.38
15 26 0.52
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (13 bp):
TTTTTTAACCGGT
Found at i:13102 original size:15 final size:15
Alignment explanation
Indices: 13084--13139 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
13074 TCGGTTTTTT
13084 AACCGGTTTTTTTCA
1 AACCGGTTTTTTTCA
13099 AACCGGTTTTTTT--
1 AACCGGTTTTTTTCA
13112 AACCGGTTTTTTTCA
1 AACCGGTTTTTTTCA
13127 AACCGGTTTTTTT
1 AACCGGTTTTTTT
13140 ACCGGATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.33
15 26 0.67
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (15 bp):
AACCGGTTTTTTTCA
Found at i:13114 original size:28 final size:28
Alignment explanation
Indices: 13078--13144 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
13068 ATAAAATCGG
13078 TTTTTTAACCGGTTTTTTTCAAACCGGT
1 TTTTTTAACCGGTTTTTTTCAAACCGGT
13106 TTTTTTAACCGGTTTTTTTCAAACCGGT
1 TTTTTTAACCGGTTTTTTTCAAACCGGT
13134 TTTTTT-ACCGG
1 TTTTTTAACCGG
13145 ATAAAAACCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (28 bp):
TTTTTTAACCGGTTTTTTTCAAACCGGT
Found at i:13246 original size:27 final size:28
Alignment explanation
Indices: 13214--13271 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
13204 AAAAAACCGG
13214 TTTTTCCCAAAACCGG-T-TTCGGATATT
1 TTTTTCCCAAAACCGGATATTCGGAT-TT
* *
13241 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCCCAAAACCGGATATTCGGATTT
13269 TTT
1 TTT
13272 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTTCCCAAAACCGGATATTCGGATTT
Found at i:19255 original size:48 final size:48
Alignment explanation
Indices: 19184--19280 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
19174 TTTCCAGAGA
* *
19184 TGAAACTGAGCTTGAATGCTGCTTGAGCAAGAACATGAATTATTAAAC
1 TGAAACTGAGCTTAAATGCTGCTTGAGCAAGAACATAAATTATTAAAC
* * *
19232 TGAAATTGAGCTTAAATGCTGCTTGTGCAAGAGCATAAATTATTAAAC
1 TGAAACTGAGCTTAAATGCTGCTTGAGCAAGAACATAAATTATTAAAC
19280 T
1 T
19281 TTTTTTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (48 bp):
TGAAACTGAGCTTAAATGCTGCTTGAGCAAGAACATAAATTATTAAAC
Found at i:22355 original size:36 final size:36
Alignment explanation
Indices: 22307--22385 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
22297 TTTAAGCTTG
* *
22307 AGCTTGACTAAGCTCA-TTTGCAGATTCTTGTACTTA
1 AGCTTGACTAAGCT-AGTTTACAGATTCTTGTACTCA
*
22343 AGCTTGATTAAGCTAGTTTACAGATTCTTGTACTCA
1 AGCTTGACTAAGCTAGTTTACAGATTCTTGTACTCA
22379 AGCTTGA
1 AGCTTGA
22386 ACTCAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (36 bp):
AGCTTGACTAAGCTAGTTTACAGATTCTTGTACTCA
Found at i:37091 original size:41 final size:41
Alignment explanation
Indices: 37019--37190 Score: 200
Period size: 41 Copynumber: 4.2 Consensus size: 41
37009 GGTAGAGGAT
* *
37019 GCATTTTGCATGAAGCGTCTTTTATTAATGTGGCAGAAGGC
1 GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
* * * ** * * * * *
37060 ACATTCTGCATGAAGCGCCTTCTGTTGATGTGGTAGAAGAC
1 GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
37101 GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
1 GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
* * *
37142 GCATTTTACATGAAGCATCTTTTGTTAATGTGACAGAAGGT
1 GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
37183 GCAATTTT
1 GC-ATTTT
37191 TTGACCCAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 104 0.95
42 5 0.05
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (41 bp):
GCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGC
Found at i:37173 original size:82 final size:82
Alignment explanation
Indices: 36997--37173 Score: 246
Period size: 82 Copynumber: 2.2 Consensus size: 82
36987 ATTGAGGGGA
* * * * *
36997 TTTTGTTGATATGGTAGAGGATGCATTTTGCATGAAGCGTCTTTTATTAATGTGGCAGAAGGCAC
1 TTTTGTTGATGTGGTAGAAGACGCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGCAC
* *
37062 ATTCTGCATGAAGCGCC
66 ATTCTACATGAAGCACC
* *
37079 TTCTGTTGATGTGGTAGAAGACGCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGCGC
1 TTTTGTTGATGTGGTAGAAGACGCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGCAC
* *
37144 ATTTTACATGAAGCATC
66 ATTCTACATGAAGCACC
*
37161 TTTTGTTAATGTG
1 TTTTGTTGATGTG
37174 ACAGAAGGTG
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (82 bp):
TTTTGTTGATGTGGTAGAAGACGCATTTTACATGAAGCATCTTTTATTAATGTGGCAGAAGGCAC
ATTCTACATGAAGCACC
Found at i:39297 original size:29 final size:29
Alignment explanation
Indices: 39236--39298 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
39226 TCTATTTTTG
* *
39236 CCCCCTAAAATTTTATAAGTTTAAATTCG
1 CCCCCTAAAATTTTATAAGTTCAAATTCA
*
39265 CCCCCTAAAATTTTATAAGTTCAAGTTCA
1 CCCCCTAAAATTTTATAAGTTCAAATTCA
39294 CCCCC
1 CCCCC
39299 AACTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (29 bp):
CCCCCTAAAATTTTATAAGTTCAAATTCA
Found at i:45678 original size:37 final size:36
Alignment explanation
Indices: 45606--45679 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
45596 GTTGGAAAAT
*
45606 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
45642 ATTTATATAGTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATT-AAAATCATAAA
45679 A
1 A
45680 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 9 0.27
37 20 0.61
38 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:46241 original size:12 final size:12
Alignment explanation
Indices: 46224--46248 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46214 AAACAGAAGA
46224 AAGTTGAAAAGC
1 AAGTTGAAAAGC
46236 AAGTTGAAAAGC
1 AAGTTGAAAAGC
46248 A
1 A
46249 TGCCAAAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGTTGAAAAGC
Found at i:47101 original size:2 final size:2
Alignment explanation
Indices: 47094--47130 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47084 ATGATAAATC
47094 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
47131 CTCAAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47554 original size:19 final size:18
Alignment explanation
Indices: 47512--47554 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
47502 TAATAATTTG
47512 TTATATATTATAAATATA
1 TTATATATTATAAATATA
47530 -TATATATATATATAATATAA
1 TTATATAT-TATA-AATAT-A
47550 TTATA
1 TTATA
47555 ACAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 5 0.24
20 1 0.05
21 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATATATTATAAATATA
Found at i:53997 original size:31 final size:30
Alignment explanation
Indices: 53902--53999 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
53892 ATAGTCCCCA
**
53902 AACTTTTAAGAATATTATATTTTGGTTATTC
1 AACTTTT-AGAATATTATATTTTAATTATTC
* * ** **
53933 AACTTTTA-AAAATTATAATACAA-TCCTC
1 AACTTTTAGAATATTATATTTTAATTATTC
53961 AAACTTTTAGGAATATTATATTTTAATTATTC
1 -AACTTTTA-GAATATTATATTTTAATTATTC
53993 AACTTTT
1 AACTTTT
54000 GAAAAATATA
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 1 0.02
31 25 0.51
32 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (30 bp):
AACTTTTAGAATATTATATTTTAATTATTC
Found at i:54030 original size:60 final size:60
Alignment explanation
Indices: 53900--54030 Score: 201
Period size: 60 Copynumber: 2.2 Consensus size: 60
53890 AAATAGTCCC
* **
53900 CAAACTTTTAAGAATATTATATTTTGGTTATTCAACTTTTAAAAATTATAATACAATCCT
1 CAAACTTTTAGGAATATTATATTTTAATTATTCAACTTTTAAAAATTATAATACAATCCT
*
53960 CAAACTTTTAGGAATATTATATTTTAATTATTCAACTTTTGAAAAA-TATAATACAGTCCT
1 CAAACTTTTAGGAATATTATATTTTAATTATTCAACTTTT-AAAAATTATAATACAATCCT
*
54020 TAAACTTTTAG
1 CAAACTTTTAG
54031 TTCGTTTCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 60 0.92
61 5 0.08
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (60 bp):
CAAACTTTTAGGAATATTATATTTTAATTATTCAACTTTTAAAAATTATAATACAATCCT
Found at i:56451 original size:3 final size:3
Alignment explanation
Indices: 56443--56474 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56433 TTAACAAGTG
56443 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56475 ATGGAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57248 original size:69 final size:69
Alignment explanation
Indices: 57137--57269 Score: 232
Period size: 69 Copynumber: 1.9 Consensus size: 69
57127 ATTCTTATTG
*
57137 TGTTTACCATCCAACAGATGAGCATGATCAGCTCATCCTCCATATCA-TTTTCGGTATACATCAA
1 TGTTTACCATCCAACAGATGAGCATGATCAGCTCATCCTCCATAT-AGTTTTCGGTATAAATCAA
57201 TATCA
65 TATCA
*
57206 TGTTTACCGTCCAACAGATGAGCATGATCAGCTCATCCTCCATATAGTTTTCGGTATAAATCAA
1 TGTTTACCATCCAACAGATGAGCATGATCAGCTCATCCTCCATATAGTTTTCGGTATAAATCAA
57270 AGTTCATTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 1 0.02
69 60 0.98
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (69 bp):
TGTTTACCATCCAACAGATGAGCATGATCAGCTCATCCTCCATATAGTTTTCGGTATAAATCAAT
ATCA
Found at i:58823 original size:167 final size:166
Alignment explanation
Indices: 58528--58850 Score: 461
Period size: 167 Copynumber: 1.9 Consensus size: 166
58518 AATTTACCGT
* * * *
58528 ATTTATGTCAAGATACTGATTAAAAAAAATGCAGGGGACCTAATGAGATTTTTCCAAATCTCACT
1 ATTTATGTAAAGATACTGATTAAAAAAAATGCAGGGGACCTAATAAGATTTTTCCAAACCTAACT
* * *
58593 CTTGACTCTAAAGTATGATTGGAGAAGATGGTCAATGATCTCAGCATAGTATAGACACAAATAAT
66 CTTGACTCTAAAGTATGATTGGAGAAGATGATCAACGATCTCAGCATAGAATAGACACAAATAAT
58658 GTAATTCCATATCTACACTAAATTAAGATTGACTGA
131 GTAATTCCATATCTACACTAAATTAAGATTGACTGA
* * ** *
58694 ATTTATTTAAAGATACTGATTAAACAAAATGCAGGGGACCTAA-AATTTTCCTTTCCGAACCTAA
1 ATTTATGTAAAGATACTGATTAAAAAAAATGCAGGGGACCTAATAAGATT--TTTCCAAACCTAA
* * * *
58758 TTCTTGACTCTCAATTATGATTGG-GAAAGATGATCAACGATCTCGGCATAGAATAGACACAAAT
64 CTCTTGACTCTAAAGTATGATTGGAG-AAGATGATCAACGATCTCAGCATAGAATAGACACAAAT
58822 AATGTAATTCCATATCTACACTAAATTAA
128 AATGTAATTCCATATCTACACTAAATTAA
58851 AAGTAACAAC
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
165 3 0.02
166 41 0.30
167 94 0.68
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (166 bp):
ATTTATGTAAAGATACTGATTAAAAAAAATGCAGGGGACCTAATAAGATTTTTCCAAACCTAACT
CTTGACTCTAAAGTATGATTGGAGAAGATGATCAACGATCTCAGCATAGAATAGACACAAATAAT
GTAATTCCATATCTACACTAAATTAAGATTGACTGA
Found at i:63968 original size:21 final size:21
Alignment explanation
Indices: 63943--64001 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
63933 GTCCGAGTTA
*
63943 CCCGCGACGGCCGCAATAGCG
1 CCCGCGATGGCCGCAATAGCG
*
63964 TCCGCGATGGCCGCAATAGCG
1 CCCGCGATGGCCGCAATAGCG
63985 CCCGCGATGGCCGCAAT
1 CCCGCGATGGCCGCAAT
64002 CACGGTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.19, C:0.39, G:0.32, T:0.10
Consensus pattern (21 bp):
CCCGCGATGGCCGCAATAGCG
Found at i:69056 original size:6 final size:6
Alignment explanation
Indices: 69047--69074 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
69037 TCAACGACAA
69047 CAATGC CAATGC CAATGC CAATGC CAAT
1 CAATGC CAATGC CAATGC CAATGC CAAT
69075 TAGGAGGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (6 bp):
CAATGC
Found at i:78032 original size:13 final size:13
Alignment explanation
Indices: 78014--78047 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
78004 TATCATTTTT
*
78014 TTTTAAATAATTA
1 TTTTAAAAAATTA
78027 TTTTAAAAAATTA
1 TTTTAAAAAATTA
78040 TTTTAAAA
1 TTTTAAAA
78048 TTAAGTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATTA
Done.