Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003317.1 Hibiscus syriacus cultivar Beakdansim tig00006988_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: 74691
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:620 original size:28 final size:28
Alignment explanation
Indices: 598--651 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
588 GTGTTTTAGA
598 TTAATTTAGGGAAGTAATATGTTTCAAG
1 TTAATTTAGGGAAGTAATATGTTTCAAG
* *
626 TTAATTTGGGGAGGTAATATGTTTCA
1 TTAATTTAGGGAAGTAATATGTTTCA
652 GGTTGGCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (28 bp):
TTAATTTAGGGAAGTAATATGTTTCAAG
Found at i:3198 original size:29 final size:29
Alignment explanation
Indices: 3145--3203 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3135 AAATCACAAG
* * *
3145 ACAAGACGAAAGGAAATCAAGTTAGTATAA
1 ACAAGACAAAAAGAAATCAAATTAGT-TAA
3175 ACAAGACAAAAAG-AATCAAATTAGTTAA
1 ACAAGACAAAAAGAAATCAAATTAGTTAA
3203 A
1 A
3204 ATGATTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 4 0.15
29 11 0.42
30 11 0.42
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (29 bp):
ACAAGACAAAAAGAAATCAAATTAGTTAA
Found at i:4140 original size:22 final size:20
Alignment explanation
Indices: 4102--4141 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4092 TTTATTATAT
*
4102 ATGACACCTCAAGGGAGAGA
1 ATGACACCACAAGGGAGAGA
4122 ATGACACACACAAGAGGAGA
1 ATGACAC-CACAAG-GGAGA
4142 CACACACGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.45, C:0.20, G:0.28, T:0.07
Consensus pattern (20 bp):
ATGACACCACAAGGGAGAGA
Found at i:5076 original size:24 final size:23
Alignment explanation
Indices: 5038--5091 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
5028 TGCCTCGACA
5038 TTTCATC-TTTTTCCCACTGCAT
1 TTTCATCTTTTTTCCCACTGCAT
5060 TTTCATCTATTTTTCCCACTGCAT
1 TTTCATCT-TTTTTCCCACTGCAT
*
5084 TTCCATCT
1 TTTCATCT
5092 GCTACACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 7 0.24
24 22 0.76
ACGTcount: A:0.15, C:0.31, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTCATCTTTTTTCCCACTGCAT
Found at i:24992 original size:44 final size:44
Alignment explanation
Indices: 24909--24998 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
24899 AACTTGATTT
* *
24909 ATCACATAAGAAGTTGGATCAACATCAGTACTTTGCTCGATTCC
1 ATCACATAAGAAGTTGGATCAACATCAGCACTTTACTCGATTCC
* *
24953 ATCATATAAGAAGTTGGATCAACAT-TGC-CATTTCACTCGATTCC
1 ATCACATAAGAAGTTGGATCAACATCAGCAC-TTT-ACTCGATTCC
24997 AT
1 AT
24999 TACAGAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 1 0.03
43 4 0.10
44 35 0.88
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (44 bp):
ATCACATAAGAAGTTGGATCAACATCAGCACTTTACTCGATTCC
Found at i:25221 original size:80 final size:79
Alignment explanation
Indices: 25072--25251 Score: 234
Period size: 80 Copynumber: 2.3 Consensus size: 79
25062 GAGGGAGAAG
* * * *
25072 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCATAAAAGGAGGTGAATCAA
1 AAGTTCATAATGAGAAGAACTTGTTCAACATTTACTCGATTCCATCACAAAAGGAAGTGAATCAA
25137 CATTTCCAATGAAA
66 CATTTCCAATGAAA
* * *
25151 AAGTTCCTAATGAGAAGAACTTGTTCAACATTTCACTCGATTCCATCACAGAAGGAAGTGGATCA
1 AAGTTCATAATGAGAAGAACTTGTTCAACATTT-ACTCGATTCCATCACAAAAGGAAGTGAATCA
* *
25216 ACATTTCTAATGGAA
65 ACATTTCCAATGAAA
** * *
25231 GGGTTCGTAATGAGAATAACT
1 AAGTTCATAATGAGAAGAACT
25252 CATCCGATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 31 0.36
80 56 0.64
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (79 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACATTTACTCGATTCCATCACAAAAGGAAGTGAATCAA
CATTTCCAATGAAA
Found at i:25245 original size:198 final size:197
Alignment explanation
Indices: 24981--25442 Score: 658
Period size: 198 Copynumber: 2.3 Consensus size: 197
24971 TCAACATTGC
* * * * * *
24981 CATTTCACTCGATTCCATTACAGAATGATGTGGACCAACATTTCCAATGAAAGGGTTCTTAATGA
1 CATTTCACTCGATTCCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAGGGTTCCTAATGA
* *
25046 GATGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTCGA
66 GAT-AACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGA
* *
25111 TTCCATCATAAAAGGAGGTGAATCAACATTTCCAATGAAAAAGTTCCTAATGAGAAGAACTTGTT
130 TTCCATCATAAAAGGAGGTGAATCAACATTTCCAATGAAAAAGTTCCTAAAGAGAAGAACTTGAT
25176 CAA
195 CAA
* * *
25179 CATTTCACTCGATTCCATCACAGAAGGAAGTGGATCAACATTTCTAATGGAAGGGTTCGTAATGA
1 CATTTCACTCGATTCCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAGGGTTCCTAATGA
*
25244 GAATAACTCATCCGATTAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGA
66 G-ATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGA
* * * *
25309 TTCCATCATAGAAGGAGGTGGATCAACATTTCCAATGAAGAAGTTCTTAAAGAGAAGAACTTGAT
130 TTCCATCATAAAAGGAGGTGAATCAACATTTCCAATGAAAAAGTTCCTAAAGAGAAGAACTTGAT
*
25374 CAG
195 CAA
* * * * * *
25377 CATTT-GCTCGATTCTATCACAGAAAGAGGTAGATTAACATTTCCAAT-GAAGAAGTTCCTAATG
1 CATTTCACTCGATTCCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAG-GGTTCCTAATG
25440 AGA
65 AGA
25443 AGAATTTGCT
Statistics
Matches: 236, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
196 5 0.02
197 46 0.19
198 183 0.78
199 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (197 bp):
CATTTCACTCGATTCCATCACAGAAAGAAGTGGATCAACATTTCCAATGGAAGGGTTCCTAATGA
GATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGAT
TCCATCATAAAAGGAGGTGAATCAACATTTCCAATGAAAAAGTTCCTAAAGAGAAGAACTTGATC
AA
Found at i:25364 original size:79 final size:79
Alignment explanation
Indices: 25266--25483 Score: 292
Period size: 79 Copynumber: 2.7 Consensus size: 79
25256 CGATTAGGGA
* * * * *
25266 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTAGATTCCATCATAGAAGGAGGTGGA
1 GAAGAAGTTCATAATGAGAAGAACTTGATCAACATTTGCTCGATTCCATCACAGAAGGAGGTAGA
25331 TCAACATTTCCAAT
66 TCAACATTTCCAAT
* * * * *
25345 GAAGAAGTTCTTAAAGAGAAGAACTTGATCAGCATTTGCTCGATTCTATCACAGAAAGAGGTAGA
1 GAAGAAGTTCATAATGAGAAGAACTTGATCAACATTTGCTCGATTCCATCACAGAAGGAGGTAGA
*
25410 TTAACATTTCCAAT
66 TCAACATTTCCAAT
* * * *
25424 GAAGAAGTTCCTAATGAGAAGAATTTGCTCAACATTTCACTCGATTCCATCACAGAAGGA
1 GAAGAAGTTCATAATGAGAAGAACTTGATCAACATTT-GCTCGATTCCATCACAGAAGGA
25484 AATAAATATT
Statistics
Matches: 119, Mismatches: 19, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
79 100 0.84
80 19 0.16
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (79 bp):
GAAGAAGTTCATAATGAGAAGAACTTGATCAACATTTGCTCGATTCCATCACAGAAGGAGGTAGA
TCAACATTTCCAAT
Found at i:25364 original size:118 final size:119
Alignment explanation
Indices: 25151--25369 Score: 316
Period size: 118 Copynumber: 1.8 Consensus size: 119
25141 TCCAATGAAA
* *
25151 AAGTTCCTAATGAGAAGAACTTGTTCAACATTTCACTCGATTCCATCACAGAAGGAAGTGGATCA
1 AAGTTCATAATGAGAAGAACTTGTTCAACATTTCACTAGATTCCATCACAGAAGGAAGTGGATCA
* * * *
25216 ACATTTCTAATGGAAGGGTTCGTAATGAGAATAACTCATCCGATTAGGGAGAAG
66 ACATTTCCAATGGAAGAGTTCGTAAAGAGAAGAACTCATCCGATTAGGGAGAAG
* * * *
25270 AAGTTCATAATGAGAAGAACTTGTTCAACCTTT-GCTAGATTCCATCATAGAAGGAGGTGGATCA
1 AAGTTCATAATGAGAAGAACTTGTTCAACATTTCACTAGATTCCATCACAGAAGGAAGTGGATCA
*
25334 ACATTTCCAAT-GAAGAAGTTCTTAAAGAGAAGAACT
66 ACATTTCCAATGGAAG-AGTTCGTAAAGAGAAGAACT
25370 TGATCAGCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
117 4 0.05
118 53 0.60
119 31 0.35
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (119 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACATTTCACTAGATTCCATCACAGAAGGAAGTGGATCA
ACATTTCCAATGGAAGAGTTCGTAAAGAGAAGAACTCATCCGATTAGGGAGAAG
Found at i:25854 original size:117 final size:116
Alignment explanation
Indices: 25616--25876 Score: 264
Period size: 116 Copynumber: 2.2 Consensus size: 116
25606 ACATTTACAA
* * * * *
25616 TGAAGAATTTCCTAATGAA-AAGAACTTGTTCAACATTTCACTCAATTCCATCACATGAGGTGGA
1 TGAAGAAGTTCATAAT-AAGAAGAACTTGTTCAACATTTCACTCAATTCCATCAAAAGAGGTAGA
* * *
25680 TCAACATTTCTAATGGAAGGATTCATAATGAGAATAACTCATCCGATGACGG
65 TCAACATTTCCAATGGAAGGATTCATAATGAGAAGAACTCATCCGAGGACGG
* * * *
25732 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTT-TCTCGATTCCATCATAAAAAGAGGTA
1 TGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTCACTCAATTCCATC---AAAAGAGGTA
* * *
25796 GATCAACATTTCCAGTGG-A-GAGTTCATAATGAGAAGAACTTATCTGAGGA-GAG
63 GATCAACATTTCCAATGGAAGGA-TTCATAATGAGAAGAACTCATCCGAGGACG-G
* * *
25849 TGAAG-AGTTCGTAATGAGGAGAACTTGT
1 TGAAGAAGTTCATAATAAGAAGAACTTGT
25877 AGCTTAAGAA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
115 13 0.11
116 54 0.45
117 30 0.25
118 23 0.19
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (116 bp):
TGAAGAAGTTCATAATAAGAAGAACTTGTTCAACATTTCACTCAATTCCATCAAAAGAGGTAGAT
CAACATTTCCAATGGAAGGATTCATAATGAGAAGAACTCATCCGAGGACGG
Found at i:28236 original size:34 final size:34
Alignment explanation
Indices: 28193--28273 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
28183 AAAATAATAA
*
28193 TAAAGATTAATGAGTTATTTGAGTATAGTAATGT
1 TAAAGATTAATGAGTTATTTGAGTATAATAATGT
28227 TAAAGATTAATGAGTTATTTGAGTATAATAATGT
1 TAAAGATTAATGAGTTATTTGAGTATAATAATGT
*
28261 TGAAGATTAATGA
1 TAAAGATTAATGA
28274 AGTGTATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.40
Consensus pattern (34 bp):
TAAAGATTAATGAGTTATTTGAGTATAATAATGT
Found at i:48743 original size:78 final size:78
Alignment explanation
Indices: 48636--48792 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 78
48626 TGCACTTAGC
*
48636 CCCAAGGGACTTAGTGCATCCGCCCCTGTATGATGTATATAATTTGTAATACCTATAGCCCGTAT
1 CCCAAGGGACTTAGTGCATCCGCCCCTGTATGATGTATATAATTTGTAACACCTATAGCCCGTAT
48701 ATGTCTCGTAATA
66 ATGTCTCGTAATA
* * * *
48714 CCCAAGGGACTTAGTGTATTCGTCCCTGTATGATGTATATAATTTGTTACACCTATAGCCCGTAT
1 CCCAAGGGACTTAGTGCATCCGCCCCTGTATGATGTATATAATTTGTAACACCTATAGCCCGTAT
48779 ATGTCTCGTAATA
66 ATGTCTCGTAATA
48792 C
1 C
48793 GAGCTAAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (78 bp):
CCCAAGGGACTTAGTGCATCCGCCCCTGTATGATGTATATAATTTGTAACACCTATAGCCCGTAT
ATGTCTCGTAATA
Found at i:50113 original size:22 final size:23
Alignment explanation
Indices: 50073--50115 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
50063 ATCATATCCT
50073 AAACATTCATAAAACATTCGTGC
1 AAACATTCATAAAACATTCGTGC
50096 AAACATT-ATAAATA-ATTCGT
1 AAACATTCATAAA-ACATTCGT
50116 ATTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (23 bp):
AAACATTCATAAAACATTCGTGC
Found at i:51629 original size:22 final size:22
Alignment explanation
Indices: 51601--51646 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
51591 TCCAATCAAC
51601 TTTCTAA-CTTAAAATTCCAGCA
1 TTTCTAATCTTAAAATT-CAGCA
51623 TTTCTAATCTTAAAATTCAGCA
1 TTTCTAATCTTAAAATTCAGCA
51645 TT
1 TT
51647 AACACTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTCTAATCTTAAAATTCAGCA
Found at i:52838 original size:29 final size:29
Alignment explanation
Indices: 52760--52840 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
52750 AATATATCAT
* * * *
52760 TTTTCAAAATTATATTTTGGTCCCTAAAC
1 TTTTCAAAATTACATTTTAGTCACAAAAC
* **
52789 TTTTCAAAGTTTACACGTTAGTCACAAAAC
1 TTTTCAAA-ATTACATTTTAGTCACAAAAC
52819 -TTTCAAAACTTACATTTTAGTC
1 TTTTCAAAA-TTACATTTTAGTC
52841 GCTAGTCAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTTCAAAATTACATTTTAGTCACAAAAC
Found at i:58182 original size:23 final size:23
Alignment explanation
Indices: 58155--58207 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
58145 AGAAGTTAGC
58155 ATGTTAGAAGTTAAGGGTTAGTA
1 ATGTTAGAAGTTAAGGGTTAGTA
*
58178 ATGTTAGAAGTTAGGGGTTAGTA
1 ATGTTAGAAGTTAAGGGTTAGTA
*
58201 AGGTTAG
1 ATGTTAG
58208 TAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (23 bp):
ATGTTAGAAGTTAAGGGTTAGTA
Found at i:59826 original size:44 final size:44
Alignment explanation
Indices: 59714--59838 Score: 164
Period size: 44 Copynumber: 2.8 Consensus size: 44
59704 GGACGAGCCA
*
59714 AAAGAGTGACGCTGATCCAACTCCTTATGTGATGGAATCGAGCGC
1 AAAGAGTGACGCTGATCCAACTCCTTATGTGATGGAACCGA-CGC
* * * *
59759 AATGA-TGACGCTGGTCTACCTCCTTATGTGATGGAACCGA-GC
1 AAAGAGTGACGCTGATCCAACTCCTTATGTGATGGAACCGACGC
*
59801 AAAGAGTTGATGCTGATCCAACTCCTTATGTGATGGAA
1 AAAGAG-TGACGCTGATCCAACTCCTTATGTGATGGAA
59839 GAGCCAAGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 6 0.09
44 58 0.85
45 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (44 bp):
AAAGAGTGACGCTGATCCAACTCCTTATGTGATGGAACCGACGC
Found at i:59953 original size:83 final size:83
Alignment explanation
Indices: 59814--59972 Score: 237
Period size: 83 Copynumber: 1.9 Consensus size: 83
59804 GAGTTGATGC
* *
59814 TGATCCAACTCCTTATGTGATGGAAGAGCCAAGGTTGAATAAGTTCTTCTCATTAGGAACTTATT
1 TGATCCAACTCCTTATGTGATGGAAGAGCCAAGGTTGAACAAGTTCTTCTCATTAGGAACTTACT
*
59879 TTCCCTCATCGAGAATGA
66 CTCCCTCATCGAGAATGA
* * * * * *
59897 TGATCTAACTCTTTATGTGATGGATGAGCCATGGTTGAACAAGTTTTTCTCATTAGGAACTTCCT
1 TGATCCAACTCCTTATGTGATGGAAGAGCCAAGGTTGAACAAGTTCTTCTCATTAGGAACTTACT
59962 CTCCCTCATCG
66 CTCCCTCATCG
59973 GACGAGTTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (83 bp):
TGATCCAACTCCTTATGTGATGGAAGAGCCAAGGTTGAACAAGTTCTTCTCATTAGGAACTTACT
CTCCCTCATCGAGAATGA
Found at i:60065 original size:116 final size:115
Alignment explanation
Indices: 59903--60229 Score: 372
Period size: 115 Copynumber: 2.8 Consensus size: 115
59893 ATGATGATCT
* * * *
59903 AACTCTTTATGTGATGGATGAGCCATGGTTGAACAAGTTTTTCTCATTAGGAACTTCCTCTCCCT
1 AACTCCTTATGTGATGGATGAGCCA-AGTTGAACAAGTTATTCTCATTAGGAACTTCTTCTCCCT
59968 CATCGGACGAGTTCTTCTCATTATAAACCCTTCCACTAAAAATGCTAATCC
65 CATCGGACGAGTTCTTCTCATTATAAACCCTTCCACTAAAAATGCTAATCC
* * *
60019 AACTCCTTATGTGAAGGATGAGCCACAGTTGAACAAGTTATTCTCATTAGAAACTTCTTCTCCCA
1 AACTCCTTATGTGATGGATGAGCCA-AGTTGAACAAGTTATTCTCATTAGGAACTTCTTCTCCCT
* *** * * * ** * *
60084 CAT-TGTTTAGTTCTTCTTATTATGAACCCTTCTACTGGAAATGTTGATCC
65 CATCGGACGAGTTCTTCTCATTATAAACCCTTCCACTAAAAATGCTAATCC
* * * * * * *
60134 AACTCCTTATGAGATGGATGAGTCAAGGTCAA-ACAGTTCTTGTCATTAGGAACTTATTCTCCCT
1 AACTCCTTATGTGATGGATGAGCCAAGTTGAACA-AGTTATTCTCATTAGGAACTTCTTCTCCCT
*
60198 CATCGGACGAGTTCTTTTCATTA-AAACCCTTC
65 CATCGGACGAGTTCTTCTCATTATAAACCCTTC
60230 TATTGGAAAT
Statistics
Matches: 173, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
113 1 0.01
114 41 0.24
115 71 0.41
116 60 0.35
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (115 bp):
AACTCCTTATGTGATGGATGAGCCAAGTTGAACAAGTTATTCTCATTAGGAACTTCTTCTCCCTC
ATCGGACGAGTTCTTCTCATTATAAACCCTTCCACTAAAAATGCTAATCC
Found at i:63720 original size:23 final size:24
Alignment explanation
Indices: 63694--63748 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
63684 ATGTGCGTTG
63694 TAAATAGTTAA-AAATATTTTGAA
1 TAAATAGTTAAGAAATATTTTGAA
63717 TAAATAGTTAAGAAATATTTTGAA
1 TAAATAGTTAAGAAATATTTTGAA
63741 TAAATAGT
1 TAAATAGT
63749 ATCTCACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (24 bp):
TAAATAGTTAAGAAATATTTTGAA
Found at i:65756 original size:19 final size:18
Alignment explanation
Indices: 65712--65752 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
65702 AAATAAACAC
65712 ATAAATGTTAGTTTTATTA
1 ATAAAT-TTAGTTTTATTA
*
65731 AT-AATTTAGTTTTTTTA
1 ATAAATTTAGTTTTATTA
65748 ATAAA
1 ATAAA
65753 ATTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 13 0.65
18 5 0.25
19 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
ATAAATTTAGTTTTATTA
Found at i:65758 original size:20 final size:19
Alignment explanation
Indices: 65712--65758 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
65702 AAATAAACAC
*
65712 ATAAATGTTAGTTTTATTA
1 ATAAATTTTAGTTTTATTA
*
65731 AT-AA-TTTAGTTTTTTTA
1 ATAAATTTTAGTTTTATTA
65748 ATAAAATTTTA
1 AT-AAATTTTA
65759 ATATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 4 0.17
20 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATAAATTTTAGTTTTATTA
Found at i:73017 original size:15 final size:15
Alignment explanation
Indices: 72999--73029 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72989 AAATTCTAAA
72999 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
73014 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
73029 T
1 T
73030 CTATTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Done.