Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006186.1 Hibiscus syriacus cultivar Beakdansim tig00014724_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: 69172
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:5468 original size:41 final size:41
Alignment explanation
Indices: 5421--5571 Score: 209
Period size: 41 Copynumber: 3.7 Consensus size: 41
5411 TAAAACACTG
* *
5421 CAATAGTGATAATCAATAGTGGCATTTTTAGACAAACG-TA
1 CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
* *
5461 GCAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAATGCCA
1 -CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
*
5503 CAATAGTTTTAATCAATAGTGGCATTTTTTA-ACAAACGCCA
1 CAATAGTGTTAATCAATAGTGGCA-TTTTTAGACAAACGCCA
*
5544 AAATAGTG-TAATCAATAGTGGCATTTTT
1 CAATAGTGTTAATCAATAGTGGCATTTTT
5572 TTTGTATAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.05
40 15 0.15
41 72 0.73
42 7 0.07
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (41 bp):
CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
Found at i:17024 original size:18 final size:16
Alignment explanation
Indices: 17001--17034 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
16991 AGAAAAACTT
17001 GATGATTTATTGTTTTTG
1 GATGATTT-TT-TTTTTG
17019 GATGATTTTTTTTTTG
1 GATGATTTTTTTTTTG
17035 AAAGGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (16 bp):
GATGATTTTTTTTTTG
Found at i:17388 original size:22 final size:23
Alignment explanation
Indices: 17346--17388 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17336 CTGACGGGCA
*
17346 TCCAGTCATCAGCTTCCAGAAGG
1 TCCAGTCAACAGCTTCCAGAAGG
*
17369 TCCAGTCAACA-CTTCTAGAA
1 TCCAGTCAACAGCTTCCAGAA
17389 AGACGAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (23 bp):
TCCAGTCAACAGCTTCCAGAAGG
Found at i:18846 original size:21 final size:22
Alignment explanation
Indices: 18813--18857 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
18803 TTCTGGGTAG
*
18813 TGTGCATCAATGCA-TCTTCAA
1 TGTGCATCAATGCACTCTTAAA
* *
18834 TGTGTATCGATGCACTCTTAAA
1 TGTGCATCAATGCACTCTTAAA
18856 TG
1 TG
18858 AATGAACATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (22 bp):
TGTGCATCAATGCACTCTTAAA
Found at i:18902 original size:19 final size:19
Alignment explanation
Indices: 18878--18929 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
18868 GAATACAATT
18878 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
18897 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
* *
18916 AGTACGTCGATGCA
1 AGTGCATCGATGCA
18930 CCCCATTAAA
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:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:19892 original size:18 final size:18
Alignment explanation
Indices: 19869--19917 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
19859 ATGGTTCTAC
19869 GTGGTCCTACGTGACATA
1 GTGGTCCTACGTGACATA
*
19887 GTGGTCCTACGGGACATA
1 GTGGTCCTACGTGACATA
*
19905 -TGTGTTCTACGTG
1 GTG-GTCCTACGTG
19918 GTCCTACAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
GTGGTCCTACGTGACATA
Found at i:19944 original size:28 final size:28
Alignment explanation
Indices: 19887--19945 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
19877 ACGTGACATA
* * *
19887 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACAGGACATATGTGTCCAAC
*
19915 GTGGTCCTACAGGATATA-GTGGTCCAAC
1 GTGGTCCTACAGGACATATGT-GTCCAAC
19943 GTG
1 GTG
19946 ACAAATTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
GTGGTCCTACAGGACATATGTGTCCAAC
Found at i:23244 original size:25 final size:25
Alignment explanation
Indices: 23210--23259 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
23200 GATCAAGGGT
*
23210 ACTGAAGCATAAACATATAGTGATA
1 ACTGAAGCATAAACATATAGAGATA
*
23235 ACTGAAGCATAAACATGTAGAGATA
1 ACTGAAGCATAAACATATAGAGATA
23260 TATTGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (25 bp):
ACTGAAGCATAAACATATAGAGATA
Found at i:23786 original size:21 final size:21
Alignment explanation
Indices: 23762--23889 Score: 97
Period size: 21 Copynumber: 6.0 Consensus size: 21
23752 AGTCGACGGT
23762 TCTACGTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
**
23783 TCTACGTGGTCCTACTAGACA
1 TCTACGTGGTCCTACGGGACA
23804 --TA-GTGGTCCTACGGGACATA
1 TCTACGTGGTCCTACGGGAC--A
*
23824 TGTGTTCTACATGGTCCTACGGGACA
1 -----TCTACGTGGTCCTACGGGACA
* *
23850 TCTACGTGGTCCTAC--TAGA
1 TCTACGTGGTCCTACGGGACA
*
23869 TATA-GTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
23889 T
1 T
23890 ATGTGTTCTA
Statistics
Matches: 84, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
18 23 0.27
19 7 0.08
20 4 0.05
21 33 0.39
26 1 0.01
27 2 0.02
28 14 0.17
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
TCTACGTGGTCCTACGGGACA
Found at i:23838 original size:28 final size:28
Alignment explanation
Indices: 23807--23914 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
23797 CTAGACATAG
23807 TGGTCCTACGGGACATATGTGTTCTACA
1 TGGTCCTACGGGACATATGTGTTCTACA
* *
23835 TGGTCCTACGGGACATCTACGTGGTCCTACTAGATATA
1 TGGTCCTACGGGACA--TATGT-GT--T-C----TACA
*
23873 GTGGTCCTACGGGACATATGTGTTCTACG
1 -TGGTCCTACGGGACATATGTGTTCTACA
23902 TGGTCCTACGGGA
1 TGGTCCTACGGGA
23915 TAAATTCTAC
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
28 28 0.44
29 2 0.03
30 4 0.06
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 4 0.06
38 3 0.05
39 15 0.23
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (28 bp):
TGGTCCTACGGGACATATGTGTTCTACA
Found at i:23868 original size:67 final size:67
Alignment explanation
Indices: 23760--23914 Score: 292
Period size: 67 Copynumber: 2.3 Consensus size: 67
23750 AAAGTCGACG
23760 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
1 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
23825 GT
66 GT
* *
23827 GTTCTACATGGTCCTACGGGACATCTACGTGGTCCTACTAGATATAGTGGTCCTACGGGACATAT
1 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
23892 GT
66 GT
23894 GTTCTACGTGGTCCTACGGGA
1 GTTCTACGTGGTCCTACGGGA
23915 TAAATTCTAC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 85 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (67 bp):
GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
GT
Found at i:37554 original size:13 final size:13
Alignment explanation
Indices: 37536--37570 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
37526 TTCCATTTTA
37536 AATAAAATATACC
1 AATAAAATATACC
37549 AATAAAATATACC
1 AATAAAATATACC
37562 AATAAAATA
1 AATAAAATA
37571 ACTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATATACC
Found at i:43924 original size:66 final size:66
Alignment explanation
Indices: 43831--44322 Score: 456
Period size: 66 Copynumber: 7.5 Consensus size: 66
43821 AGGGTTGATG
* * * * *
43831 GTTTCAAGAGAAA-TCGTCTCAAAAGAGACAAAACATGTTTCAAGGGAAAAAATCTCAAAGGTTG
1 GTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAACATGTTTCAAGGGAAAAGATCTCAAAGATTT
43895 GT
65 GT
* *
43897 GTTTGAAGGGAAACTGTCTCAAGAGAGACAAAATTCA--TTTCAAGGGAAACGATCTCAAAGATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--CATGTTTCAAGGGAAAAGATCTCAAAGATT
43960 TGT
64 TGT
* * * ** *
43963 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATTA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAA-AGATCTCAAAGATTT
44027 GT
65 GT
* * * *
44029 GTTTCAAGGGAAATTGTCTTAAGAGAGAGAAAATTCA--TTTCAAGGGAAACGATCTCAAAGATT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--CATGTTTCAAGGGAAAAGATCTCAAAGATT
44092 TGT
64 TGT
* * * *
44095 GTTTCAAGAGAAATTGTCTCAATG-GATACAAAATC-TGTTTCAAGGGAAACAAAT-TCAAAGAT
1 GTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAA-CATGTTTCAAGGGAAA-AGATCTCAAAGAT
*
44157 TGGT
63 TTGT
* * * * *
44161 GTTTCAAGGGAAAATGTCTCAAGAAAGACAAAA-TTCGTTTCAAGGGAAACGATCTCATAGACTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACAT-GTTTCAAGGGAAAAGATCTCAAAGA-TT
*
44225 TTT
64 TGT
* ** * *
44228 GTTTCAA-GGAAACTGTCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACAGA-CTCAAAGACTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAA-AGATCTCAAAGATTT
44291 -T
65 GT
* *
44292 -TTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
44323 TTTGTTTTGA
Statistics
Matches: 355, Mismatches: 50, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
62 2 0.01
63 25 0.07
64 1 0.00
65 11 0.03
66 293 0.83
67 21 0.06
68 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (66 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAAAGATCTCAAAGATTTG
T
Found at i:43968 original size:30 final size:31
Alignment explanation
Indices: 43934--44041 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 31
43924 ACAAAATTCA
43934 TTTCAAGGGAAAC-GATCTCAAAGATTTGTG
1 TTTCAAGGGAAACAGATCTCAAAGATTTGTG
* * *
43964 TTTCAAGAGAAACTG-TCTCAAGGGAGAAAAAATT-TG
1 TTTCAAGGGAAACAGATCTCAA---AG----ATTTGTG
*
44000 TTTCAAGGGAAACAGAT-TCAAAGATTAGTG
1 TTTCAAGGGAAACAGATCTCAAAGATTTGTG
44030 TTTCAAGGGAAA
1 TTTCAAGGGAAA
44042 TTGTCTTAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
29 2 0.03
30 32 0.52
31 1 0.02
33 4 0.06
36 19 0.31
37 4 0.06
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (31 bp):
TTTCAAGGGAAACAGATCTCAAAGATTTGTG
Found at i:44068 original size:132 final size:132
Alignment explanation
Indices: 43831--44324 Score: 678
Period size: 132 Copynumber: 3.8 Consensus size: 132
43821 AGGGTTGATG
** ** *
43831 GTTTCAAGAGAAA-TCGTCTCAAAAGAGACAAAACATGTTTCAAGGGAAA-AAATCTCAAAGGTT
1 GTTTCAAGAGAAACT-GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAAT-TCAAAGATT
* *
43894 GGTGTTTGAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGAT
64 GGTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGAT
43959 TTGT
129 TTGT
* * *
43963 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTAG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
* *
44028 TGTTTCAAGGGAAATTGTCTTAAGAGAGAGAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
66 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
44093 GT
131 GT
* * * *
44095 GTTTCAAGAGAAATTGTCTCAATGGATACAAAATCTGTTTCAAGGGAAACAAATTCAAAGATTGG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
* * * *
44160 TGTTTCAAGGGAAAATGTCTCAAGAAAGACAAAATTCGTTTCAAGGGAAACGATCTCATAGACTT
66 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGA-TT
*
44225 TTT
130 TGT
* * *
44228 GTTTCAAG-GAAACTGTCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACAGACTCAAAGACTT-
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGA-TTG
*
44291 -T-TTT-AAGAGAAATTGTCTCAAGAGAGACAAAATT
65 GTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
44325 TGTTTTGAGT
Statistics
Matches: 322, Mismatches: 36, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
129 27 0.08
130 3 0.01
131 1 0.00
132 273 0.85
133 18 0.06
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (132 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
GT
Found at i:44137 original size:21 final size:20
Alignment explanation
Indices: 44105--44147 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
44095 GTTTCAAGAG
* *
44105 AAATTGTCTCAATGGATACA
1 AAATTGTCTCAAGGGAAACA
*
44125 AAATCTGTTTCAAGGGAAACA
1 AAAT-TGTCTCAAGGGAAACA
44146 AA
1 AA
44148 TTCAAAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (20 bp):
AAATTGTCTCAAGGGAAACA
Found at i:44181 original size:198 final size:196
Alignment explanation
Indices: 43831--44329 Score: 550
Period size: 198 Copynumber: 2.5 Consensus size: 196
43821 AGGGTTGATG
* ** *
43831 GTTTCAAGAGAAA-TCGTCTCAAAAGAGACAAAA--CATGTTTCAAGGGAAAAAATCTCAAAGGT
1 GTTTCAAG-GAAACT-GTCTCAAGAGAGACAAAATTCA--TTTCAAGGGAAACGATCTCAAAGAT
* * * * *
43893 TGGTGTTTGAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGA
62 TTGTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAATT-GTTTCAAGGGAAACAATCTCAAAGA
* * ** *
43958 TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAGAT-TCAAA
125 TTGGTGTTTCAAGAGAAAATGTCTCAAGAAAGAAAAAATTCGTTTCAAGGGAAAC-GATCTCAAA
44022 GA-TTAGT
189 GACTTAGT
* * *
44029 GTTTCAAGGGAAATTGTCTTAAGAGAGAGAAAATTCATTTCAAGGGAAACGATCTCAAAGATTTG
1 GTTTCAA-GGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTTG
*
44094 TGTTTCAAGAGAAATTGTCTCAATG-GATACAAAATCTGTTTCAAGGGAAACAAAT-TCAAAGAT
65 TGTTT-AAGAGAAATTGTCTCAA-GAGAGACAAAAT-TGTTTCAAGGGAAAC-AATCTCAAAGAT
* * *
44157 TGGTGTTTCAAGGGAAAATGTCTCAAGAAAGACAAAATTCGTTTCAAGGGAAACGATCTCATAGA
126 TGGTGTTTCAAGAGAAAATGTCTCAAGAAAGAAAAAATTCGTTTCAAGGGAAACGATCTCAAAGA
**
44222 CTTTTT
191 CTTAGT
* ** * *
44228 GTTTCAAGGAAACTGTCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACAGA-CTCAAAGACTT-
1 GTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAAC-GATCTCAAAGATTTG
44291 T-TTTAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTT
65 TGTTTAAGAGAAATTGTCTCAAGAGAGACAAAA-TTGTTT
44330 TGAGTAAAAA
Statistics
Matches: 257, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
194 1 0.00
195 30 0.12
196 4 0.02
197 4 0.02
198 198 0.77
199 18 0.07
200 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (196 bp):
GTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTTGT
GTTTAAGAGAAATTGTCTCAAGAGAGACAAAATTGTTTCAAGGGAAACAATCTCAAAGATTGGTG
TTTCAAGAGAAAATGTCTCAAGAAAGAAAAAATTCGTTTCAAGGGAAACGATCTCAAAGACTTAG
T
Found at i:44823 original size:16 final size:16
Alignment explanation
Indices: 44802--44835 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44792 TTCATGTATC
*
44802 ATGTATGTATGTGTTG
1 ATGTATGTATATGTTG
44818 ATGTATGTATATGTTG
1 ATGTATGTATATGTTG
44834 AT
1 AT
44836 CTTTGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
ATGTATGTATATGTTG
Found at i:45854 original size:2 final size:2
Alignment explanation
Indices: 45847--45881 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45837 GCTTTATTGT
45847 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
45882 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45886 original size:2 final size:2
Alignment explanation
Indices: 45881--45906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45871 ACACACACAC
45881 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
45907 TATGGGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51907 original size:31 final size:30
Alignment explanation
Indices: 51872--51951 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
51862 GGAGTACATT
51872 GGGGCCTGC-GAGCCTACCAAAGAAAATTCTC
1 GGGGCC-GCAGAGCCTACCAAAGAAAA-TCTC
* * *
51903 GGGGCCACGGAGGCCTACCCAAGAAAATCTC
1 GGGGCCGCAGA-GCCTACCAAAGAAAATCTC
* *
51934 AGGGTCGCAGAGCCTACC
1 GGGGCCGCAGAGCCTACC
51952 CAAGGGTCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 8 0.20
31 19 0.46
32 14 0.34
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.12
Consensus pattern (30 bp):
GGGGCCGCAGAGCCTACCAAAGAAAATCTC
Found at i:51951 original size:30 final size:31
Alignment explanation
Indices: 51881--51955 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
51871 TGGGGCCTGC
* * *
51881 GAGCCTACCAAAGAAAATTCTCGGGGCCACG
1 GAGCCTACCCAAGAAAATTCTCAGGGCCACA
* *
51912 GAGGCCTACCCAAGAAAA-TCTCAGGGTCGCA
1 GA-GCCTACCCAAGAAAATTCTCAGGGCCACA
51943 GAGCCTACCCAAG
1 GAGCCTACCCAAG
51956 GGTCGTCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 11 0.29
31 13 0.34
32 14 0.37
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.12
Consensus pattern (31 bp):
GAGCCTACCCAAGAAAATTCTCAGGGCCACA
Found at i:54501 original size:3 final size:3
Alignment explanation
Indices: 54493--54540 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
54483 AAATTCTTTA
54493 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54541 GTATATAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:58470 original size:3 final size:3
Alignment explanation
Indices: 58462--58536 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
58452 ATGGGCTTTA
*
58462 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58510 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
58537 TTGTTTTAGC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58810 original size:54 final size:54
Alignment explanation
Indices: 58693--58810 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
58683 GAAGTGCTAA
* * * *
58693 ACTCACACCAAACGAAACAAATCACGTAAGGTGGACAAAACCATAGATTCTAAT
1 ACTCACACCAAACGAAACAAATCAAGTAAGGTGGACAAAACCAAAGATCCCAAT
* * * * *
58747 ACTTACACCAACCTAAACAAATCAAGTAAGGTGGACGAACCCGAAAG-TCCCAAT
1 ACTCACACCAAACGAAACAAATCAAGTAAGGTGGACAAAACC-AAAGATCCCAAT
*
58801 ACTCGCACCA
1 ACTCACACCA
58811 TACATAACCA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 49 0.94
55 3 0.06
ACGTcount: A:0.43, C:0.28, G:0.14, T:0.15
Consensus pattern (54 bp):
ACTCACACCAAACGAAACAAATCAAGTAAGGTGGACAAAACCAAAGATCCCAAT
Found at i:61380 original size:17 final size:17
Alignment explanation
Indices: 61358--61393 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
61348 AATTAAAGGT
61358 TGGAATGATATATGCTC
1 TGGAATGATATATGCTC
*
61375 TGGAATGATTTATGCTC
1 TGGAATGATATATGCTC
61392 TG
1 TG
61394 ATCGGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (17 bp):
TGGAATGATATATGCTC
Found at i:65665 original size:15 final size:15
Alignment explanation
Indices: 65629--65671 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
65619 AGTTGGTGTT
* * *
65629 TCAAGGAAAATGATT
1 TCAAGGGAAATAATC
65644 TCAAGGGAAATAATC
1 TCAAGGGAAATAATC
*
65659 TCAAGGGAGATAA
1 TCAAGGGAAATAA
65672 ATTTGGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (15 bp):
TCAAGGGAAATAATC
Done.