Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007691.1 Hibiscus syriacus cultivar Beakdansim tig00109880_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: 74725
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:407 original size:150 final size:147
Alignment explanation
Indices: 102--373 Score: 384
Period size: 150 Copynumber: 1.8 Consensus size: 147
92 ATCACTCAGG
102 GACAAAGTCTAGGACTTCTAATTAGACAAGAAAAATAAAGCAACAGAATATGGAGTACTTACAAT
1 GACAAAGTCTAGGACTTCTAATTAGACAAGAAAAATAAAGCAACAGAATATGGAGTACTTACAAT
*
167 GAACTACTTTGGTTAAATATCATACCTGATTTATCATATTCATCTCACAATTTTTTAATACACAG
66 GAACTACTTTGGTTAAATATCATACCTGATTTATCATATTCATCTCACAATTTTTGAATACACA-
** * * ***
232 GAGGTTTAGTATCACTCGGG
130 GAGCATAAGAATCA--CAAA
* * * *
252 GACAAAGTCTAGGACTTCTAATTAGACATGCAAAATCAAGCAACAGAATATGGAGTACTTATAAT
1 GACAAAGTCTAGGACTTCTAATTAGACAAGAAAAATAAAGCAACAGAATATGGAGTACTTACAAT
* *
317 GAACT-CTTTGGTTAAATATCATACGTGGTTTATCATATTCATCTCACAATTTTTGAA
66 GAACTACTTTGGTTAAATATCATACCTGATTTATCATATTCATCTCACAATTTTTGAA
374 CTGATCATCC
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
149 49 0.43
150 66 0.57
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (147 bp):
GACAAAGTCTAGGACTTCTAATTAGACAAGAAAAATAAAGCAACAGAATATGGAGTACTTACAAT
GAACTACTTTGGTTAAATATCATACCTGATTTATCATATTCATCTCACAATTTTTGAATACACAG
AGCATAAGAATCACAAA
Found at i:6264 original size:19 final size:20
Alignment explanation
Indices: 6240--6283 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6230 TTATTTCATA
*
6240 TTTAAAATGAA-TTTAATAT
1 TTTAAAAGGAATTTTAATAT
*
6259 TTTAAAAGGAATTTTATTAT
1 TTTAAAAGGAATTTTAATAT
6279 TTTAA
1 TTTAA
6284 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTAAAAGGAATTTTAATAT
Found at i:21021 original size:65 final size:65
Alignment explanation
Indices: 20917--21044 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
20907 ATAACACTAG
20917 GTTGGTTTAGGAATTCTGAAGGAGCTCTCAATTCTGGTGTGTCTGGTTCTTCTTGAACTTCTTCA
1 GTTGGTTTAGGAATTCTGAAGGAGCTCTCAATTCTGGTGTGTCTGGTTCTTCTTGAACTTCTTCA
* * *
20982 GTTGGTTTAGGAATTCTGGAGGAGCTCTCAGTTCTGGTGTGTTTGGTTCTTCTTGAACTTCTT
1 GTTGGTTTAGGAATTCTGAAGGAGCTCTCAATTCTGGTGTGTCTGGTTCTTCTTGAACTTCTT
21045 TAGGACTGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.15, C:0.16, G:0.27, T:0.43
Consensus pattern (65 bp):
GTTGGTTTAGGAATTCTGAAGGAGCTCTCAATTCTGGTGTGTCTGGTTCTTCTTGAACTTCTTCA
Found at i:21834 original size:15 final size:15
Alignment explanation
Indices: 21814--21843 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21804 GAGATGATAC
21814 CCATACATCAATATG
1 CCATACATCAATATG
21829 CCATACATCAATATG
1 CCATACATCAATATG
21844 AACAAACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
CCATACATCAATATG
Found at i:27800 original size:3 final size:3
Alignment explanation
Indices: 27792--27862 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
27782 TTTTTATCCA
*
27792 TAT TAT TAT TAT TAA 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
27840 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
27863 ATTTATATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:29325 original size:22 final size:20
Alignment explanation
Indices: 29284--29328 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
29274 ATAGAATTAT
**
29284 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
29304 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
29326 TAT
1 TAT
29329 ATATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:40677 original size:19 final size:19
Alignment explanation
Indices: 40648--40710 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
40638 TATTATGCTT
*
40648 GAAAAAAAGAAAGAAAAAGA
1 GAAAAAGAGAAA-AAAAAGA
40668 -AAAAAGAGAAAAAAAAGA
1 GAAAAAGAGAAAAAAAAGA
40686 GAAAAACGA-AAAAAAAAGA
1 GAAAAA-GAGAAAAAAAAGA
40705 GAAAAA
1 GAAAAA
40711 AAAGGGGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 7 0.17
19 31 0.77
20 2 0.05
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (19 bp):
GAAAAAGAGAAAAAAAAGA
Found at i:40681 original size:11 final size:11
Alignment explanation
Indices: 40667--40714 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
40657 AAAGAAAAAG
40667 AAAAAAGAGAA
1 AAAAAAGAGAA
40678 AAAAAAGAG--
1 AAAAAAGAGAA
*
40687 AAAAACGA-AA
1 AAAAAAGAGAA
40697 AAAAAAGAGAA
1 AAAAAAGAGAA
40708 AAAAAAG
1 AAAAAAG
40715 GGGGTCAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.22
10 7 0.22
11 18 0.56
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:40689 original size:30 final size:29
Alignment explanation
Indices: 40649--40714 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
40639 ATTATGCTTG
*
40649 AAAAAAAGA-AAGAAA-AAGAAAAAAGAGA
1 AAAAAAAGAGAA-AAACAAAAAAAAAGAGA
40677 AAAAAAAGAGAAAAACGAAAAAAAAAGAGA
1 AAAAAAAGAGAAAAAC-AAAAAAAAAGAGA
40707 AAAAAAAG
1 AAAAAAAG
40715 GGGGTCAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.35
29 2 0.06
30 20 0.59
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAGAAAAACAAAAAAAAAGAGA
Found at i:41732 original size:51 final size:51
Alignment explanation
Indices: 41656--41953 Score: 537
Period size: 51 Copynumber: 5.8 Consensus size: 51
41646 TATGTGCTCA
41656 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
41707 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
41758 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
*
41809 ATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGG-TGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
*
41859 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
*
41911 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
41954 TGGCAGAACC
Statistics
Matches: 242, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
49 3 0.01
50 45 0.19
51 142 0.59
52 52 0.21
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (51 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAAC
Found at i:42072 original size:52 final size:52
Alignment explanation
Indices: 41994--42149 Score: 287
Period size: 52 Copynumber: 3.0 Consensus size: 52
41984 GAATTTGCTA
41994 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42046 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42098 ACAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
42150 CAATCATTGA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
52 98 0.96
53 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:42122 original size:187 final size:188
Alignment explanation
Indices: 41809--42233 Score: 786
Period size: 187 Copynumber: 2.3 Consensus size: 188
41799 TTAGAAGAAC
41809 ATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGG-TGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
41872 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACACAGCATCTTCTGGAAGTGTTCTTTG
41937 AGTTATCTGATATGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCT-A
131 AGTTATCTGATATGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTAA
41994 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
42059 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACACAGCATCTTCTGGAAGTGTTCTTTG
66 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACACAGCATCTTCTGGAAGTGTTCTTTG
* *
42124 AGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTAA
131 AGTTATCTGATATGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTAA
42182 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
42234 CAATCATTGA
Statistics
Matches: 233, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
185 22 0.09
186 18 0.08
187 141 0.61
188 48 0.21
189 4 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (188 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACACAGCATCTTCTGGAAGTGTTCTTTG
AGTTATCTGATATGGTTTGGCAGAACCAATCATTGAATTTGAAAGATGAATTTGCTAA
Found at i:42321 original size:83 final size:83
Alignment explanation
Indices: 42100--42393 Score: 518
Period size: 83 Copynumber: 3.5 Consensus size: 83
42090 GACAGAACAC
42100 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
42165 GAAGATGAATTTGCTAAAT
66 GAAGATGAATTTGCT-AAT
42184 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
42249 GAAGATGAATTTGCTAAT
66 GAAGATGAATTTGCTAAT
* *
42267 AGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATCAATCATTGAATTT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAATTT
*
42331 GGAAGATGAATTTGTTAAT
65 GGAAGATGAATTTGCTAAT
* *
42350 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGTTTTGG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
42394 TAAGAACTAC
Statistics
Matches: 202, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
82 4 0.02
83 114 0.56
84 84 0.42
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
GAAGATGAATTTGCTAAT
Found at i:43288 original size:112 final size:114
Alignment explanation
Indices: 42995--43553 Score: 973
Period size: 114 Copynumber: 4.8 Consensus size: 114
42985 CAAAGATTCA
*
42995 AATTCATCACTTGATGGATCA-TCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAG-AA-AGTTCATAATGAGAAGAA--C-TCATC
43059 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
43113 AATTCATCAATTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATC-ACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
43178 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43228 AATTCATCAC-TGATGGATCATTC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
43291 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43340 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
43405 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43454 AATTCATCACTTGATGGATCATTC-TTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCACTTGATGGATCATTCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATC
43518 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
61 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
43554 CATCAAGAGC
Statistics
Matches: 429, Mismatches: 3, Indels: 18
0.95 0.01 0.04
Matches are distributed among these distances:
112 99 0.23
113 34 0.08
114 117 0.27
115 85 0.20
116 1 0.00
117 1 0.00
118 67 0.16
119 14 0.03
120 11 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (114 bp):
AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:43417 original size:226 final size:231
Alignment explanation
Indices: 42995--43553 Score: 1022
Period size: 226 Copynumber: 2.4 Consensus size: 231
42985 CAAAGATTCA
42995 AATTCATCACTTGATGGATCA-TCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCACTTGATGGATCATTC-TTTCCAGAG-AAGAGTTCATAATGAGAAGAAC-CGTCATC
*
43059 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAT
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAC
43124 TTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
128 TTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
43189 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
193 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43228 AATTCATCAC-TGATGGATCATTCTTTCCAGAGAA-AGTTCATAATGAGAAGAA-C-TCATCTGA
1 AATTCATCACTTGATGGATCATTCTTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTCATCTGA
43289 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-ACTTG
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAACTTG
43353 ATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
131 ATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
43418 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
196 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
43454 AATTCATCACTTGATGGATCATTCTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCATTCTTTCCAGA-GAAGAGTTCATAATGAGAAGAAC-CGTCATCT
43519 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
43554 CATCAAGAGC
Statistics
Matches: 318, Mismatches: 1, Indels: 15
0.95 0.00 0.04
Matches are distributed among these distances:
226 115 0.36
227 88 0.28
228 4 0.01
229 18 0.06
230 18 0.06
231 3 0.01
232 60 0.19
233 12 0.04
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (231 bp):
AATTCATCACTTGATGGATCATTCTTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAACTTG
ATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:43803 original size:3 final size:3
Alignment explanation
Indices: 43795--43873 Score: 126
Period size: 3 Copynumber: 26.7 Consensus size: 3
43785 ATTTTATCCA
*
43795 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
43843 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43874 ATTTATATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 65 0.92
4 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:43806 original size:15 final size:14
Alignment explanation
Indices: 43794--43883 Score: 116
Period size: 15 Copynumber: 6.4 Consensus size: 14
43784 AATTTTATCC
43794 ATATTATTATTATT
1 ATATTATTATTATT
43808 AATATTATTATTATT
1 -ATATTATTATTATT
43823 ATTATTATTATTATT
1 A-TATTATTATTATT
43838 ATA-T-TTATTA-T
1 ATATTATTATTATT
43849 -TATTATTATTATT
1 ATATTATTATTATT
43862 ATATTATTATTAATTT
1 ATATTATTATT-A-TT
43878 ATATTA
1 ATATTA
43884 AATATATTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 13
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.03
11 2 0.03
12 12 0.18
13 2 0.03
14 13 0.19
15 29 0.43
16 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTATTATTATT
Found at i:47399 original size:2 final size:2
Alignment explanation
Indices: 47392--47416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47382 ACGTATAATT
47392 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
47417 AAATCCTAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49930 original size:2 final size:2
Alignment explanation
Indices: 49923--49947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49913 CTAGGTTTTA
49923 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
49948 AAACACTATT
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:60989 original size:35 final size:35
Alignment explanation
Indices: 60933--61003 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
60923 GTTAAAAACT
*
60933 ATATCAATATACTAAATTAAAAGCAGGGCCCATAA
1 ATATCAATAAACTAAATTAAAAGCAGGGCCCATAA
*
60968 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
1 ATATCAATAAACTAAATTAAAAGCAGGGCCCATAA
61003 A
1 A
61004 CTTATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (35 bp):
ATATCAATAAACTAAATTAAAAGCAGGGCCCATAA
Found at i:64758 original size:23 final size:24
Alignment explanation
Indices: 64712--64759 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
64702 AGATATAATG
*
64712 TAAATCACTTTTCAAATAATTCAA
1 TAAATCACTTTTCAAATAAATCAA
64736 TAAATCA-TTTTCTAAA-AAATCAA
1 TAAATCACTTTTC-AAATAAATCAA
64759 T
1 T
64760 TACATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATCACTTTTCAAATAAATCAA
Found at i:70205 original size:20 final size:18
Alignment explanation
Indices: 70168--70206 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
70158 AAATCATCTT
*
70168 ACAACAAACGGTATATGA
1 ACAACAAACCGTATATGA
70186 ACAAGCAAACCGTAATATGA
1 ACAA-CAAACCGT-ATATGA
70206 A
1 A
70207 GAATTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (18 bp):
ACAACAAACCGTATATGA
Found at i:70721 original size:2 final size:2
Alignment explanation
Indices: 70714--70739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
70704 TGACACGTAC
70714 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
70740 TACAAACAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:74610 original size:2 final size:2
Alignment explanation
Indices: 74598--74642 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
74588 AGAAATTACA
*
74598 AT AT AT GT 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 AT
74640 AT A
1 AT A
74643 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.