Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006877.1 Hibiscus syriacus cultivar Beakdansim tig00017522_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: 94360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5011 original size:30 final size:31
Alignment explanation
Indices: 4958--5020 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
4948 AGCTTATGTA
*
4958 AAAACATACCAAAGCTGATAGTTTAGGTACT
1 AAAACATACCAAAGCTAATAGTTTAGGTACT
4989 AAAACATACCAAA-CTAATAGTTTAGGTACT
1 AAAACATACCAAAGCTAATAGTTTAGGTACT
5019 AA
1 AA
5021 CGTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (31 bp):
AAAACATACCAAAGCTAATAGTTTAGGTACT
Found at i:7527 original size:30 final size:30
Alignment explanation
Indices: 7493--7551 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
7483 CATTTTTACA
* *
7493 ATGAATTTTCTATTTT-TTACAATTTAATCC
1 ATGAACTTTATATTTTGTT-CAATTTAATCC
*
7523 ATGAACTTTATATTTTGTTTAATTTAATC
1 ATGAACTTTATATTTTGTTCAATTTAATC
7552 TTCCAACTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (30 bp):
ATGAACTTTATATTTTGTTCAATTTAATCC
Found at i:14937 original size:20 final size:21
Alignment explanation
Indices: 14907--14945 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
14897 ACTACAGGTA
14907 CAAATATGACAAAACCGGTCC
1 CAAATATGACAAAACCGGTCC
14928 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
14946 AAAACGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCC
Found at i:15673 original size:182 final size:180
Alignment explanation
Indices: 15199--15675 Score: 647
Period size: 182 Copynumber: 2.6 Consensus size: 180
15189 AAATTAAACT
15199 AAAAGTGTCGACACTTTATGAAAATG-ATCGATTCATAACAATATAACAGGTAAAAATATGATAA
1 AAAAGTGTCGACACTTTATGAAAATGTATCGA-TCATAACAATATAACAGGTAAAAATATGATAA
* * *
15263 AATTGATCTCAAAAATGACAAAA-CA-TGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATT
65 AATTGGTCTC-AAAATGACAAAACCAGT-AAAAAG-TACCAGATATGTTGAAAGTGTCGATAATT
* * *
15326 AAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAATTATAGCGCTTA
127 AAATATAAGTATCGACACTTTATGAATTTAAAAGAGAAGAAATTATAGCACTTA
* *
15380 AAAAGTGTCGACACTTTATTAAAATGTATCGATCATTACCAATATAACAGGTAAAAATATGATAA
1 AAAAGTGTCGACACTTTATGAAAATGTATCGATCA-TAACAATATAACAGGTAAAAATATGATAA
** * * * * * *
15445 AATAAGTCTAAAAAATGACAACACC-GAAAAAAGTAACTGAATATGTTGAAAGTGTCGATAATTT
65 AATTGGTCT-CAAAATGACAAAACCAGTAAAAAGTACCAG-ATATGTTGAAAGTGTCGATAATTA
* * *
15509 AATATAAGTATCGACATTTTATGAATTTAAAATAGAAGAATTTATAGCACTTA
128 AATATAAGTATCGACACTTTATGAATTTAAAAGAGAAGAAATTATAGCACTTA
*
15562 AAAAGTGTCGACACTTTATGAAAATGTATCGATCCAGAACAATATAACAGGTAAAAATATGATAA
1 AAAAGTGTCGACACTTTATGAAAATGTATCGAT-CATAACAATATAACAGGTAAAAATATGATAA
* *
15627 AATTGGTCTCAAAATGATAAAACCAGTAAATAGATACCAGATATGTTGA
65 AATTGGTCTCAAAATGACAAAACCAGTAAAAAG-TACCAGATATGTTGA
15676 TCCAGAATTA
Statistics
Matches: 257, Mismatches: 30, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
181 44 0.17
182 206 0.80
183 7 0.03
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (180 bp):
AAAAGTGTCGACACTTTATGAAAATGTATCGATCATAACAATATAACAGGTAAAAATATGATAAA
ATTGGTCTCAAAATGACAAAACCAGTAAAAAGTACCAGATATGTTGAAAGTGTCGATAATTAAAT
ATAAGTATCGACACTTTATGAATTTAAAAGAGAAGAAATTATAGCACTTA
Found at i:16111 original size:15 final size:15
Alignment explanation
Indices: 16091--16148 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
16081 TTTCTCAAAT
16091 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* * *
16106 CTCTTCCCAACTCAG
1 CTCTTCTCAACCCAC
16121 CTCTTCTCAACCACAAC
1 CTCTTCTCAACC-C-AC
16138 CTCCTTCTCAA
1 CT-CTTCTCAA
16149 ACAATCACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 22 0.65
16 1 0.03
17 3 0.09
18 8 0.24
ACGTcount: A:0.22, C:0.48, G:0.02, T:0.28
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:18279 original size:2 final size:2
Alignment explanation
Indices: 18272--18327 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
18262 TAGACACGTG
18272 AT AT AT AT 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
18314 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
18328 GTTGAAGGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18507 original size:2 final size:2
Alignment explanation
Indices: 18500--18527 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18490 TATCAATACA
18500 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
18528 TTAATCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19104 original size:12 final size:12
Alignment explanation
Indices: 19087--19111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19077 ACTCCATAAA
19087 AAGGCTCTTTTT
1 AAGGCTCTTTTT
19099 AAGGCTCTTTTT
1 AAGGCTCTTTTT
19111 A
1 A
19112 CTTAAGTTAC
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (12 bp):
AAGGCTCTTTTT
Found at i:21015 original size:64 final size:64
Alignment explanation
Indices: 20876--21036 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
20866 AATTGTTCAG
* * *
20876 TGTGTATCGATGCACAGGAAGT-TCATCGATGCA-CCCATTAAAATAGAAACATTGAATGCAATT
1 TGTGTATCGATGCATAGGAAGTGT-ATCGATGCACCCCATTAAAATAGAAACATCGAAGGCAATT
* * * **
20939 AGTGCATCGATGCATAAGG-AGTGTATCGATGCACCCCCTTAAAATTA-AAACATCGAAGGTGAT
1 TGTGTATCGATGCAT-AGGAAGTGTATCGATGCACCCCATTAAAA-TAGAAACATCGAAGGCAAT
21002 T
64 T
* *
21003 TGTGTATCGATGCATGGGTAGTGTATCGATGCAC
1 TGTGTATCGATGCATAGGAAGTGTATCGATGCAC
21037 ATGTTAAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
63 26 0.32
64 54 0.66
65 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAAGTGTATCGATGCACCCCATTAAAATAGAAACATCGAAGGCAATT
Found at i:21069 original size:20 final size:20
Alignment explanation
Indices: 21044--21081 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21034 CACATGTTAA
21044 AGAATGCATCGATACACTAT
1 AGAATGCATCGATACACTAT
* *
21064 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
21082 TAAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTAT
Found at i:22867 original size:23 final size:23
Alignment explanation
Indices: 22800--22884 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
22790 CGTATAAATT
*
22800 TGCACCGAAGTGCCACGTAGAATT
1 TGCACCGAAGTGCCACGTAGAA-A
* *
22824 TGTC-CCGAAG-GACCGCATAGAAA
1 TG-CACCGAAGTG-CCACGTAGAAA
* *
22847 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAA
*
22870 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
22885 TATAATATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
22 1 0.02
23 29 0.60
24 17 0.35
25 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:24975 original size:23 final size:23
Alignment explanation
Indices: 24907--24967 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
24897 ACATTTTATA
*
24907 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
*
24930 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
24953 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
24968 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:34141 original size:94 final size:94
Alignment explanation
Indices: 33980--34169 Score: 335
Period size: 94 Copynumber: 2.0 Consensus size: 94
33970 GACCTAATAA
**
33980 TATCTTCAATTGAGATGTAGGGGTAAATTTCATTGATTCCACTTACTGATTATTGGTGGGAAATT
1 TATCTTCAATTGAGATGTAGGGGTAAATTTCATTGATTCCACTTACTGATTATTGGTGAAAAATT
* *
34045 AAATTAAATAGATTAATACGTGTCCTTTT
66 AAATTAAATAAACTAATACGTGTCCTTTT
*
34074 TATCTTCAATTGAGATGTAGGGGTAAATTTCATTGATTCCACTTACTGATTTTTGGTGAAAAATT
1 TATCTTCAATTGAGATGTAGGGGTAAATTTCATTGATTCCACTTACTGATTATTGGTGAAAAATT
34139 AAATTAAATAAACTAATACGTGTCCTTTT
66 AAATTAAATAAACTAATACGTGTCCTTTT
34168 TA
1 TA
34170 AGAAATTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (94 bp):
TATCTTCAATTGAGATGTAGGGGTAAATTTCATTGATTCCACTTACTGATTATTGGTGAAAAATT
AAATTAAATAAACTAATACGTGTCCTTTT
Found at i:37245 original size:30 final size:30
Alignment explanation
Indices: 37202--37266 Score: 71
Period size: 31 Copynumber: 2.1 Consensus size: 30
37192 CATATTATAG
*
37202 AAAAGTATTAATAA-AATAAGTTAAAGTGATT
1 AAAAGTATAAATAATAA-AAGTT-AAGTGATT
37233 AAAA-TATAAATAATTTAAAAGTTAAGTGATT
1 AAAAGTATAAATAA--TAAAAGTTAAGTGATT
37264 AAA
1 AAA
37267 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
30 8 0.27
31 15 0.50
32 5 0.17
33 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAAGTATAAATAATAAAAGTTAAGTGATT
Found at i:52202 original size:3 final size:3
Alignment explanation
Indices: 52194--52236 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
52184 TAAACACTTC
52194 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52237 AAGATTTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61955 original size:26 final size:27
Alignment explanation
Indices: 61904--61955 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
61894 TTATTAATAA
* * *
61904 AAATAAAAATATTGGTATATTTTATTT
1 AAATAAAAATATTGATAAATTATATTT
61931 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
61956 AATTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTT
Found at i:62126 original size:27 final size:26
Alignment explanation
Indices: 62059--62130 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
62049 ATATTAATAT
62059 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATTCATTA
* * *
62086 TTAATAATTTAATAATATTATTTA-TA
1 TAAATAA-TAAATAATATTATTCATTA
62112 TGAAATTAATAAATAATAT
1 T-AAA-TAATAAATAATAT
62131 AAAATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 4 0.11
27 30 0.81
28 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TAAATAATAAATAATATTATTCATTA
Found at i:62201 original size:23 final size:23
Alignment explanation
Indices: 62171--62221 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
62161 TTAAAATAAA
* *
62171 AATATAATATCTTGTATTATTAT
1 AATATAATATATTATATTATTAT
* *
62194 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
62217 AATAT
1 AATAT
62222 TAAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:62206 original size:18 final size:18
Alignment explanation
Indices: 62185--62219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62175 TAATATCTTG
62185 TATTATTATAATATAATT
1 TATTATTATAATATAATT
* *
62203 TATTATTTTATTATAAT
1 TATTATTATAATATAAT
62220 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATAATATAATT
Found at i:62239 original size:22 final size:23
Alignment explanation
Indices: 62211--62257 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
62201 TTTATTATTT
62211 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
62233 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
62256 TA
1 TA
62258 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:62244 original size:30 final size:33
Alignment explanation
Indices: 62185--62263 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
62175 TAATATCTTG
* * *
62185 TATTATTATAATATAATTTATTATTTTATTA-TAA
1 TATTAATA-AATATAA-TTATTATATTATTAGAAA
62219 TATTAA-AAATATAA-TATTATATTATTAGAAA
1 TATTAATAAATATAATTATTATATTATTAGAAA
62250 TATTAATAAATATA
1 TATTAATAAATATA
62264 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.30
31 8 0.20
32 14 0.35
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
TATTAATAAATATAATTATTATATTATTAGAAA
Found at i:62262 original size:22 final size:22
Alignment explanation
Indices: 62219--62262 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
62209 TTTATTATAA
*
62219 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
62241 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
62263 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:68452 original size:2 final size:2
Alignment explanation
Indices: 68445--68475 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68435 ACAATTTAAA
68445 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 A
68476 ATTCATCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68630 original size:2 final size:2
Alignment explanation
Indices: 68621--68652 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
68611 TACATAATGT
68621 TA TA -A 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 TA TA TA T
68653 TGGTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69900 original size:26 final size:26
Alignment explanation
Indices: 69857--69909 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
69847 TAGGCACATG
*
69857 ATATATATCACATCATCA-TTTATAAC
1 ATATATATCAAATCATCACTTTA-AAC
* *
69883 ATATATATTAAATTATCACTTTAAAC
1 ATATATATCAAATCATCACTTTAAAC
69909 A
1 A
69910 AATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATATATCAAATCATCACTTTAAAC
Found at i:71377 original size:34 final size:34
Alignment explanation
Indices: 71339--71420 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
71329 GAATGGGGAT
71339 GCAGTTCAATAACACTGATAAA-TTCCAAAGAGAC
1 GCAGTTCAATAACACTGA-AAATTTCCAAAGAGAC
* * * *
71373 GCAGTTGAATGACACTGAAAATTTCCAACGAGAT
1 GCAGTTCAATAACACTGAAAATTTCCAAAGAGAC
71407 GCAGTTCAATAACA
1 GCAGTTCAATAACA
71421 TTAAAAGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 3 0.07
34 38 0.93
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (34 bp):
GCAGTTCAATAACACTGAAAATTTCCAAAGAGAC
Found at i:72467 original size:45 final size:45
Alignment explanation
Indices: 72403--72496 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
72393 ACCTTCTATG
72403 ATCCTCGTGCTTAATTAAAGCGTGATCTTGCTTTGCTTGCTTGTT
1 ATCCTCGTGCTTAATTAAAGCGTGATCTTGCTTTGCTTGCTTGTT
72448 ATCCTCGTGCTTAATTAAAGCGTGATCTTGCTTTGCTTGCTTGTT
1 ATCCTCGTGCTTAATTAAAGCGTGATCTTGCTTTGCTTGCTTGTT
72493 ATCC
1 ATCC
72497 GGGTTGGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (45 bp):
ATCCTCGTGCTTAATTAAAGCGTGATCTTGCTTTGCTTGCTTGTT
Found at i:78272 original size:94 final size:94
Alignment explanation
Indices: 78153--78532 Score: 649
Period size: 94 Copynumber: 4.1 Consensus size: 94
78143 TAGATTGCTT
* *
78153 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
78218 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
78247 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
78312 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
78341 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
78406 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
78435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGATAAACTATGTATTCTTTAATACTAT-ACAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGA-AGTTAG
78499 TATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
78528 AGTAA
1 AGTAA
78533 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
93 27 0.10
94 250 0.90
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:78645 original size:17 final size:17
Alignment explanation
Indices: 78620--78668 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
78610 AAAAATGACT
78620 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
* *
78637 ATCGTAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
78651 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
78668 A
1 A
78669 AATTGCAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 4 0.16
17 9 0.36
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:78687 original size:33 final size:33
Alignment explanation
Indices: 78620--78711 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
78610 AAAAATGACT
* * *
78620 ATCGCAACGCGAAATG--AATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
78651 ATCGCAACGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* **
78684 ATCGCAATGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
78712 CGAAACTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 16 0.31
33 35 0.69
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:78726 original size:19 final size:19
Alignment explanation
Indices: 78680--78717 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
78670 ATTGCAACGA
*
78680 CAAAATCGCAATGCGAAAC
1 CAAAATCGCAACGCGAAAC
78699 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
78718 TATAATCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.08
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:78786 original size:20 final size:20
Alignment explanation
Indices: 78761--78812 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
78751 GATTCTCTCG
*
78761 TTGCGATAGTTAAATTCACA
1 TTGCGATAGTCAAATTCACA
** *
78781 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCACA
78801 TTGCGATAGTCA
1 TTGCGATAGTCA
78813 TTTTCGCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCACA
Found at i:78813 original size:20 final size:20
Alignment explanation
Indices: 78779--78827 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
78769 GTTAAATTCA
78779 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
78799 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
78819 CGTTGCGAT
1 CATTGCGAT
78828 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:80795 original size:14 final size:14
Alignment explanation
Indices: 80776--80811 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
80766 ATTGTTTAAT
80776 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
80790 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
80804 TGATTTGT
1 TGATTTGT
80812 TTAATTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:81033 original size:19 final size:19
Alignment explanation
Indices: 80967--81130 Score: 230
Period size: 19 Copynumber: 8.8 Consensus size: 19
80957 AATCGCAACG
*
80967 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
80986 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
* *
81004 A---CCCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
81020 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
81039 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
81058 ATTTCGCATTGTGATTTTC
1 ATTTCGCATTGCGATTTTC
81077 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
81096 ATTTCGTATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
81115 ATTTCGCATTACGATT
1 ATTTCGCATTGCGATT
81131 CTCTCGTTGC
Statistics
Matches: 129, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
14 8 0.06
16 4 0.03
18 4 0.03
19 101 0.78
20 12 0.09
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:81160 original size:20 final size:20
Alignment explanation
Indices: 81135--81223 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
81125 ACGATTCTCT
81135 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
81155 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
81175 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
81195 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
81215 CGTTGCGAT
1 CGTTGCGAT
81224 TTCTGCGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:83672 original size:24 final size:24
Alignment explanation
Indices: 83638--83691 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
83628 CTGAAAAATC
83638 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
83662 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
83686 ATCAAA
1 ATCAAA
83692 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:83705 original size:24 final size:24
Alignment explanation
Indices: 83638--83705 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
83628 CTGAAAAATC
* * *
83638 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
83662 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
83686 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
83706 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:84709 original size:19 final size:20
Alignment explanation
Indices: 84681--84773 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
84671 CGATACCGGA
*
84681 GATCGAGTTGCGAA-TTATC-
1 GATCGCGTTGCGAATTTA-CG
84700 GATCGCGTTGC-AATTTACG
1 GATCGCGTTGCGAATTTACG
*
84719 GATACGCGTTGCGATTTTACG
1 GAT-CGCGTTGCGAATTTACG
* *
84740 TATTGTCGTTGCG-ATTTACG
1 GATCG-CGTTGCGAATTTACG
*
84760 GATACTCGTTGCGA
1 GAT-CGCGTTGCGA
84774 TAGTCAGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.05
19 16 0.27
20 24 0.41
21 16 0.27
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
GATCGCGTTGCGAATTTACG
Found at i:84772 original size:20 final size:20
Alignment explanation
Indices: 84705--84774 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
84695 TTATCGATCG
* *
84705 CGTTGCAATTTACGGATACG
1 CGTTGCGATTTACGGATACT
* **
84725 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGGATACT
84746 CGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGGATACT
84766 CGTTGCGAT
1 CGTTGCGAT
84775 AGTCAGAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACT
Found at i:84806 original size:20 final size:20
Alignment explanation
Indices: 84783--84835 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
84773 ATAGTCAGAA
*
84783 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
84803 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
84823 TCACGTTGCGATT
1 TCGCGTTGCGATT
84836 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:84913 original size:20 final size:19
Alignment explanation
Indices: 84864--84917 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
84854 AATTTGTACT
84864 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
*
84883 AACTG-GTTTGCGATTCTGGAG
1 ATC-GCG-TTGCGATTCTGG-G
84904 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
84918 TTTATTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:85794 original size:21 final size:21
Alignment explanation
Indices: 85770--85812 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
85760 AAAATAGAAC
*
85770 AAAACTAGTAGTTT-TTATATT
1 AAAA-TAGTAGTTTCTCATATT
*
85791 AAAATTGTAGTTTCTCATATT
1 AAAATAGTAGTTTCTCATATT
85812 A
1 A
85813 TTGTTAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (21 bp):
AAAATAGTAGTTTCTCATATT
Found at i:88828 original size:29 final size:29
Alignment explanation
Indices: 88792--88851 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
88782 CTTTATTAAA
* * *
88792 TCCCTCAACTATTAAAAGTTATAAAATGG
1 TCCCTCAAATATTAAAAGTAACAAAATGG
88821 TCCCTCAAATATTAAAAGTAACAAAATGG
1 TCCCTCAAATATTAAAAGTAACAAAATGG
88850 TC
1 TC
88852 ACACGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (29 bp):
TCCCTCAAATATTAAAAGTAACAAAATGG
Found at i:88862 original size:29 final size:29
Alignment explanation
Indices: 88797--88862 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
88787 TTAAATCCCT
* * * *
88797 CAACTATTAAAAGTTATAAAATGGTCCCT
1 CAACTATTAAAAGTAACAAAATGGTCACA
*
88826 CAAATATTAAAAGTAACAAAATGGTCACA
1 CAACTATTAAAAGTAACAAAATGGTCACA
*
88855 CGACTATT
1 CAACTATT
88863 CATTGAGTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (29 bp):
CAACTATTAAAAGTAACAAAATGGTCACA
Found at i:90009 original size:21 final size:21
Alignment explanation
Indices: 89983--90095 Score: 121
Period size: 21 Copynumber: 5.6 Consensus size: 21
89973 GTTTCCAGAT
89983 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
90004 TCGCAATGCGAA--T-GTA-AA
1 TCGCAATGCGAACTTCG-ACTA
*
90022 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
90043 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
90064 TCGCAATGCG-ACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
90084 TCGCAATACGAA
1 TCGCAATGCGAA
90096 TATGTAAATC
Statistics
Matches: 80, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.16
19 3 0.04
20 22 0.28
21 42 0.52
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:90029 original size:39 final size:39
Alignment explanation
Indices: 89983--90114 Score: 151
Period size: 39 Copynumber: 3.3 Consensus size: 39
89973 GTTTCCAGAT
89983 TCGCAATGCGAACTTCGACTATCGCAATGCGAATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATGTAAA
* * *
90022 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAA--TGTA-AA
* *
90064 TCGCAATGCG-ACTTGGACTATCGCAATACGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCG-A-ATGTAAA
90104 TCGCAATGCGA
1 TCGCAATGCGA
90115 TAGTCGAAGT
Statistics
Matches: 77, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
39 30 0.39
40 13 0.17
41 21 0.27
42 12 0.16
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (39 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAATGTAAA
Found at i:90827 original size:19 final size:19
Alignment explanation
Indices: 90760--90828 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
90750 TTAAGAAACA
90760 AATCGCAACGAATTTGGAAT
1 AATCGCAACGAATTT-GAAT
* *
90780 AAATCGCAACGCGAA-CTGACT
1 -AATCGCAA--CGAATTTGAAT
*
90801 -ATCACAACGAATTTGAAT
1 AATCGCAACGAATTTGAAT
90819 AATCGCAACG
1 AATCGCAACG
90829 CGAACTTGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 14 0.37
21 11 0.29
22 1 0.03
23 4 0.11
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (19 bp):
AATCGCAACGAATTTGAAT
Found at i:90829 original size:38 final size:41
Alignment explanation
Indices: 90765--90921 Score: 148
Period size: 43 Copynumber: 4.1 Consensus size: 41
90755 AAACAAATCG
90765 CAACGAATTTGGAATAAATCGCAACGCGAAC-TGACTATCA
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTGACTATCA
90805 CAACGAATTT-GAAT-AATCGCAACGCGAACTTGACTAT--
1 CAACGAATTTGGAATAAATCGCAACGCGAACTTGACTATCA
*
90842 ---C------GGAAT-AATCGCAACGCGAACTTCGACTATCG
1 CAACGAATTTGGAATAAATCGCAACGCGAACTT-GACTATCA
*
90874 CAACG-ATTTGGAAATAATATCGCAACGCGAACTTCGACTATCG
1 CAACGAATTTGG-AATAA-ATCGCAACGCGAACTT-GACTATCA
90917 CAACG
1 CAACG
90922 CGAACTTCGA
Statistics
Matches: 101, Mismatches: 0, Indels: 29
0.78 0.00 0.22
Matches are distributed among these distances:
29 21 0.21
30 6 0.06
34 1 0.01
35 1 0.01
38 15 0.15
39 11 0.11
40 12 0.12
41 3 0.03
42 1 0.01
43 30 0.30
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
CAACGAATTTGGAATAAATCGCAACGCGAACTTGACTATCA
Found at i:90857 original size:29 final size:30
Alignment explanation
Indices: 90815--90873 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
90805 CAACGAATTT
90815 GAATAATCGCAACGCGAACTT-GACTATCG
1 GAATAATCGCAACGCGAACTTCGACTATCG
90844 GAATAATCGCAACGCGAACTTCGACTATCG
1 GAATAATCGCAACGCGAACTTCGACTATCG
90874 CAACGATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (30 bp):
GAATAATCGCAACGCGAACTTCGACTATCG
Found at i:90860 original size:67 final size:74
Alignment explanation
Indices: 90775--90916 Score: 210
Period size: 72 Copynumber: 2.0 Consensus size: 74
90765 CAACGAATTT
90775 GGAATAAATCGCAACGCGAAC-T-GACTATCACAACGAATTT-G-AAT-A-ATCGCAACGCGAAC
1 GGAATAAATCGCAACGCGAACTTCGACTATCACAACG-ATTTGGAAATAATATCGCAACGCGAAC
90834 TT-GACTATC
65 TTCGACTATC
*
90843 GGAAT-AATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAAATAATATCGCAACGCGAACT
1 GGAATAAATCGCAACGCGAACTTCGACTATCACAACGATTTGGAAATAATATCGCAACGCGAACT
90907 TCGACTATC
66 TCGACTATC
90916 G
1 G
90917 CAACGCGAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
67 15 0.23
68 10 0.15
69 13 0.20
70 3 0.05
71 1 0.02
72 16 0.24
73 8 0.12
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (74 bp):
GGAATAAATCGCAACGCGAACTTCGACTATCACAACGATTTGGAAATAATATCGCAACGCGAACT
TCGACTATC
Found at i:90875 original size:21 final size:21
Alignment explanation
Indices: 90849--90939 Score: 98
Period size: 21 Copynumber: 4.3 Consensus size: 21
90839 TATCGGAATA
90849 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
90870 ATCGCAA--CG-ATTTGGAAAT
1 ATCGCAACGCGAACTTCG-ACT
90889 AATATCGCAACGCGAACTTCGACT
1 ---ATCGCAACGCGAACTTCGACT
90913 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
90934 ATCGCA
1 ATCGCA
90940 TACGAATAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 4 0.07
19 4 0.07
21 34 0.60
22 7 0.12
24 4 0.07
25 4 0.07
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Done.