Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001905.1 Hibiscus syriacus cultivar Beakdansim tig00003858_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: 62503
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:124 original size:19 final size:19
Alignment explanation
Indices: 100--137 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
90 CTGGGCAAGG
100 GGAATCGGTACCCATTCAA
1 GGAATCGGTACCCATTCAA
*
119 GGAATCGTTACCCATTCAA
1 GGAATCGGTACCCATTCAA
138 TGGGAAATCG
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:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (19 bp):
GGAATCGGTACCCATTCAA
Found at i:152 original size:22 final size:19
Alignment explanation
Indices: 100--153 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
90 CTGGGCAAGG
*
100 GGAATCGGTACCCATTCAA
1 GGAATCGATACCCATTCAA
*
119 GGAATCGTTACCCATTCAA
1 GGAATCGATACCCATTCAA
138 TGGGAAATCGATACCC
1 --GG-AATCGATACCC
154 CTAAAGCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 18 0.60
21 2 0.07
22 10 0.33
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (19 bp):
GGAATCGATACCCATTCAA
Found at i:207 original size:20 final size:21
Alignment explanation
Indices: 182--223 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
172 TCTAGAATCT
182 CATAGG-GGAACCGATTCCCC
1 CATAGGAGGAACCGATTCCCC
*
202 CATAGGAGGAATCGATTCCCC
1 CATAGGAGGAACCGATTCCCC
223 C
1 C
224 TAAAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (21 bp):
CATAGGAGGAACCGATTCCCC
Found at i:230 original size:22 final size:21
Alignment explanation
Indices: 188--230 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
178 ATCTCATAGG
*
188 GGAACCGATTCCCCCATAGGA
1 GGAACCGATTCCCCCAAAGGA
*
209 GGAATCGATTCCCCCTAAAGGA
1 GGAACCGATTCCCCC-AAAGGA
231 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
GGAACCGATTCCCCCAAAGGA
Found at i:1590 original size:103 final size:103
Alignment explanation
Indices: 1411--1619 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 103
1401 CTACGCGGTT
* *
1411 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTT
1 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
* * *
1476 GGCATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 AGCATATGTATATGATTCTTAAGGAATGACATGTGATC
1514 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
1 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
*
1579 AGTATATGTATATGATTCTTAAGGAATGACATGTGATC
66 AGCATATGTATATGATTCTTAAGGAATGACATGTGATC
1617 CTT
1 CTT
1620 ATGGACATTA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (103 bp):
CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
AGCATATGTATATGATTCTTAAGGAATGACATGTGATC
Found at i:1663 original size:23 final size:23
Alignment explanation
Indices: 1635--1726 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
1625 CATTATTATA
**
1635 TGGCACTATGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
1658 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
1681 TGGCACTCCGGTGCAATTCTATG
1 TGGCACTCCGGTGCAATTCTACG
* *
1704 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTCTACG
1727 AGCTATGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:10973 original size:19 final size:19
Alignment explanation
Indices: 10937--10978 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
10927 CCCCCTTTGA
**
10937 AGGGGAACCGATTTCCCCT
1 AGGGGAACCGATACCCCCT
*
10956 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATACCCCCT
10975 -GGGG
1 AGGGG
10979 TTCTGGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:15084 original size:21 final size:21
Alignment explanation
Indices: 15058--15120 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
15048 GTCGAGGGTT
15058 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
15079 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
15101 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
15121 ATTTAATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:15111 original size:22 final size:22
Alignment explanation
Indices: 15057--15123 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
15047 AGTCGAGGGT
15057 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
15078 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
15100 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
15122 TT
1 TT
15124 TAATATGCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:21694 original size:16 final size:15
Alignment explanation
Indices: 21646--21695 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
21636 TTTTATTATT
21646 TTAATTTTAATTTTAA
1 TTAA-TTTAATTTTAA
*
21662 ATAATTTAATTTTTAA
1 TTAATTTAA-TTTTAA
*
21678 TTAGTCTTAATTTTAA
1 TTAAT-TTAATTTTAA
21694 TT
1 TT
21696 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTAATTTAATTTTAA
Found at i:21714 original size:38 final size:35
Alignment explanation
Indices: 21631--21714 Score: 82
Period size: 38 Copynumber: 2.3 Consensus size: 35
21621 ATTAATGTTG
*
21631 ATATATTTT-ATTATTTTAATTTTAATTTTAAATA
1 ATATATTTTAATTATCTTAATTTTAATTTTAAATA
*
21665 ATTTAATTTTTAATTAGTCTTAATTTTAATTTTTTTAAA-A
1 ATAT-A-TTTTAATTA-TCTTAATTTTAA---TTTTAAATA
21705 ATATATTTTA
1 ATATATTTTA
21715 TTACATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
34 3 0.08
35 1 0.03
36 4 0.10
37 4 0.10
38 16 0.40
39 1 0.03
40 4 0.10
41 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (35 bp):
ATATATTTTAATTATCTTAATTTTAATTTTAAATA
Found at i:22345 original size:45 final size:46
Alignment explanation
Indices: 22271--22358 Score: 110
Period size: 45 Copynumber: 1.9 Consensus size: 46
22261 TAAATTTTTC
* *
22271 AAACTCAACTCGAAATAAAATATTAAAACTCGACTCAAACTCAAAA
1 AAACTCAACTCGAAATAAAATATCAAAACTCAACTCAAACTCAAAA
*
22317 AAACTCAAACTC-AAA-AAAAT-TCATAAACTCAATTCAAACTCA
1 AAACTC-AACTCGAAATAAAATATCA-AAACTCAACTCAAACTCA
22359 TTTTTGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 2 0.05
45 21 0.57
46 9 0.24
47 5 0.14
ACGTcount: A:0.55, C:0.23, G:0.02, T:0.20
Consensus pattern (46 bp):
AAACTCAACTCGAAATAAAATATCAAAACTCAACTCAAACTCAAAA
Found at i:22348 original size:18 final size:16
Alignment explanation
Indices: 22303--22335 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
22293 TTAAAACTCG
22303 ACTCAAACTCAAAAAA
1 ACTCAAACTCAAAAAA
22319 ACTCAAACTCAAAAAA
1 ACTCAAACTCAAAAAA
22335 A
1 A
22336 TTCATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (16 bp):
ACTCAAACTCAAAAAA
Found at i:22368 original size:23 final size:23
Alignment explanation
Indices: 22342--22423 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
22332 AAAATTCATA
*
22342 AACTCAATTCAAACTCATTTTTG
1 AACTCAATTCAAACTCATTTTTT
* * *
22365 AACTCGATTCAAGCTTATTTTTTT
1 AACTCAATTCAAACTCA-TTTTTT
* *
22389 AACTCCATTCAAACTCGTTTTTT
1 AACTCAATTCAAACTCATTTTTT
22412 AACT-AGATTCAA
1 AACTCA-ATTCAA
22424 GCTAGAAGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 30 0.62
24 18 0.38
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (23 bp):
AACTCAATTCAAACTCATTTTTT
Found at i:24289 original size:32 final size:31
Alignment explanation
Indices: 24253--24328 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
24243 CGGGGCCGTG
*
24253 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
24285 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
24316 GAGCCTACCTAAG
1 GGGCCTACCTAAG
24329 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:24312 original size:63 final size:63
Alignment explanation
Indices: 24206--24328 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
24196 ACCTAAGGGA
* * ** *
24206 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
24269 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
24329 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:29411 original size:32 final size:31
Alignment explanation
Indices: 29375--29450 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
29365 CGGGGCCGTG
*
29375 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
29407 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
29438 GAGCCTACCTAAG
1 GGGCCTACCTAAG
29451 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:29434 original size:63 final size:63
Alignment explanation
Indices: 29328--29450 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
29318 ACCTAAGGGA
* * ** *
29328 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
29391 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
29451 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:33367 original size:7 final size:7
Alignment explanation
Indices: 33355--33472 Score: 107
Period size: 7 Copynumber: 16.9 Consensus size: 7
33345 GTGCATAACT
33355 TAAACCC
1 TAAACCC
33362 TAAACCC
1 TAAACCC
33369 TAAACCC
1 TAAACCC
33376 T-AACTCC
1 TAAAC-CC
*
33383 TAAACTC
1 TAAACCC
*
33390 TAAACTC
1 TAAACCC
33397 T-AACTCC
1 TAAAC-CC
33404 TAAACCC
1 TAAACCC
33411 TAAACCC
1 TAAACCC
33418 TAAACCC
1 TAAACCC
* *
33425 TAATCTC
1 TAAACCC
*
33432 TAAACCT
1 TAAACCC
*
33439 TAAAACC
1 TAAACCC
* *
33446 T-ATCACA
1 TAAAC-CC
33453 TAAACCC
1 TAAACCC
*
33460 TAAAACC
1 TAAACCC
33467 TAAACC
1 TAAACC
33473 TTAACACATA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
6 7 0.08
7 74 0.83
8 8 0.09
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:33912 original size:25 final size:25
Alignment explanation
Indices: 33860--33912 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
33850 TTTATTCACT
* * * * *
33860 AATAATGTATTTTTAATATATTTTA
1 AATAATGTAATTTTAAAAAATCTAA
33885 AATAATGTAATTTTAAAAAATCTAA
1 AATAATGTAATTTTAAAAAATCTAA
33910 AAT
1 AAT
33913 TATAATATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATCTAA
Found at i:39861 original size:27 final size:27
Alignment explanation
Indices: 39813--39869 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
39803 CGAGCATATT
* * *
39813 AAAGTGGATGTTCATCTGGTTCGGGAC
1 AAAGTGGATGGTCAACTAGTTCGGGAC
39840 AAAGTGGATGGTCAACTAGTTCGGGAC
1 AAAGTGGATGGTCAACTAGTTCGGGAC
39867 AAA
1 AAA
39870 CTTAAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.25
Consensus pattern (27 bp):
AAAGTGGATGGTCAACTAGTTCGGGAC
Found at i:44101 original size:12 final size:12
Alignment explanation
Indices: 44084--44108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44074 TCTAGCAGGG
44084 GGAAATGTGAGT
1 GGAAATGTGAGT
44096 GGAAATGTGAGT
1 GGAAATGTGAGT
44108 G
1 G
44109 AAAAATGTGT
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:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (12 bp):
GGAAATGTGAGT
Found at i:47648 original size:21 final size:21
Alignment explanation
Indices: 47622--47666 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47612 GATTTCTGGG
* *
47622 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
47643 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
47664 CAA
1 CAA
47667 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:49060 original size:14 final size:14
Alignment explanation
Indices: 49041--49068 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49031 GAAAAGAAGC
49041 TATGTGATACGTGA
1 TATGTGATACGTGA
49055 TATGTGATACGTGA
1 TATGTGATACGTGA
49069 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:49441 original size:151 final size:149
Alignment explanation
Indices: 49169--49485 Score: 521
Period size: 151 Copynumber: 2.1 Consensus size: 149
49159 GAGTCGAGGG
*
49169 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTAAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTAAAGTCTTGAAAGACACAT
*
49234 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATCATTA
*
49299 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGCGCAAT
* *
49318 TCTACGCGGTCCTTCGGGATATATATATATAT-TATGTGGAACATGTGTGAAGTCTTGAAAGACA
1 TCTACGCGGTCCTTCGGGACATATATATAT-TCT-T-TGGAACATGTGTAAAGTCTTGAAAGACA
**
49382 CATACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTT
63 CATACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATCA
49447 TTATATGGCACTACGGCGCAAT
128 TTATATGGCACTACGGCGCAAT
49469 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
49486 TGCAATTATA
Statistics
Matches: 157, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
149 29 0.18
150 3 0.02
151 125 0.80
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTAAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGCGCAAT
Found at i:49490 original size:23 final size:23
Alignment explanation
Indices: 49453--49497 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49443 ATTTTTATAT
*
49453 GGCACTACGGCGCAATTCTACGC
1 GGCACTACGGCGCAATTATACGC
* *
49476 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGCGCAATTATACG
49498 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (23 bp):
GGCACTACGGCGCAATTATACGC
Found at i:52798 original size:21 final size:21
Alignment explanation
Indices: 52755--52799 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52745 GATTTCTGGG
* * *
52755 CAAGGGGAATCGGTTCCCATT
1 CAAGGGGAACCGATACCCATT
*
52776 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
52797 CAA
1 CAA
52800 ACGAACAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:54179 original size:14 final size:14
Alignment explanation
Indices: 54160--54187 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54150 GAAAAGAAGC
54160 TATGTGATACGTGA
1 TATGTGATACGTGA
54174 TATGTGATACGTGA
1 TATGTGATACGTGA
54188 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:54470 original size:148 final size:149
Alignment explanation
Indices: 54283--54586 Score: 529
Period size: 148 Copynumber: 2.0 Consensus size: 149
54273 GAGTCGAGGG
* * * *
54283 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACATAT
1 TCTACGCAGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
54348 ACTTGATCCCTAGTATATGTATATGATTCTTAA-GAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
*
54412 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGCGCAAT
*
54431 TCTACGCAGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCAGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
**
54496 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
54561 TATGGCACTACGGCGCAAT
131 TATGGCACTACGGCGCAAT
54580 TCTACGC
1 TCTACGC
54587 GGCACTTCGG
Statistics
Matches: 147, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
148 93 0.63
149 54 0.37
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCAGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGCGCAAT
Found at i:54601 original size:23 final size:23
Alignment explanation
Indices: 54564--54608 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54554 ATTTTTATAT
*
54564 GGCACTACGGCGCAATTCTACGC
1 GGCACTACGGCGCAATTATACGC
* *
54587 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGCGCAATTATACG
54609 AGATGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (23 bp):
GGCACTACGGCGCAATTATACGC
Done.