Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001511.1 Hibiscus syriacus cultivar Beakdansim tig00002957_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: 68085
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3887 original size:56 final size:56
Alignment explanation
Indices: 3779--3888 Score: 130
Period size: 56 Copynumber: 2.0 Consensus size: 56
3769 CTTGGGTCTG
* * * * * **
3779 AGACATTGGTGCAAGTGTCCGATAGGGAGGTTCTAGACAGAGTATCGGGCTTGCTA
1 AGACATTGGTGCAAATGTCCGACAGAGAGGCTCAAGACAGAGTATCAAGCTTGCTA
* * *
3835 AGACATTGGTGCAAATTTTCGACAGAGAGGCTCAAGATAGAGTATCAAGCTTGC
1 AGACATTGGTGCAAATGTCCGACAGAGAGGCTCAAGACAGAGTATCAAGCTTGC
3889 CAAGGCCACC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (56 bp):
AGACATTGGTGCAAATGTCCGACAGAGAGGCTCAAGACAGAGTATCAAGCTTGCTA
Found at i:12191 original size:2 final size:2
Alignment explanation
Indices: 12174--12248 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
12164 GTAAACTATC
* *
12174 AT AT AT AC AT AC 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
12216 AT 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 AT A
12249 ATTTGTTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13214 original size:17 final size:18
Alignment explanation
Indices: 13192--13232 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
13182 TTAAATATAC
*
13192 TAATTATAAAATTTAAG-
1 TAATTAGAAAATTTAAGA
*
13209 TAATTAGAATATTTAAGA
1 TAATTAGAAAATTTAAGA
13227 TAATTA
1 TAATTA
13233 AAGTAGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
TAATTAGAAAATTTAAGA
Found at i:13861 original size:26 final size:26
Alignment explanation
Indices: 13832--13888 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
13822 ATGCTTAATT
13832 TAAAATTTATAA-AATTTTAGAGAAAA
1 TAAAATTTA-AAGAATTTTAGAGAAAA
* *
13858 T-AAACTTAAAGAATTTTATAGAAAA
1 TAAAATTTAAAGAATTTTAGAGAAAA
*
13883 AAAAAT
1 TAAAAT
13889 AAATTACCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (26 bp):
TAAAATTTAAAGAATTTTAGAGAAAA
Found at i:20524 original size:8 final size:8
Alignment explanation
Indices: 20511--20551 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20501 CTCATTTTCA
20511 GAGAATTT
1 GAGAATTT
20519 GAGAATTT
1 GAGAATTT
*
20527 -AGAGTTT
1 GAGAATTT
*
20534 GGGAATTT
1 GAGAATTT
20542 GAGAATTT
1 GAGAATTT
20550 GA
1 GA
20552 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:20862 original size:128 final size:128
Alignment explanation
Indices: 20632--21238 Score: 1117
Period size: 128 Copynumber: 4.7 Consensus size: 128
20622 ACTATTCACA
*
20632 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
20697 TTATGTCACTCATGTCCCTCGGAGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
20760 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
20825 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
**
20888 TGAAGGCGCGTTCCCGGGGGCGCGCCTTTTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
20953 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
21016 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
21081 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
21144 TGAAGGCGCGTTCCCGGGGGCACGCCTTCCACTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
21209 TTATATCCCTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
21239 GATGGATTGT
Statistics
Matches: 465, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
127 1 0.00
128 463 1.00
129 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:21641 original size:34 final size:34
Alignment explanation
Indices: 21602--21708 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
21592 TAAGTTGAAA
* * *
21602 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTTGAATAATATAATTTATAT
* *
21636 TTTAATTTTAAATTTTGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTTGAATAATATAATTTATAT
* *
21670 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTTGAATAATATAATTTATAT
21704 TTTAA
1 TTTAA
21709 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTAATTTTAAATTTTGAATAATATAATTTATAT
Found at i:22259 original size:21 final size:21
Alignment explanation
Indices: 22229--22322 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
22219 TATGGTATAA
*
22229 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
22250 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
22271 AACCCTGCGGGCTCGGAATAT
1 AACCCTGCGGGCTAGGAATGT
22292 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
22313 AACCCTGCGG
1 AACCCTGCGG
22323 AGATGACATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
20 3 0.05
21 59 0.91
22 3 0.05
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:22334 original size:42 final size:41
Alignment explanation
Indices: 22256--22335 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 41
22246 ATGTAACCTG
*
22256 GCGGGCTAGGAATGTAACCCTGCGGGCTCGGAATATAACCCT
1 GCGGGCTAGGAATGTAACCCTGCGGGATC-GAATATAACCCT
22298 GCGGGCTCA-GAATGTAACCCTGCGGAGAT-GACATATAA
1 GCGGGCT-AGGAATGTAACCCTGCGG-GATCGA-ATATAA
22336 ACTGGTGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
41 2 0.06
42 29 0.85
43 3 0.09
ACGTcount: A:0.28, C:0.24, G:0.30, T:0.19
Consensus pattern (41 bp):
GCGGGCTAGGAATGTAACCCTGCGGGATCGAATATAACCCT
Found at i:24169 original size:31 final size:33
Alignment explanation
Indices: 24104--24183 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
24094 TTAATAATTC
* *
24104 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
24138 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
24169 TATAAAATATAATAA
1 TA-AAAAAATAATAA
24184 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:34905 original size:179 final size:176
Alignment explanation
Indices: 34572--34928 Score: 552
Period size: 179 Copynumber: 2.0 Consensus size: 176
34562 GGCAAAACTG
* * **
34572 GTAAAGAGCTACCGAAATTGTTGAAATTTGTATGGACACGTTTATAAGTATATGTACCAAAGTAT
1 GTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAACACGTTTATAAGTATATGTACCAAAGTAT
* *
34637 CAGTACTGTAGAATTTAAAAGAATTACAATAATAGCGGCTATAAAGTATCGATACCTTACACACA
66 CAGTACTGTAGAATTTAAAAGAACTACAATAATAGCAGCTATAAAGTATCGATACCTTACACACA
*
34702 TGTATCGATACATGACAATATAACATGTTGAAATTTGAAAAAGACCT
131 TCTATCGATACATGACAATATAACATGTTGAAATTTGAAAAA-ACCT
*
34749 GTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAATACGTTTATAAGTATATGTACCAAAGTAT
1 GTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAACACGTTTATAAGTATATGTACCAAAGTAT
* * * * *
34814 CGGTACTTTAGGAATTTTAAAAGAACTGCAATAGTAGCAGCTATAAAGTATCGATACCTTAGACA
66 CAGTACTGTA-GAA-TTTAAAAGAACTACAATAATAGCAGCTATAAAGTATCGATACCTTACACA
* *
34879 CATCTATCGATACATGACAATATAACATGTTTAAATTTGACAAAACCT
129 CATCTATCGATACATGACAATATAACATGTTGAAATTTGAAAAAACCT
34927 GT
1 GT
34929 TTCAATTTGA
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
177 68 0.42
178 9 0.06
179 86 0.53
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (176 bp):
GTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAACACGTTTATAAGTATATGTACCAAAGTAT
CAGTACTGTAGAATTTAAAAGAACTACAATAATAGCAGCTATAAAGTATCGATACCTTACACACA
TCTATCGATACATGACAATATAACATGTTGAAATTTGAAAAAACCT
Found at i:34935 original size:20 final size:20
Alignment explanation
Indices: 34906--34944 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34896 CAATATAACA
34906 TGTTTAAATTTGACAAAACC
1 TGTTTAAATTTGACAAAACC
*
34926 TGTTTCAATTTGACAAAAC
1 TGTTTAAATTTGACAAAAC
34945 TGGTAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TGTTTAAATTTGACAAAACC
Found at i:35118 original size:197 final size:196
Alignment explanation
Indices: 34733--35229 Score: 725
Period size: 197 Copynumber: 2.5 Consensus size: 196
34723 AACATGTTGA
* * *
34733 AATTTGAAAAAGACCTGTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAATACGTTTATAAGT
1 AATTTGACAAA-ACCGGT-AAAAGCTACCAAAATTGTTGAAATTTGTATCGATACGTTTATAAGT
* *
34798 ATATGTACCAAAGTATCGGTACTTTAGGAATTTTAAAAGAACTGCAATAGTAGCAGCTATAAAGT
64 ATATGTACCAAAGTATCGGTACTTTAGGAA-TTTAAAAGAACTGCAATAATAGCACCTATAAAGT
* * *
34863 ATCGATACCTTAGACACATCTATCGATACATGACAATATAACATGTTTAAATTTGACAAAACCTG
128 ATCGATACCTTAAACACATCTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACC-G
34928 -TTTC
192 ATTTC
* *
34932 AATTTGACAAAACTGGTAAAGAGCTACCAAAATTGTTGAAATTTGTATCGATACTTTTATAAGTA
1 AATTTGACAAAACCGGTAAA-AGCTACCAAAATTGTTGAAATTTGTATCGATACGTTTATAAGTA
* * *
34997 TATGTACCAAAGTATCGGTACTTTTGGAATTTAAAATAATTGCAATAATAGCACCTATAAAGTAT
65 TATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAACTGCAATAATAGCACCTATAAAGTAT
* *
35062 CGATACCTTAAACACATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAATCGATT
130 CGATACCTTAAACACATCTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCGATT
35127 TC
195 TC
** *
35129 AATTTGACAAAACCGGTAAAACGCT-TTAGGAATTGTTGAAA---GTATCGATACGTTTATAAGT
1 AATTTGACAAAACCGGTAAAA-GCTACCA-AAATTGTTGAAATTTGTATCGATACGTTTATAAGT
*
35190 ATATGTACCATAGTATCGGTACTTTAGGAATTTAAAAGAA
64 ATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAA
35230 ATAAAAAAAG
Statistics
Matches: 271, Mismatches: 23, Indels: 13
0.88 0.07 0.04
Matches are distributed among these distances:
194 56 0.21
196 3 0.01
197 128 0.47
198 74 0.27
199 10 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (196 bp):
AATTTGACAAAACCGGTAAAAGCTACCAAAATTGTTGAAATTTGTATCGATACGTTTATAAGTAT
ATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAACTGCAATAATAGCACCTATAAAGTATC
GATACCTTAAACACATCTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCGATTT
C
Found at i:35258 original size:197 final size:196
Alignment explanation
Indices: 34733--35288 Score: 669
Period size: 197 Copynumber: 2.8 Consensus size: 196
34723 AACATGTTGA
* * * *
34733 AATTTGAAAAAGACCTGTAAAAAGCTACCAAAATTGTTGAAATTTGTATCAATACGTTTATAAGT
1 AATTTGACAAA-ACCGGTAAAGAGCTACCAAAATTGTTGAAA--TGTATCGATACGTTTATAAGT
* ** *
34798 ATATGTACCAAAGTATCGGTACTTTAGGAATTTTAAAAGAACTGCAATAGTAGCA-GCTATAAAG
63 ATATGTACCAAAGTATCGGTACTTTAGGAA-TTTAAAAGAAATAAAAAAGTAGCACGCTATAAAG
* * * *
34862 TATCGATACCTTAGACACATCTATCGATACATGACAATATAACATGTTTAAATTTGACAAAACCT
127 TATCGATACCTTAAACACATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCT
34927 GTTTC
192 GTTTC
* *
34932 AATTTGACAAAACTGGTAAAGAGCTACCAAAATTGTTGAAATTTGTATCGATACTTTTATAAGTA
1 AATTTGACAAAACCGGTAAAGAGCTACCAAAATTGTTGAAA--TGTATCGATACGTTTATAAGTA
* * * * *
34997 TATGTACCAAAGTATCGGTACTTTTGGAATTTAAAATAATTGCAATAA-TAGCAC-CTATAAAGT
64 TATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAAT-AAAAAAGTAGCACGCTATAAAGT
*
35060 ATCGATACCTTAAACACATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAATC-G
128 ATCGATACCTTAAACACATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCTG
35124 ATTTC
193 -TTTC
** *
35129 AATTTGACAAAACCGGTAAA-ACGCT-TTAGGAATTGTTGAAA-GTATCGATACGTTTATAAGTA
1 AATTTGACAAAACCGGTAAAGA-GCTACCA-AAATTGTTGAAATGTATCGATACGTTTATAAGTA
* * **
35191 TATGTACCATAGTATCGGTACTTTAGGAATTTAAAAGAAATAAAAAAAGGAAAACGTCT-TGAAA
64 TATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAAT-AAAAAAGTAGCACG-CTAT-AAA
* * *
35255 GTATCGATACCTTACACAAAAGTATCGATACATG
126 GTATCGATACCTTAAACACATGTATCGATACATG
35289 GGGAATGATA
Statistics
Matches: 312, Mismatches: 36, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
194 61 0.20
195 3 0.01
196 4 0.01
197 155 0.50
198 79 0.25
199 10 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (196 bp):
AATTTGACAAAACCGGTAAAGAGCTACCAAAATTGTTGAAATGTATCGATACGTTTATAAGTATA
TGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAATAAAAAAGTAGCACGCTATAAAGTATC
GATACCTTAAACACATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCTGTTT
C
Found at i:40172 original size:20 final size:20
Alignment explanation
Indices: 40143--40182 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40133 AGAGCACATA
*
40143 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
40163 TAGGAGCATATAGTTGCATT
1 TAGGAGCATATAGATGCATT
40183 AGTGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:43456 original size:30 final size:30
Alignment explanation
Indices: 43422--43501 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 30
43412 CCTATATGGT
* *
43422 CCGAAGAACATAGGTAATTATCCATATATC
1 CCGAAGGACATAGGTAACTATCCATATATC
* *
43452 CCGAAGGACATAAGTAACACTGTCCATATATC
1 CCGAAGGACATAGGT-A-ACTATCCATATATC
43484 CCGAAGGACATAGGTAAC
1 CCGAAGGACATAGGTAAC
43502 CCTCGACTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 15 0.35
31 2 0.05
32 26 0.60
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (30 bp):
CCGAAGGACATAGGTAACTATCCATATATC
Found at i:44684 original size:30 final size:30
Alignment explanation
Indices: 44641--44730 Score: 76
Period size: 32 Copynumber: 2.9 Consensus size: 30
44631 AAAAACCTAC
*
44641 CCATATGGT-CCGAAGAACATAGGTAA-TTGT
1 CCATAT-GTCCCGAAG-ACATAGGTAACCTGT
*
44671 CCATATGTCCCGAATGACATAAGTAACCCTGT
1 CCATATGTCCCGAA-GACATAGGTAA-CCTGT
* * *
44703 TCATATATCCCAAAGGACATAGGTAACC
1 CCATATGTCCCGAA-GACATAGGTAACC
44731 CTCGACTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 2 0.04
30 20 0.41
31 3 0.06
32 24 0.49
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (30 bp):
CCATATGTCCCGAAGACATAGGTAACCTGT
Found at i:44722 original size:32 final size:32
Alignment explanation
Indices: 44672--44732 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
44662 GGTAATTGTC
* * *
44672 CATATGTCCCGAATGACATAAGTAACCCTGTT
1 CATATATCCCAAAGGACATAAGTAACCCTGTT
*
44704 CATATATCCCAAAGGACATAGGTAACCCT
1 CATATATCCCAAAGGACATAAGTAACCCT
44733 CGACTCTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (32 bp):
CATATATCCCAAAGGACATAAGTAACCCTGTT
Found at i:47434 original size:2 final size:2
Alignment explanation
Indices: 47427--47463 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47417 GCCCCACGTG
47427 AT AT AT 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 AT AT AT A
47464 GCTTACAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48158 original size:20 final size:21
Alignment explanation
Indices: 48133--48176 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
48123 CCAATTCATG
*
48133 AATGAAATG-AAACCTA-TATA
1 AATG-AATGTAAAACTATTATA
48153 AATGAATGTAAAACTATTATA
1 AATGAATGTAAAACTATTATA
48174 AAT
1 AAT
48177 CAATAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 7 0.33
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (21 bp):
AATGAATGTAAAACTATTATA
Found at i:48972 original size:23 final size:23
Alignment explanation
Indices: 48931--49010 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
48921 GCACCGAAGT
*
48931 ACCACATAGAATTTTTCCTGAAAG
1 ACCACATAG-ATTTGTCCTGAAAG
*
48955 ACCACATAGATTTGTCCTGAAGG
1 ACCACATAGATTTGTCCTGAAAG
* * *
48978 GCCACATAGATTTGTCCCGAATG
1 ACCACATAGATTTGTCCTGAAAG
*
49001 ACCGCATAGA
1 ACCACATAGA
49011 ACCCTCGACT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 40 0.82
24 9 0.18
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (23 bp):
ACCACATAGATTTGTCCTGAAAG
Found at i:49187 original size:15 final size:15
Alignment explanation
Indices: 49144--49200 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
49134 TTATTACATG
**
49144 TTCACATAGA-CATT
1 TTCACATAGATCACA
*
49158 TTCACATAGAACACA
1 TTCACATAGATCACA
* *
49173 TTTACATATATCACA
1 TTCACATAGATCACA
49188 TTCACATAGATCA
1 TTCACATAGATCA
49201 TTTTTCACGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (15 bp):
TTCACATAGATCACA
Found at i:49443 original size:2 final size:2
Alignment explanation
Indices: 49436--49471 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49426 ATTTCACATA
49436 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
49472 CATAACAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55125 original size:23 final size:23
Alignment explanation
Indices: 55062--55160 Score: 89
Period size: 23 Copynumber: 4.3 Consensus size: 23
55052 ACAACTGCTT
55062 ATATA-ATTTG-CACCGAAGTG-CC
1 ATATAGATTTGTC-CCGAA-TGACC
* *
55084 ACATAGAATTTGTCTCGAATGACC
1 ATATAG-ATTTGTCCCGAATGACC
55108 ATATAGATTTGTCCCGAA-GAACC
1 ATATAGATTTGTCCCGAATG-ACC
* * *
55131 ACATAGATTTATCCTGAATGACC
1 ATATAGATTTGTCCCGAATGACC
55154 ATATAGA
1 ATATAGA
55161 ACCCTCGACT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 5 0.08
23 40 0.63
24 17 0.27
25 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (23 bp):
ATATAGATTTGTCCCGAATGACC
Found at i:55592 original size:2 final size:2
Alignment explanation
Indices: 55585--55613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55575 ATTTCACATA
55585 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 A
55614 CTCATAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56108 original size:21 final size:20
Alignment explanation
Indices: 56063--56112 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
56053 CTTGCTCTTG
56063 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
* *
56083 ATATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTCCACATCA
56104 GTATCGATA
1 GTATCGATA
56113 TCGTTCATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Done.