Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021097.1 Corchorus olitorius cultivar O-4 contig21130, 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: 31226
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:17622 original size:156 final size:157
Alignment explanation
Indices: 17325--17648 Score: 503
Period size: 157 Copynumber: 2.1 Consensus size: 157
17315 GGATTTCTGT
* *
17325 TTGGA-TTTTGGACACGGGTATTCGCTCTGTCTGAATCCATTTAGACCGGCTTTGAATCGTGTCA
1 TTGGACTTTTGGACACGAGTATTCGCTCCGTCTGAATCCATTTAGACCGGCTTTGAATCGTGTCA
*
17389 TATGAATATCACCTTTTAGGTCAGATTTGAATCGTGATATATGGATATTGAGCGAATTTGGATTT
66 TATGAATATCA-CTTTTAGGTCAGATTTGAATCGTGATATATGGATACTGAGCGAATTTGGATTT
*
17454 TTAATTATTTTTTTTT-CATTTACTAAA
130 TTAATTATTTTTTTTTCCATTCACTAAA
* * * *
17481 TTGGACTTTTGGACATGAGTATTCGCTCCGTCTGAATCCGTTTAGACCGGGTTTGAATCGTGTTA
1 TTGGACTTTTGGACACGAGTATTCGCTCCGTCTGAATCCATTTAGACCGGCTTTGAATCGTGTCA
* *
17546 TATGAATATCA-TGTTTAGGTCGGATTTGAATCGTGATATATGGATACCT-ATCGAATTTGGATT
66 TATGAATATCACT-TTTAGGTCAGATTTGAATCGTGATATATGGATA-CTGAGCGAATTTGGATT
17609 TTTAATTATTTTTTTTTCCATTCACTAAA
129 TTTAATTATTTTTTTTTCCATTCACTAAA
17638 TTGGACTTTTG
1 TTGGACTTTTG
17649 TGTCTTAGGT
Statistics
Matches: 154, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
155 1 0.01
156 67 0.44
157 86 0.56
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (157 bp):
TTGGACTTTTGGACACGAGTATTCGCTCCGTCTGAATCCATTTAGACCGGCTTTGAATCGTGTCA
TATGAATATCACTTTTAGGTCAGATTTGAATCGTGATATATGGATACTGAGCGAATTTGGATTTT
TAATTATTTTTTTTTCCATTCACTAAA
Found at i:17895 original size:16 final size:16
Alignment explanation
Indices: 17874--17905 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17864 CTCTCCAAAC
*
17874 TTTTTTGTTTGTATTT
1 TTTTTTGTTTATATTT
17890 TTTTTTGTTTATATTT
1 TTTTTTGTTTATATTT
17906 CTCGAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTATATTT
Found at i:19030 original size:22 final size:22
Alignment explanation
Indices: 19005--19402 Score: 161
Period size: 22 Copynumber: 18.1 Consensus size: 22
18995 ATTTTTTATG
19005 ACCTCCTTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
19027 ACCTCCCTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
* * * *
19049 ACATTCATATGAAATTTTAATA
1 ACCTCCTTATGAAATTTTGATA
* * * * *
19071 ACGATAC-TATGGAATTTCGAGA
1 AC-CTCCTTATGAAATTTTGATA
** * * **
19093 ACCTTTTTATTAATTTTTTTTA
1 ACCTCCTTATGAAATTTTGATA
*
19115 A---CCTTATGAAATTTTGTTA
1 ACCTCCTTATGAAATTTTGATA
* * *
19134 ACCTCCCTAAGGAATTTTGA-A
1 ACCTCCTTATGAAATTTTGATA
*
19155 GACCTCAC--AGTGAGATTTTGATA
1 -ACCTC-CTTA-TGAAATTTTGATA
* **
19178 ACTTCCCAATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
* * *
19200 ACCAACAC-TATGAGATGTTGATA
1 ACC-TC-CTTATGAAATTTTGATA
* * *
19223 ACCTCCATATGATATATTGATA
1 ACCTCCTTATGAAATTTTGATA
* * * * * *
19245 ACCACGTTATAAAAATTTAAAA
1 ACCTCCTTATGAAATTTTGATA
* *
19267 ACCTCCGTATG-AATTGTT-AGCA
1 ACCTCCTTATGAAATT-TTGA-TA
* * *
19289 ATCACAC-TCTGAAATTTTGATA
1 ACCTC-CTTATGAAATTTTGATA
* * * * * *
19311 ATCACATTATAAAATTGTAATA
1 ACCTCCTTATGAAATTTTGATA
*
19333 ACCTCGTTATGAAATTTTGATAA
1 ACCTCCTTATGAAATTTTGAT-A
* *
19356 ACCTCCCTATAAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
19378 ACCTCCTTATGGAAATCTTGATA
1 ACCTCCTTAT-GAAATTTTGATA
19401 AC
1 AC
19403 TACAAATTTT
Statistics
Matches: 276, Mismatches: 78, Indels: 43
0.70 0.20 0.11
Matches are distributed among these distances:
19 14 0.05
21 9 0.03
22 193 0.70
23 59 0.21
24 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
ACCTCCTTATGAAATTTTGATA
Found at i:19066 original size:44 final size:44
Alignment explanation
Indices: 19012--19635 Score: 131
Period size: 44 Copynumber: 14.7 Consensus size: 44
19002 ATGACCTCCT
19012 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
* * * * * * * **
19056 TATGAAATTTTAATAACGAT-ACTATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAAC-CTCCCTATGAAATTTTGATAACATTCA
* * ** * * * *
19100 TATTAATTTTTTTTAACCT---TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
* * * *
19141 TAAGGAATTTTGA-AGACCTCAC-AGTGAGATTTTGATAAC-TTCCCA
1 TATGAAATTTTGATA-ACCTCCCTA-TGAAATTTTGATAACATT--CA
* * * * * *
19186 -ATGAAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACATTCA
* * * ** * * * * * * *
19230 TATGATATATTGATAACCACGTTATAAAAATTTAAAAACCTCCG
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
* * * * *
19274 TATG-AATTGTT-AGCAATCACACTCTGAAATTTTGATAATCA--CA
1 TATGAAATT-TTGA-TAACCTCCCTATGAAATTTTGATAA-CATTCA
* * * ** * * *
19317 TTATAAAATTGTAATAACCTCGTTATGAAATTTTGATAAACCTCCC
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATTCA
* * *
19363 TATAAAATTTTGATAACCTCCTTATGGAAATCTTGAT-A-A--C-
1 TATGAAATTTTGATAACCTCCCTAT-GAAATTTTGATAACATTCA
* * **
19403 TA-CAAATTTTGATAATCTCCCTATG--ATTTT--T-TGA-T-A
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
* * * *
19439 -ATGAAATTTTGTTAATCT-CCTGATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGAT-AACATTCA
* * **
19482 TATGAAATTTTGATAA-CTCTCTTATGAAATTTTGAAAAC-TAAA
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACATTCA
* *
19525 CTATGAAATTTTGATATCCTCCC--TGAAATTTTGATTAC-TTCA
1 -TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
* * * * * *
19567 TAATAAAAGTTTAATAACCTTCC--T--AA-TTTGGTAATCATAC-
1 T-ATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATTCA
19607 TATGAAATTTTGATAACCTCCCTA-GAAAT
1 TATGAAATTTTGATAACCTCCCTATGAAAT
19636 ACCACTATGA
Statistics
Matches: 422, Mismatches: 108, Indels: 101
0.67 0.17 0.16
Matches are distributed among these distances:
34 1 0.00
35 5 0.01
36 21 0.05
38 6 0.01
39 42 0.10
40 8 0.02
41 30 0.07
42 37 0.09
43 11 0.03
44 178 0.42
45 70 0.17
46 13 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACATTCA
Found at i:19471 original size:36 final size:37
Alignment explanation
Indices: 19367--19522 Score: 118
Period size: 36 Copynumber: 4.0 Consensus size: 37
19357 CCTCCCTATA
* *
19367 AAATTTTGATAACCTCCTTATGGAAATCTTGATAACTAC
1 AAATTTTGATAATCTCC-TAT-GAAATTTTGATAACTAC
** *
19406 AAATTTTGATAATCTCCCTATGATTTTTTGATAA-T-G
1 AAATTTTGATAATCT-CCTATGAAATTTTGATAACTAC
* *
19442 AAATTTTGTTAATCTCCTGATGAAATTTTGATCTACATACTATG
1 AAATTTTGATAATCTCCT-ATGAAATTTTGA--T--A-ACTA-C
* *
19486 AAATTTTGATAACTCTCTTATGAAATTTTGAAAACTA
1 AAATTTTGATAA-TCTCCTATGAAATTTTGATAACTA
19523 AACTATGAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
35 3 0.03
36 24 0.25
37 1 0.01
38 11 0.12
39 21 0.22
40 4 0.04
41 1 0.01
42 1 0.01
44 24 0.25
45 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (37 bp):
AAATTTTGATAATCTCCTATGAAATTTTGATAACTAC
Found at i:19507 original size:22 final size:23
Alignment explanation
Indices: 19439--19540 Score: 92
Period size: 22 Copynumber: 4.6 Consensus size: 23
19429 TTTTTTGATA
* *
19439 ATGAAATTTTGTTAA-T-CTCCT
1 ATGAAATTTTGATAACTACTACT
19460 GATGAAATTTTGAT--CTACATACT
1 -ATGAAATTTTGATAACTAC-TACT
19483 ATGAAATTTTGATAACT-CT-CTT
1 ATGAAATTTTGATAACTACTAC-T
* *
19505 ATGAAATTTTGAAAACTA-AACT
1 ATGAAATTTTGATAACTACTACT
19527 ATGAAATTTTGATA
1 ATGAAATTTTGATA
19541 TCCTCCCTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.03
22 58 0.87
23 5 0.07
24 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (23 bp):
ATGAAATTTTGATAACTACTACT
Found at i:19694 original size:21 final size:22
Alignment explanation
Indices: 19665--20049 Score: 160
Period size: 22 Copynumber: 17.6 Consensus size: 22
19655 AATCATATTT
* *
19665 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
19687 TGAAATTTTGAT-ACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
19708 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
19730 TGAAATTTTGATATTAAC-AT-TA
1 TGAAATTTTGATA--ACCTCTCTA
* * * *
19752 TGTAATTTTAATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
*
19774 TGAATTTTTGATAA-----C-A
1 TGAAATTTTGATAACCTCTCTA
** *
19790 ACAAATTTTGATAATCT-TCTTA
1 TGAAATTTTGATAACCTCTC-TA
19812 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * * *
19836 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCTCTCTA
*
19858 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* * * **
19878 TCAAATTTTGGTAGTCCTCATGAAA
1 TGAAATTTTGATA-ACCTC-T-CTA
*
19903 TTGAGACTTTT-ATAACCT-TCATA
1 -TGA-AATTTTGATAACCTCTC-TA
* *
19926 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
19948 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
* *
19970 TGATATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
19992 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
20014 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
20036 T-AACATTTTGATAA
1 TGAA-ATTTTGATAA
20050 TCCCTTTGAT
Statistics
Matches: 268, Mismatches: 62, Indels: 66
0.68 0.16 0.17
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
20 9 0.03
21 55 0.21
22 151 0.56
23 7 0.03
24 8 0.03
25 17 0.06
26 4 0.01
27 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:19841 original size:25 final size:22
Alignment explanation
Indices: 19792--19851 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 22
19782 TGATAACAAC
*
19792 AAATTTTGATAAT-CTTCTTAT
1 AAATTTTGATAATCCATCTTAT
19813 AAATTTTGATAATCCGATCTCTAT
1 AAATTTTGATAATCC-ATCT-TAT
*
19837 GAAATTTCGATAATC
1 -AAATTTTGATAATC
19852 ACTTTATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.39
22 1 0.03
23 3 0.09
24 3 0.09
25 13 0.39
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCCATCTTAT
Found at i:20029 original size:44 final size:43
Alignment explanation
Indices: 19924--20254 Score: 167
Period size: 44 Copynumber: 7.7 Consensus size: 43
19914 ATAACCTTCA
* * *
19924 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTT-ATAACCTCACTATGAAATTTTGATAACCACAC
* * * *
19968 CATGATATATTAGTAACCTC-CTTATGAAATTTTGTTAACCACAC
1 TATGAAATTTTA-TAACCTCAC-TATGAAATTTTGATAACCACAC
* *
20012 TATGAAATTCTTATAACCTCGCTAT-AACATTTTGATAATC-C-C
1 TATGAAATT-TTATAACCTCACTATGAA-ATTTTGATAACCACAC
* * *
20054 TTTGATAA-CTT-T----T--CTATGAAATTGTGATAACCACAC
1 TATGA-AATTTTATAACCTCACTATGAAATTTTGATAACCACAC
* * *
20090 TATGAAATTTCAATAACCTTC-CTAAGAAATTTTAATAACCTGATC-C
1 TATGAAATTT-TATAACC-TCACTATGAAATTTTGATAACC--A-CAC
* *
20136 TATGAAATTTTGGTAACCAT-ACTATGAAATTTTGATAACCTTC-C
1 TATGAAATTTT-ATAACC-TCACTATGAAATTTTGATAACC-ACAC
* * * *
20180 CATGAAATTTTGATAACTTC-CATATGAAATTTTGGTAACTACAC
1 TATGAAATTTT-ATAACCTCAC-TATGAAATTTTGATAACCACAC
* *
20224 TATGGAATTTTGATAGCCTC-CTCATGAAATT
1 TATGAAATTTT-ATAACCTCACT-ATGAAATT
20255 ATAATAATTA
Statistics
Matches: 221, Mismatches: 39, Indels: 54
0.70 0.12 0.17
Matches are distributed among these distances:
34 14 0.06
35 5 0.02
36 7 0.03
38 1 0.00
40 1 0.00
41 2 0.01
42 5 0.02
43 12 0.05
44 134 0.61
45 4 0.02
46 35 0.16
47 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (43 bp):
TATGAAATTTTATAACCTCACTATGAAATTTTGATAACCACAC
Found at i:20153 original size:46 final size:44
Alignment explanation
Indices: 20054--20285 Score: 168
Period size: 44 Copynumber: 5.2 Consensus size: 44
20044 TGATAATCCC
* * * * *
20054 TTTGATAACTTTTCTATGAAATTGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTCCTATGAAATTTTAATAACCTTC-CTATGAAAT
** *
20098 TTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCTTCCTATGAAATTTTAATAACCT--TCCTATGAAAT
* * * * *
20144 TTTGGTAACCATACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAATTTTAATAACCTTCCTATGAAAT
** * *
20188 TTTGATAA-CTTCCATATGAAATTTTGGTAA-CTACACTATGGAAT
1 TTTGATAACCTTCC-TATGAAATTTTAATAACCTTC-CTATGAAAT
* * * *
20232 TTTGATAGCC-TCCTCATGAAATTATAATAA-TTATCTTATGAAAT
1 TTTGATAACCTTCCT-ATGAAATTTTAATAACCT-TCCTATGAAAT
*
20276 CTTGATAACC
1 TTTGATAACC
20286 ACACAGAGAC
Statistics
Matches: 147, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
43 7 0.05
44 102 0.69
45 2 0.01
46 35 0.24
47 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TTTGATAACCTTCCTATGAAATTTTAATAACCTTCCTATGAAAT
Found at i:20254 original size:22 final size:21
Alignment explanation
Indices: 20067--20254 Score: 153
Period size: 22 Copynumber: 8.5 Consensus size: 21
20057 GATAACTTTT
* *
20067 CTATGAAATTGTGATAACCAC
1 CTATGAAATTTTGATAACCTC
**
20088 ACTATGAAATTTCAATAACCTTC
1 -CTATGAAATTTTGATAACC-TC
* *
20111 CTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAACC---TC
* *
20135 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACC-TC
20157 CTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAACC-TC
* *
20179 CCATGAAATTTTGATAACTTC
1 CTATGAAATTTTGATAACCTC
*
20200 CATATGAAATTTTGGTAA-CTAC
1 C-TATGAAATTTTGATAACCT-C
* *
20222 ACTATGGAATTTTGATAGCCTC
1 -CTATGAAATTTTGATAACCTC
20244 CTCATGAAATT
1 CT-ATGAAATT
20255 ATAATAATTA
Statistics
Matches: 135, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
21 6 0.04
22 107 0.79
23 4 0.03
24 18 0.13
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:20272 original size:66 final size:68
Alignment explanation
Indices: 20058--20289 Score: 251
Period size: 66 Copynumber: 3.5 Consensus size: 68
20048 AATCCCTTTG
* * ** *
20058 ATAACTTTTC-TATGAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCT-AAGAAATT
1 ATAACTTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATT
20121 TTA
66 TTA
* * * *
20124 ATAACCTGATCCTATGAAATTTTGGTAACCATACTATGAAATTTTGATAACCTTCC-CATGAAAT
1 ATAA-CTTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAAT
*
20188 TTTG
65 TTTA
* * * * *
20192 ATAACTT-CCATATGAAATTTTGGTAACTACACTATGGAATTTTGATAGCC-TCCTCATGAAATT
1 ATAACTTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATT
*
20255 ATA
66 TTA
* *
20258 ATAA-TTATCTTATGAAATCTTGATAACCACAC
1 ATAACTTATCATATGAAATTTTGATAACCACAC
20290 AGAGACAAGA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
65 5 0.04
66 75 0.54
67 6 0.04
68 52 0.38
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (68 bp):
ATAACTTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATT
TTA
Found at i:26912 original size:15 final size:16
Alignment explanation
Indices: 26892--26924 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
26882 AGATATATAT
26892 ATCTAATCTAAC-ATA
1 ATCTAATCTAACAATA
26907 ATCTAATCTAACAATA
1 ATCTAATCTAACAATA
26923 AT
1 AT
26925 AAAAGTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (16 bp):
ATCTAATCTAACAATA
Found at i:26939 original size:23 final size:23
Alignment explanation
Indices: 26913--26958 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
26903 CATAATCTAA
26913 TCTAACAATAATAAAAGTTAACC
1 TCTAACAATAATAAAAGTTAACC
*
26936 TCTAACAATGATAAAAGTTAACC
1 TCTAACAATAATAAAAGTTAACC
26959 ACAATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (23 bp):
TCTAACAATAATAAAAGTTAACC
Found at i:29891 original size:36 final size:36
Alignment explanation
Indices: 29844--29913 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
29834 TTCAATAACC
* *
29844 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
29880 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
29914 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:30798 original size:202 final size:204
Alignment explanation
Indices: 30429--30839 Score: 736
Period size: 202 Copynumber: 2.0 Consensus size: 204
30419 GCTTAATAAC
*
30429 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAATGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTCAAGTCTAAAATTACTAACAAAGTTGTAATGAATAA
* * *
30494 GATACAACACATTATTATTATATATATATAACTATACCAAAAACAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
30559 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
30624 TCCGATTTA
196 TCCGATTTA
* * *
30633 TTTATCAATGGTGAATGTTATTAATTTTTCAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTCAAGTCTAAAATTACTAACAAAGTTGTAATGAATAA
*
30698 GATACAACAGATTACTA-T-TATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
30761 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
30826 TCCGATTTA
196 TCCGATTTA
30835 TTTAT
1 TTTAT
30840 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
202 122 0.61
203 1 0.01
204 76 0.38
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (204 bp):
TTTATCAATGATGAATGTTATTAATTTTTCAAGTCTAAAATTACTAACAAAGTTGTAATGAATAA
GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
TCCGATTTA
Done.