Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018827.1 Corchorus olitorius cultivar O-4 contig18860, 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: 21718
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:3817 original size:201 final size:201
Alignment explanation
Indices: 3472--3846 Score: 750
Period size: 201 Copynumber: 1.9 Consensus size: 201
3462 ATTTTTGTAG
3472 TCAAGGAGCATGTATAGTTGTCGTAGAAAAATTGAATTAGTTGAGAGCATTTGCAGGAGCATATG
1 TCAAGGAGCATGTATAGTTGTCGTAGAAAAATTGAATTAGTTGAGAGCATTTGCAGGAGCATATG
3537 TAATTTAGACAATGCATCACAAAATGATTGTAGGTTAACTATGTGCTTTTGGGAATGTGGAAATA
66 TAATTTAGACAATGCATCACAAAATGATTGTAGGTTAACTATGTGCTTTTGGGAATGTGGAAATA
3602 TACTAAACATAAGCAACTAATAGAAACCTCAATAAAAAGGAAGTATAGTTGTCGTAACCTCAATA
131 TACTAAACATAAGCAACTAATAGAAACCTCAATAAAAAGGAAGTATAGTTGTCGTAACCTCAATA
3667 GAAACC
196 GAAACC
3673 TCAAGGAGCATGTATAGTTGTCGTAGAAAAATTGAATTAGTTGAGAGCATTTGCAGGAGCATATG
1 TCAAGGAGCATGTATAGTTGTCGTAGAAAAATTGAATTAGTTGAGAGCATTTGCAGGAGCATATG
3738 TAATTTAGACAATGCATCACAAAATGATTGTAGGTTAACTATGTGCTTTTGGGAATGTGGAAATA
66 TAATTTAGACAATGCATCACAAAATGATTGTAGGTTAACTATGTGCTTTTGGGAATGTGGAAATA
3803 TACTAAACATAAGCAACTAATAGAAACCTCAATAAAAAGGAAGT
131 TACTAAACATAAGCAACTAATAGAAACCTCAATAAAAAGGAAGT
3847 CGAATGATAA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 174 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (201 bp):
TCAAGGAGCATGTATAGTTGTCGTAGAAAAATTGAATTAGTTGAGAGCATTTGCAGGAGCATATG
TAATTTAGACAATGCATCACAAAATGATTGTAGGTTAACTATGTGCTTTTGGGAATGTGGAAATA
TACTAAACATAAGCAACTAATAGAAACCTCAATAAAAAGGAAGTATAGTTGTCGTAACCTCAATA
GAAACC
Found at i:4888 original size:15 final size:13
Alignment explanation
Indices: 4852--4883 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4842 ATTCTCGCTG
4852 ATATAT-AATATA
1 ATATATAAATATA
4864 ATATATAAATATA
1 ATATATAAATATA
4877 ATATATA
1 ATATATA
4884 TAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATAAATATA
Found at i:5494 original size:27 final size:27
Alignment explanation
Indices: 5459--5538 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
5449 ATCCTAGGGA
*
5459 ACTAACTTTGATTGG-GAAACTGACTTG
1 ACTAACTTTGAATGGAG-AACTGACTTG
*
5486 ACTAGCTTTGAATGGAGAACTGACTTG
1 ACTAACTTTGAATGGAGAACTGACTTG
*
5513 ACTAACTTGGAAT-GAGAGACTGACTT
1 ACTAACTTTGAATGGAGA-ACTGACTT
5539 TGAATGATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.09
27 42 0.89
28 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (27 bp):
ACTAACTTTGAATGGAGAACTGACTTG
Found at i:9977 original size:18 final size:19
Alignment explanation
Indices: 9933--9978 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
9923 ACTTGACTAG
*
9933 CTTTGAATG-GAGATTTGA
1 CTTTGAATGAGAGATCTGA
9951 C-TTGAAATGAGAGA-CTGA
1 CTTTG-AATGAGAGATCTGA
9969 CTTTGAATGA
1 CTTTGAATGA
9979 TCCTTAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 14 0.58
19 7 0.29
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (19 bp):
CTTTGAATGAGAGATCTGA
Found at i:13522 original size:30 final size:30
Alignment explanation
Indices: 12434--13504 Score: 1018
Period size: 30 Copynumber: 35.8 Consensus size: 30
12424 CTTGTAGTAA
* * * *
12434 TATGGAGGTGGTGGTGGTGACTTGTAGACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * * * *
12464 TATGGGGGAGGTGGTGGTGATTTATAGACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12494 TATGGTGGAGGGGGAGGGGAGC-TGTAGACG
1 TATGGAGGAGGTGGAGGTGA-CTTGTACACG
* * * *
12524 TATGGTGGAGGCGGTGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * * *
12554 TATGGTGGAGGAGGTGGTGACTTGTAGATG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12584 TATGGAGGAGGAGGTGGTGACTTGTAGAGG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * * * * *
12614 TATGGTGGTGGAGGGGGTGATTTATAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12644 TATGGAGGAGGGGGTGGTGACTTGTAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12674 TATGGTGGAGGTGGGGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12704 TATGGTGGAGGTGG-GGTGATTTGTAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12733 TATGGAGGAGGGGGTGGTGACTTGTAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12763 TATGGTGGAGGTGGGGGTGATTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12793 TATGGAGGAGGAGGTGGTGACTTGTAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
*
12823 TATGGTGGAGGTGG-GGTGACTTGTACACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12852 TATGGTGGAGGTGGAGGGGACTTGTAAACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12882 TAAGGAGGAGGAGGATGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
12912 TATGGTGGTGGTGGAGGTGACTTGTAAACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
12942 TAGGGAGGTGGTGGTGGTGACTTGTAGACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
*
12972 TATGGAGGAGGTGGAGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
13002 TATGGAGGAGGAGGAGGTGATTTATACACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
*
13032 TATGGAGGAGGAGGAGGTGACTTGTACACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
13062 TATGGTGGTGGTGGAGGTGACTTATACACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* *
13092 TATGGAGGAGGTGGTGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* *
13122 TATGGTGGAGGTGGAGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * * *
13152 TAAGGAGGTGGTGGTGGTGACTTGTAAACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * *
13182 TATGGAGGTGGTGGAGGTGACTTATAAACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
13212 TATGGAGGAGGTGGTGGTGACTTGTAGACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
*
13242 TATGGAGGAGGTGGAGGTGACTTGTACACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
** * *
13272 TATGGAGGAGGTGTTGGTGACTTGTAAATG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* *
13302 TATGGTGGTA-GTGGAGGTGA-TTCATACACG
1 TATGGAGG-AGGTGGAGGTGACTT-GTACACG
*
13332 TATGGAGGAGGTGGTGGTGACTTGTACACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
13362 TATGGTGGTGGTGGAGGTGACTTGTAAACG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * *
13392 TATGGAGGAGGTGGTGGTGACTTGTAAACA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * **
13422 TATGGAGGAGGAGGCGGTGACTTGTAGGCG
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
* * * * **
13452 TAGGGAGGTGGTGGTGGTGACTTGTAAATA
1 TATGGAGGAGGTGGAGGTGACTTGTACACG
*
13482 TATGGAGGTGGTGGAGGTGACTT
1 TATGGAGGAGGTGGAGGTGACTT
13505 ATAAATGTAG
Statistics
Matches: 880, Mismatches: 153, Indels: 16
0.84 0.15 0.02
Matches are distributed among these distances:
29 56 0.06
30 821 0.93
31 3 0.00
ACGTcount: A:0.23, C:0.07, G:0.44, T:0.26
Consensus pattern (30 bp):
TATGGAGGAGGTGGAGGTGACTTGTACACG
Found at i:15846 original size:2 final size:2
Alignment explanation
Indices: 15839--15879 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
15829 ATTTGCTTTC
15839 TA TA TA TA TA TA TA 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 TA TA TA TA T
15880 GCAGCCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16550 original size:44 final size:46
Alignment explanation
Indices: 16481--16585 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 46
16471 TTATATTATT
* * * *** *
16481 AAATTTTGATAA--ACCTAGAATGAAATTTTACTACTTTCCCTATG
1 AAATTTTGATAACCACATAGAATGAAATTTAAATAAGCTCCCTATA
*
16525 AAATTTTGATAACCACATA-AA-GAAATTTAAATAAGCTCTCTATA
1 AAATTTTGATAACCACATAGAATGAAATTTAAATAAGCTCCCTATA
16569 AAATTTTGATAACCACA
1 AAATTTTGATAACCACA
16586 CTATGAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 45 0.88
45 2 0.04
46 4 0.08
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (46 bp):
AAATTTTGATAACCACATAGAATGAAATTTAAATAAGCTCCCTATA
Found at i:16580 original size:22 final size:22
Alignment explanation
Indices: 16520--16717 Score: 125
Period size: 22 Copynumber: 9.0 Consensus size: 22
16510 ACTACTTTCC
*
16520 CTATGAAATTTTGATAACCACAT
1 CTATGAAATTTTGATAACCTC-T
* * ** *
16543 -AAAGAAATTTAAATAAGCTCT
1 CTATGAAATTTTGATAACCTCT
* * *
16564 CTATAAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTCT
* ** *
16586 CTATGAAATATTGATGGTCATC-
1 CTATGAAATTTTGAT-AACCTCT
*
16608 CTATGAAATTTTGGTAACCTCT
1 CTATGAAATTTTGATAACCTCT
* * *
16630 TTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAACCTCT
* * *
16652 CTAAGAAATTTTGATGACCAT-A
1 CTATGAAATTTTGATAACC-TCT
* * *
16674 CTATGAAACTTTCATAACCGC-
1 CTATGAAATTTTGATAACCTCT
16695 CTTATGAAATTTTGATAACCTCT
1 C-TATGAAATTTTGATAACCTCT
16718 TTGATATTCT
Statistics
Matches: 126, Mismatches: 42, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
21 5 0.04
22 118 0.94
23 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCT
Found at i:16617 original size:44 final size:44
Alignment explanation
Indices: 16517--17006 Score: 193
Period size: 44 Copynumber: 11.5 Consensus size: 44
16507 TTTACTACTT
* * *
16517 TCCCTATGAAATTTTGATAACCACA-TAAAGAAAT-TTAAATAAGC
1 TCCCTATGAAATTTTGATAACCACACT-ATGAAATATT-GATAATC
* * **
16561 TCTCTATAAAATTTTGATAACCACACTATGAAATATTGATGGTC
1 TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
* * ** *
16605 AT-CCTATGAAATTTTGGTAACCTCTTTATGAAATTTTGATAATC
1 -TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
* * * * *
16649 TCCCTAAGAAATTTTGATGACCATACTATGAAACT-TTCATAACC
1 TCCCTATGAAATTTTGATAACCACACTATGAAA-TATTGATAATC
* * * *
16693 GCCTTATGAAATTTTGAT-A--AC-C--T---CT-TTGATATTC
1 TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
** * * * *
16727 TCCCTATTTAATTTTGATAACCACAATGTAAAAT-TTTATAATC
1 TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
* * ** *
16770 TTCCTAT-AACGTTTTGATAACTTTC-CTATGAAATTTTGATAATC
1 TCCCTATGAA-ATTTTGATAAC-CACACTATGAAATATTGATAATC
* * * * * * *
16814 TTCTTATGGAATTTTGATAATCC-CCCTATGAAATTTTGGTAACC
1 TCCCTATGAAATTTTGATAA-CCACACTATGAAATATTGATAATC
* * * ** * * *
16858 ACACTATGAAAATTTGATAACTTC-CTTATGAAATTTTAATAATT
1 TCCCTATGAAATTTTGATAACCACAC-TATGAAATATTGATAATC
* * * * *
16902 TTCCTAGGAAATTTTG--GA-CAC-C-ATGAAATTTTGAGAATC
1 TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
* * *
16941 TCCTTATGAAAATTTTGGTAACCACACCATGAAAT-TGTGATAATC
1 TCCCTATG-AAATTTTGATAACCACACTATGAAATAT-TGATAATC
***
16986 TTTTTATGAAATTTTGATAAC
1 TCCCTATGAAATTTTGATAAC
17007 ATTATTATCA
Statistics
Matches: 331, Mismatches: 86, Indels: 58
0.70 0.18 0.12
Matches are distributed among these distances:
34 21 0.06
35 1 0.00
37 2 0.01
38 1 0.00
39 19 0.06
40 10 0.03
41 3 0.01
42 3 0.01
43 38 0.11
44 206 0.62
45 27 0.08
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (44 bp):
TCCCTATGAAATTTTGATAACCACACTATGAAATATTGATAATC
Found at i:16660 original size:66 final size:66
Alignment explanation
Indices: 16555--16714 Score: 176
Period size: 66 Copynumber: 2.4 Consensus size: 66
16545 AGAAATTTAA
* * * * ** * *
16555 ATAAGCTCTCTATAAAATTTTGATAACCACACTATGAAATATTGATGGTCATCCTATGAAATTTT
1 ATAACCTCTTTATGAAATTTTGATAACCACACTAAGAAATATTGATGACCATACTATGAAACTTT
*
16620 G
66 C
* * * * *
16621 GTAACCTCTTTATGAAATTTTGATAATCTCCCTAAGAAATTTTGATGACCATACTATGAAACTTT
1 ATAACCTCTTTATGAAATTTTGATAACCACACTAAGAAATATTGATGACCATACTATGAAACTTT
16686 C
66 C
* *
16687 ATAACCGCCTTATGAAATTTTGATAACC
1 ATAACCTCTTTATGAAATTTTGATAACC
16715 TCTTTGATAT
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (66 bp):
ATAACCTCTTTATGAAATTTTGATAACCACACTAAGAAATATTGATGACCATACTATGAAACTTT
C
Found at i:16789 original size:22 final size:22
Alignment explanation
Indices: 16757--17005 Score: 153
Period size: 22 Copynumber: 11.5 Consensus size: 22
16747 CCACAATGTA
16757 AAATTTT-ATAATCTTCCTAT-
1 AAATTTTGATAATCTTCCTATG
*
16777 AACGTTTTGATAA-CTTTCCTATG
1 AA-ATTTTGATAATC-TTCCTATG
*
16800 AAATTTTGATAATCTTCTTATG
1 AAATTTTGATAATCTTCCTATG
* **
16822 GAATTTTGATAATCCCCCTATG
1 AAATTTTGATAATCTTCCTATG
* **
16844 AAATTTTGGTAA-CCACACTATG
1 AAATTTTGATAATCTTC-CTATG
*
16866 AAAATTTGATAA-CTTCCTTATG
1 AAATTTTGATAATCTTCC-TATG
* * *
16888 AAATTTTAATAATTTTCCTAGG
1 AAATTTTGATAATCTTCCTATG
* *
16910 AAATTTTG--GA-C-ACC-ATG
1 AAATTTTGATAATCTTCCTATG
*
16927 AAATTTTGAGAATC-TCCTTATG
1 AAATTTTGATAATCTTCC-TATG
* ** *
16949 AAAATTTTGGTAA-CCACACCATG
1 -AAATTTTGATAATCTTC-CTATG
* **
16972 AAATTGTGATAATCTTTTTATG
1 AAATTTTGATAATCTTCCTATG
16994 AAATTTTGATAA
1 AAATTTTGATAA
17006 CATTATTATC
Statistics
Matches: 175, Mismatches: 37, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
17 10 0.06
18 2 0.01
19 1 0.01
20 6 0.03
21 9 0.05
22 124 0.71
23 22 0.13
24 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAATCTTCCTATG
Found at i:16865 original size:66 final size:62
Alignment explanation
Indices: 16794--16957 Score: 179
Period size: 66 Copynumber: 2.6 Consensus size: 62
16784 TGATAACTTT
* *
16794 CCTATGAAATTTTGATAATCTTCTTATGGAATTTTGATAATCCCCCTATGAAATTTTGGTAACCA
1 CCTATGAAATTTTGATAATCTTCTTATGAAATTTTGATAATCCCCCTAGGAAATTTTGG--A-CA
* * ***
16859 CACTATGAAAATTTGATAA-CTTCCTTATGAAATTTTAATAATTTTCCTAGGAAATTTTGGACA
1 C-CTATGAAATTTTGATAATCTT-CTTATGAAATTTTGATAATCCCCCTAGGAAATTTTGGACA
* *
16922 CC-ATGAAATTTTGAGAATCTCCTTATGAAAATTTTG
1 CCTATGAAATTTTGATAATCTTCTTATG-AAATTTTG
16958 GTAACCACAC
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
61 19 0.23
62 10 0.12
63 3 0.04
64 1 0.01
65 4 0.05
66 47 0.56
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (62 bp):
CCTATGAAATTTTGATAATCTTCTTATGAAATTTTGATAATCCCCCTAGGAAATTTTGGACA
Found at i:16986 original size:45 final size:44
Alignment explanation
Indices: 16919--17006 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
16909 GAAATTTTGG
* *
16919 ACACCATGAAATTTTGAGAATCTCCTTATGAAAATTTTGGTAACC
1 ACACCATGAAATTGTGAGAATCTCCTTATG-AAATTTTGATAACC
* **
16964 ACACCATGAAATTGTGATAATCTTTTTATGAAATTTTGATAAC
1 ACACCATGAAATTGTGAGAATCTCCTTATGAAATTTTGATAAC
17007 ATTATTATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 12 0.32
45 26 0.68
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (44 bp):
ACACCATGAAATTGTGAGAATCTCCTTATGAAATTTTGATAACC
Found at i:17014 original size:22 final size:22
Alignment explanation
Indices: 16969--17014 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16959 TAACCACACC
*
16969 ATGAAATTGTGATAATCTTTTT
1 ATGAAATTGTGATAATCTTATT
*
16991 ATGAAATTTTGATAA-CATTATT
1 ATGAAATTGTGATAATC-TTATT
17013 AT
1 AT
17015 CAAACTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGAAATTGTGATAATCTTATT
Found at i:17036 original size:2 final size:2
Alignment explanation
Indices: 17029--17054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17019 CTTCGACAAC
17029 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17055 CTATGAAAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17089 original size:22 final size:22
Alignment explanation
Indices: 17054--17117 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
17044 ATATATATAT
17054 ACTATGAAAA-TTTGATAACCTC
1 ACTAT-AAAATTTTGATAACCTC
* * * * *
17076 CCTATTAAGTTTTGAAAATCTC
1 ACTATAAAATTTTGATAACCTC
17098 ACTATAAAATTTTGATAACC
1 ACTATAAAATTTTGATAACC
17118 ACACAAAGTC
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
ACTATAAAATTTTGATAACCTC
Done.