Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013190.1 Kokia drynarioides strain JFW-HI SEQ_128209, 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: 53186
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:659 original size:29 final size:28
Alignment explanation
Indices: 618--954 Score: 148
Period size: 29 Copynumber: 11.5 Consensus size: 28
608 AAATTGTACA
*
618 AAAATTACATTTTTACCCTCAAACTTTCC
1 AAAATTCCATTTTTACCC-CAAACTTTCC
* ** **
647 AAAATTCCATTTTCGACCTTAAACTTTTTG
1 AAAATTCCATTTT-TACCCCAAAC-TTTCC
** * *
677 AAAATTATATTCTTACCCCTAAATTTTCC
1 AAAATTCCATTTTTACCCC-AAACTTTCC
* **
706 AAAATTCCATTTTTGACCCCGATTTTTCC
1 AAAATTCCATTTTT-ACCCCAAACTTTCC
* *
735 AAAAATTACATTTTTACCCCTAACTTTCC
1 -AAAATTCCATTTTTACCCCAAACTTTCC
** * *
764 AAAATTCCATTTTTGACCTTAATCTCTCC
1 AAAATTCCATTTTT-ACCCCAAACTTTCC
*
793 AAAAATT--ATCGTTTTACCCCTGAAC-TTCC
1 -AAAATTCCAT--TTTTACCCC-AAACTTTCC
* **
822 AAAAATTCCATTTTTGACCCCGATTTTTCC
1 -AAAATTCCATTTTT-ACCCCAAACTTTCC
* * *
852 AAAATTTTCA-TTTTACTCTCGAAC-TTCC
1 AAAA-TTCCATTTTTAC-CCCAAACTTTCC
* * **
880 ACAAATTCTATTTTTTACCCTAATTTTTCC
1 A-AAATTCCA-TTTTTACCCCAAACTTTCC
910 AAAAATTACCA-TTTTACCCCCCAAAC-TTCC
1 -AAAATT-CCATTTTTA--CCCCAAACTTTCC
*
940 AAAAAATCCATTTTT
1 -AAAATTCCATTTTT
955 TAACCTCGAT
Statistics
Matches: 230, Mismatches: 53, Indels: 49
0.69 0.16 0.15
Matches are distributed among these distances:
28 25 0.11
29 104 0.45
30 91 0.40
31 10 0.04
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCAAACTTTCC
Found at i:710 original size:59 final size:59
Alignment explanation
Indices: 607--954 Score: 247
Period size: 59 Copynumber: 5.9 Consensus size: 59
597 GTTCTTGGTC
* * *
607 TAAATTGTACAAAAATTACATTTTTA-CCCTCAAACTTTCCAAAATTCCATTTTCGACCT
1 TAAATTTTTCAAAAATTACATTTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCT
* * * *
666 TAAACTTTTT-GAAAATTATATTCTTACCCCTAAATTTTCCAAAATTCCATTTTTGACC-
1 TAAA-TTTTTCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
***
724 CCGATTTTTCCAAAAATTACATTTTTACCCCT-AACTTTCCAAAATTCCATTTTTGACCT
1 TAAATTTTT-CAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
* * * *
783 T-AATCTCTCCAAAAATTATC-GTTTTACCCCTGAAC-TTCCAAAAATTCCATTTTTGACC-
1 TAAAT-TTTTCAAAAATTA-CATTTTTACCCCTAAACTTTCC-AAAATTCCATTTTTGACCT
*** * * * * * * *
841 CCGATTTTTCCAAAATTTTCA-TTTTA-CTCTCGAAC-TTCCACAAATTCTATTTTTTACCC
1 TAAATTTTT-CAAAAATTACATTTTTACCCCT-AAACTTTCCA-AAATTCCATTTTTGACCT
* *
900 T-AATTTTTCCAAAAATTACCA-TTTTACCCCCCAAAC-TTCCAAAAAATCCATTTTT
1 TAAATTTTT-CAAAAATTA-CATTTTTA-CCCCTAAACTTTCC-AAAATTCCATTTTT
955 TAACCTCGAT
Statistics
Matches: 233, Mismatches: 37, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
57 9 0.04
58 96 0.41
59 100 0.43
60 25 0.11
61 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (59 bp):
TAAATTTTTCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT
Found at i:827 original size:117 final size:117
Alignment explanation
Indices: 616--984 Score: 415
Period size: 117 Copynumber: 3.1 Consensus size: 117
606 CTAAATTGTA
* * ***
616 CAAAAATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTCGACCTTAAACTTTTTGAAAA
1 CAAAAATTACATTTTTACCC-CAAACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAA
*
681 TTAT-ATTCTTACCCCTAAATTTTCC-AAAATTCCATTTTTGACCCCGATTTTTC
65 TTATCATT-TTACCCCTAAA-CTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
* *
734 CAAAAATTACATTTTTACCCCTAACTTTCCAAAATTCCATTTTTGACCTTAATCTCTCCAAAAAT
1 CAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAAT
* *
799 TATCGTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
66 TATCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
* * * * * * * *
851 CAAAATTTTCA-TTTTACTCTCGAAC-TTCCACAAATTCTATTTTTTACCCTAATTTTTCCAAAA
1 CAAAAATTACATTTTTAC-CCCAAACTTTCCA-AAATTCCATTTTTGACCTTAATCTTTCCAAAA
* * * * *
914 ATTACCATTTTACCCCCCAAACTTCCAAAAAATCCATTTTTTAACCTCGA-TTTTC
64 ATTATCATTTTA-CCCCTAAACTTCCAAAAATTCCA-TTTTTGACCCCGATTTTTC
*
969 CCAAAATTACCATTTT
1 CAAAAATTA-CATTTT
985 ATTCGGATGT
Statistics
Matches: 214, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
116 15 0.07
117 130 0.61
118 53 0.25
119 13 0.06
120 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (117 bp):
CAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTGACCTTAATCTTTCCAAAAAT
TATCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTC
Found at i:1972 original size:28 final size:25
Alignment explanation
Indices: 1916--1976 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
1906 TTTTTGGGTA
*
1916 TAAAATAAAACTTTTTAGGTACAATT
1 TAAAA-AAAACTTTTTAGGTACAAAT
*
1942 TAAAAAAAACATGTTTTAGGTATGAAAT
1 TAAAAAAAAC-T-TTTTAGGTA-CAAAT
1970 TAAAAAA
1 TAAAAAA
1977 TGCACTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 6 0.20
27 9 0.30
28 10 0.33
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (25 bp):
TAAAAAAAACTTTTTAGGTACAAAT
Found at i:7935 original size:42 final size:41
Alignment explanation
Indices: 7856--7935 Score: 92
Period size: 42 Copynumber: 1.9 Consensus size: 41
7846 TAATTTATTG
* * *
7856 TTTATTTATTTATATGTTATCATAGATTTTTTGTTTTAATT
1 TTTAATTATTTATATGTTATCATAGATTTATTATTTTAATT
7897 TTTAATTATATTATATGTTAT-AT-GCATTCTATTATTTTA
1 TTTAATTAT-TTATATGTTATCATAG-ATT-TATTATTTTA
7936 TTTAGTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
40 1 0.03
41 13 0.39
42 19 0.58
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (41 bp):
TTTAATTATTTATATGTTATCATAGATTTATTATTTTAATT
Found at i:8870 original size:19 final size:20
Alignment explanation
Indices: 8839--8890 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
8829 AAAAATACAA
*
8839 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AATTTTTAAAAATT
8859 ATTTTAAA-TTTTAAAAATT
1 ATTTTAAATTTTTAAAAATT
*
8878 ATTTTTAATTTTT
1 ATTTTAAATTTTT
8891 TAATTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
20 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTAAATTTTTAAAAATT
Found at i:9479 original size:20 final size:17
Alignment explanation
Indices: 9454--9496 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
9444 AGAAAAATGA
9454 TTTTAACCTTTTATTTAAAT
1 TTTTAACC-TTT-TTT-AAT
9474 TTTTAACCTTTTTTAAT
1 TTTTAACCTTTTTTAAT
9491 TTTTAA
1 TTTTAA
9497 ACTTGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 3 0.13
19 3 0.13
20 8 0.35
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAACCTTTTTTAAT
Found at i:10161 original size:14 final size:15
Alignment explanation
Indices: 10137--10174 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
10127 GAATGAGAAT
10137 AAATCTTTAATTAA-A
1 AAAT-TTTAATTAATA
10152 AAATTTTAATTAATTA
1 AAATTTTAATTAA-TA
10168 AAATTTT
1 AAATTTT
10175 TAAACCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTTAATTAATA
Found at i:11393 original size:20 final size:20
Alignment explanation
Indices: 11363--11400 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11353 GATTTAATAA
11363 AAAAATATAAATTTAAAGATT
1 AAAAATATAAA-TTAAAGATT
11384 AAAAAT-TAAATTAAAGA
1 AAAAATATAAATTAAAGA
11401 CTAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAATATAAATTAAAGATT
Found at i:15963 original size:21 final size:20
Alignment explanation
Indices: 15937--16020 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 20
15927 AAAAATATAA
15937 AAAAAATACTTAAATTTTATT
1 AAAAAATACTTAAATTTTA-T
15958 AAAAAATACTTAAA--TTAT
1 AAAAAATACTTAAATTTTAT
15976 -AAAAAT-CTTAAAATTTTTAT
1 AAAAAATACTT-AAA-TTTTAT
** *
15996 AAAAAATTGTAAAATTTTAT
1 AAAAAATACTTAAATTTTAT
16016 AAAAA
1 AAAAA
16021 TCGTAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
16 3 0.05
17 9 0.16
18 1 0.02
19 3 0.05
20 15 0.27
21 23 0.42
22 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAAAATACTTAAATTTTAT
Found at i:15990 original size:17 final size:16
Alignment explanation
Indices: 15955--15987 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15945 CTTAAATTTT
15955 ATTAAAAAATACTTAA
1 ATTAAAAAATACTTAA
15971 ATTATAAAAAT-CTTAA
1 ATTA-AAAAATACTTAA
15987 A
1 A
15988 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAAAATACTTAA
Found at i:16011 original size:38 final size:39
Alignment explanation
Indices: 15938--16028 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 39
15928 AAAATATAAA
*
15938 AAAAATACTT-AAATTTTATTAAAAAATACTTAAA-TTAT
1 AAAAAT-CTTAAAATTTTATTAAAAAATACTAAAATTTAT
**
15976 AAAAATCTTAAAATTTT-TATAAAAAATTGTAAAATTTTAT
1 AAAAATCTTAAAATTTTAT-TAAAAAATACTAAAA-TTTAT
*
16016 AAAAATCGTAAAA
1 AAAAATCTTAAAA
16029 AAATATAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 4 0.09
38 25 0.56
40 16 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.37
Consensus pattern (39 bp):
AAAAATCTTAAAATTTTATTAAAAAATACTAAAATTTAT
Found at i:16021 original size:19 final size:20
Alignment explanation
Indices: 15972--16028 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
15962 AATACTTAAA
15972 TTATAAAAATCT-TAAAATTT
1 TTATAAAAAT-TGTAAAATTT
15992 TTATAAAAAATTGTAAAA-TT
1 TTAT-AAAAATTGTAAAATTT
*
16012 TTATAAAAATCGTAAAA
1 TTATAAAAATTGTAAAA
16029 AAATATAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.35
20 11 0.32
21 11 0.32
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
TTATAAAAATTGTAAAATTT
Found at i:16030 original size:21 final size:20
Alignment explanation
Indices: 15972--16029 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
15962 AATACTTAAA
* *
15972 TTATAAAAATCTTAAAATTT
1 TTATAAAAATCGTAAAAATT
*
15992 TTATAAAAAATTGT-AAAATT
1 TTAT-AAAAATCGTAAAAATT
16012 TTATAAAAATCGTAAAAA
1 TTATAAAAATCGTAAAAA
16030 AATATAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTATAAAAATCGTAAAAATT
Found at i:16096 original size:29 final size:29
Alignment explanation
Indices: 15969--16104 Score: 96
Period size: 29 Copynumber: 4.6 Consensus size: 29
15959 AAAAATACTT
* *
15969 AAATTATAAAAATCTTA-AAATTTTTATAAA
1 AAATTAT-AAAATTTTATAAATTTGTA-AAA
* * *
15999 AAATTGTAAAATTTTATAAAAATCGTAAAA
1 AAATTATAAAATTTTAT-AAATTTGTAAAA
* * * * *
16029 AAA-TATAAAGTATATAGAAATATAGAAAAA
1 AAATTATAAAAT-TTTATAAAT-TTGTAAAA
*
16059 AAGATTATAAAATTTTATAAATTTGTAAGA
1 AA-ATTATAAAATTTTATAAATTTGTAAAA
*
16089 AAATTATAAAAATTTA
1 AAATTATAAAATTTTA
16105 AAGAAATATA
Statistics
Matches: 81, Mismatches: 19, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
29 30 0.37
30 30 0.37
31 14 0.17
32 7 0.09
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATTATAAAATTTTATAAATTTGTAAAA
Found at i:16110 original size:20 final size:20
Alignment explanation
Indices: 16085--16137 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
16075 ATAAATTTGT
16085 AAGAAAATTATAAAAAT-TTA
1 AAGAAAA-TATAAAAATCTTA
16105 AAG-AAATAT-AAAATGCTTA
1 AAGAAAATATAAAAAT-CTTA
16124 AA-AAAATATAAAAA
1 AAGAAAATATAAAAA
16138 ATAGCATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.17
18 3 0.10
19 14 0.48
20 7 0.24
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AAGAAAATATAAAAATCTTA
Found at i:17007 original size:19 final size:18
Alignment explanation
Indices: 16983--17022 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
16973 TATAAATAAA
*
16983 ATAATAAATATGTAATTAT
1 ATAATAAATATATAA-TAT
17002 ATAATAAATATATAATAT
1 ATAATAAATATATAATAT
17020 ATA
1 ATA
17023 TCATTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAATAAATATATAATAT
Found at i:17014 original size:2 final size:2
Alignment explanation
Indices: 16999--17073 Score: 63
Period size: 2 Copynumber: 40.0 Consensus size: 2
16989 AATATGTAAT
* * * *
16999 TA TA TA -A TA AA TA TA TA -A TA TA TA TCA T- TA TG T- TA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
17038 TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17074 ATTACATATT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
1 6 0.10
2 53 0.87
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17028 original size:28 final size:27
Alignment explanation
Indices: 16970--17077 Score: 79
Period size: 28 Copynumber: 4.1 Consensus size: 27
16960 ACTCTTTTAT
*
16970 TTATATAAATAAA-ATAATAA-ATATGTAA
1 TTATAT-AATAAATAT-ATAATATATAT-A
16998 TTATATAATAAATATATAATATATATCA
1 TTATATAATAAATATATAATATATAT-A
*
17026 TTATGTTAA-AAATAT-T-ATATATATA
1 TTAT-ATAATAAATATATAATATATATA
* *
17051 -TATAT-ATATATATATATTATATA-A
1 TTATATAATAAATATATAATATATATA
17075 TTA
1 TTA
17078 CATATTTATT
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
22 1 0.01
23 6 0.09
24 5 0.07
25 9 0.13
26 8 0.12
27 11 0.16
28 24 0.36
29 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (27 bp):
TTATATAATAAATATATAATATATATA
Found at i:26175 original size:20 final size:20
Alignment explanation
Indices: 26150--26188 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
26140 AAGTTATAAT
*
26150 ATTTTTCCGTCCATAGAGTG
1 ATTTTTCCATCCATAGAGTG
26170 ATTTTTCCATCCATAGAGT
1 ATTTTTCCATCCATAGAGT
26189 ACCCACTAAG
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:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTTTTCCATCCATAGAGTG
Found at i:26794 original size:19 final size:19
Alignment explanation
Indices: 26770--26817 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
26760 AAATATTTTC
*
26770 ATTTTTTTATACTTTTT-GA
1 ATTTTTTAATA-TTTTTAGA
*
26789 ATTTTTTAATATTTTTATA
1 ATTTTTTAATATTTTTAGA
26808 ATTTTTTAAT
1 ATTTTTTAAT
26818 CTCTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTTTTAATATTTTTAGA
Found at i:32245 original size:31 final size:31
Alignment explanation
Indices: 32199--32280 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
32189 TTCGATAAAC
* * *
32199 CATCGTTGTCAAGCAATTCGAGGTGGTAGGT
1 CATCATTGTCAAGCAATCCGAGGTGATAGGT
* *
32230 CATCATTGTCGAGCAATCCGGGGTGATAGGT
1 CATCATTGTCAAGCAATCCGAGGTGATAGGT
* *
32261 CATCATTGCCAGGCAATCCG
1 CATCATTGTCAAGCAATCCG
32281 GGATGACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (31 bp):
CATCATTGTCAAGCAATCCGAGGTGATAGGT
Found at i:32771 original size:74 final size:75
Alignment explanation
Indices: 32634--32798 Score: 242
Period size: 74 Copynumber: 2.2 Consensus size: 75
32624 CAATATCAAC
* *
32634 CCAAATAAACAACACGAGTCTAAGTAAACAATAACAACAATACAACAAGATTATAATAAAAAAAC
1 CCAAATAAACAACACGAGTCGAAGTAAAC-A-AACAACAACACAACAAGATTATAATAAAAAAAC
32699 ATAAGCAAAAAT
64 ATAAGCAAAAAT
* *
32711 CCAAGTAAACAACATGAGTCGAAGTAAAC-AACAACAACACAACAAGATTATAATAAAAAAACAT
1 CCAAATAAACAACACGAGTCGAAGTAAACAAACAACAACACAACAAGATTATAATAAAAAAACAT
*
32775 AAGCAAAAGT
66 AAGCAAAAAT
32785 CCAAAATACAACAA
1 CC-AAATA-AACAA
32799 AAACCTACAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
74 45 0.56
75 4 0.05
76 5 0.06
77 26 0.32
ACGTcount: A:0.60, C:0.18, G:0.08, T:0.14
Consensus pattern (75 bp):
CCAAATAAACAACACGAGTCGAAGTAAACAAACAACAACACAACAAGATTATAATAAAAAAACAT
AAGCAAAAAT
Found at i:34413 original size:35 final size:34
Alignment explanation
Indices: 34362--34432 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 34
34352 AAAGTGAGCT
* * *
34362 CAGCTCTAGTTGGATAAATCAACAATATTTGTGCC
1 CAGCGCTAGTTGGATAAACCAACAA-ATGTGTGCC
*
34397 CAGCGCTAGTTGGATAAACCAACGAATGTGTGCC
1 CAGCGCTAGTTGGATAAACCAACAAATGTGTGCC
34431 CA
1 CA
34433 ACACTAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (34 bp):
CAGCGCTAGTTGGATAAACCAACAAATGTGTGCC
Found at i:34440 original size:34 final size:35
Alignment explanation
Indices: 34367--34449 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
34357 GAGCTCAGCT
* * * *
34367 CTAGTTGGATAAATCAACAATATTTGTGCCCAGCG
1 CTAGTTGGATAAACCAACAATATGTGTGCCCAACA
*
34402 CTAGTTGGATAAACCAACGA-ATGTGTGCCCAACA
1 CTAGTTGGATAAACCAACAATATGTGTGCCCAACA
**
34436 CTAGTCAGATAAAC
1 CTAGTTGGATAAAC
34450 TGACGATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 23 0.56
35 18 0.44
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (35 bp):
CTAGTTGGATAAACCAACAATATGTGTGCCCAACA
Found at i:36297 original size:22 final size:22
Alignment explanation
Indices: 36272--36313 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36262 AAAGTCCAAT
36272 AAACCAACAAAAATAACACAAC
1 AAACCAACAAAAATAACACAAC
* * *
36294 AAACTAATAACAATAACACA
1 AAACCAACAAAAATAACACA
36314 TCAGTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.24, G:0.00, T:0.10
Consensus pattern (22 bp):
AAACCAACAAAAATAACACAAC
Found at i:40414 original size:27 final size:25
Alignment explanation
Indices: 40368--40436 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
40358 AATAAAAGAA
40368 AATGCCTTTGTGGCAAACTCTATAAGG
1 AATGCCTTTGTGGCAAACTCTA-AA-G
**
40395 AATGCCTTTGTGGCGTACTCTAAAG
1 AATGCCTTTGTGGCAAACTCTAAAG
40420 AATGATCC-TTGTGGCAA
1 AATG--CCTTTGTGGCAA
40437 CAATCTGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
26 9 0.25
27 22 0.61
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (25 bp):
AATGCCTTTGTGGCAAACTCTAAAG
Found at i:40900 original size:107 final size:107
Alignment explanation
Indices: 40714--40930 Score: 416
Period size: 107 Copynumber: 2.0 Consensus size: 107
40704 TGATGAATTC
*
40714 AAAGTATAAGCCAAGTATACCTGAAGAACAAATCTGAGTAAGGGCTACGTTTCATAAATTGAAGA
1 AAAGTATAAGCCAAGTATACCTGAAGAACAAATATGAGTAAGGGCTACGTTTCATAAATTGAAGA
*
40779 AGGTTAATTTACTGTAATTATTAGAAGAAAAAGGGTAGTTAA
66 AGGTTAATTTACTGTAATTATTAGAAAAAAAAGGGTAGTTAA
40821 AAAGTATAAGCCAAGTATACCTGAAGAACAAATATGAGTAAGGGCTACGTTTCATAAATTGAAGA
1 AAAGTATAAGCCAAGTATACCTGAAGAACAAATATGAGTAAGGGCTACGTTTCATAAATTGAAGA
40886 AGGTTAATTTACTGTAATTATTAGAAAAAAAAGGGTAGTTAA
66 AGGTTAATTTACTGTAATTATTAGAAAAAAAAGGGTAGTTAA
40928 AAA
1 AAA
40931 AAGATCAGGT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (107 bp):
AAAGTATAAGCCAAGTATACCTGAAGAACAAATATGAGTAAGGGCTACGTTTCATAAATTGAAGA
AGGTTAATTTACTGTAATTATTAGAAAAAAAAGGGTAGTTAA
Found at i:45088 original size:15 final size:16
Alignment explanation
Indices: 45063--45096 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45053 AAAATGTAAT
45063 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
45079 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
45094 TTT
1 TTT
45097 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:47507 original size:14 final size:14
Alignment explanation
Indices: 47490--47520 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
47480 TTTAATACTT
47490 TTTAAAAATAAAAA
1 TTTAAAAATAAAAA
47504 TTTAAAAATAAAAA
1 TTTAAAAATAAAAA
47518 TTT
1 TTT
47521 TCAACTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTAAAAATAAAAA
Found at i:51378 original size:16 final size:16
Alignment explanation
Indices: 51357--51387 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51347 TCCTAATCCA
51357 ATTTTTTGTTACTATC
1 ATTTTTTGTTACTATC
*
51373 ATTTTTTTTTACTAT
1 ATTTTTTGTTACTAT
51388 ATGCATTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTTGTTACTATC
Found at i:53011 original size:12 final size:12
Alignment explanation
Indices: 52984--53052 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
52974 TTTTTTATTG
*
52984 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
*
52997 TTTCG-TGTTAT
1 TTTTGTTGTTAT
53008 TTTTGTTGTTA-
1 TTTTGTTGTTAT
* *
53019 TTTTGTTGCTGT
1 TTTTGTTGTTAT
53031 TTTTGTTGTTAT
1 TTTTGTTGTTAT
53043 TTTTGTTGTT
1 TTTTGTTGTT
53053 TTTAATGTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
11 18 0.38
12 25 0.53
13 4 0.09
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:53020 original size:23 final size:23
Alignment explanation
Indices: 53005--53050 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52995 ATTTTCGTGT
53005 TATTTTTGTTGTTATTTTGTTGC
1 TATTTTTGTTGTTATTTTGTTGC
*
53028 TGTTTTTGTTGTTATTTTTGTTG
1 TATTTTTGTTGTTA-TTTTGTTG
53051 TTTTTAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.72
Consensus pattern (23 bp):
TATTTTTGTTGTTATTTTGTTGC
Found at i:53041 original size:35 final size:35
Alignment explanation
Indices: 52984--53052 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
52974 TTTTTTATTG
52984 TTTTGATTGCTATTTTCGTGTTATTTTTGTTGTTA
1 TTTTGATTGCTATTTTCGTGTTATTTTTGTTGTTA
* *
53019 TTTTG-TTGCTGTTTTTGTTGTTATTTTTGTTGTT
1 TTTTGATTGCTATTTTCG-TGTTATTTTTGTTGTT
53053 TTTAATGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 10 0.32
35 21 0.68
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (35 bp):
TTTTGATTGCTATTTTCGTGTTATTTTTGTTGTTA
Found at i:53124 original size:17 final size:17
Alignment explanation
Indices: 53102--53175 Score: 107
Period size: 17 Copynumber: 4.4 Consensus size: 17
53092 TTGGAAATTG
53102 AATTTATTTTAAAA-TTA
1 AATTTA-TTTAAAATTTA
*
53119 AGTTTATTTAAAATTTA
1 AATTTATTTAAAATTTA
53136 AATTTATTTAAAATTTA
1 AATTTATTTAAAATTTA
53153 AATTTA-TTATAAATTTA
1 AATTTATTTA-AAATTTA
53170 AATTTA
1 AATTTA
53176 AAATGTCCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.19
17 43 0.81
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (17 bp):
AATTTATTTAAAATTTA
Found at i:53138 original size:6 final size:6
Alignment explanation
Indices: 53124--53177 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
53114 AATTAAGTTT
53124 ATTTAAA ATTTAA ATTT-- ATTTAAA ATTTAA ATTT-- ATTATAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATT-TAA ATTTAA
53171 ATTTAA A
1 ATTTAA A
53178 ATGTCCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.17
5 1 0.02
6 22 0.54
7 11 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Done.