Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011741.1 Kokia drynarioides strain JFW-HI SEQ_126735, 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: 38119
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:63 original size:4 final size:4
Alignment explanation
Indices: 43--108 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
33 AACACATTAC
* * * * *
43 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTAT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
91 CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT CTTT C
109 CCGTTTATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.80
5 7 0.14
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:77 original size:17 final size:15
Alignment explanation
Indices: 43--109 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 15
33 AACACATTAC
43 CTTTCTTTCCTTCTT
1 CTTTCTTTCCTTCTT
58 CTTTCTTTCC-TC-T
1 CTTTCTTTCCTTCTT
*
71 CCTTC-TTCCTTTCTAT
1 CTTTCTTTCC-TTCT-T
87 CTTTCTTTCC-T-TT
1 CTTTCTTTCCTTCTT
100 CTTTCTTTCC
1 CTTTCTTTCC
110 CGTTTATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 4 0.09
13 16 0.36
14 5 0.11
15 11 0.24
16 5 0.11
17 4 0.09
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.63
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:90 original size:29 final size:27
Alignment explanation
Indices: 49--106 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
39 TTACCTTTCT
49 TTCCTTCTTCTTTCTTTCCTCTCCTTC
1 TTCCTTCTTCTTTCTTTCCTCTCCTTC
* *
76 TTCCTTTCTATCTTTCTTTCCTTTCTTTC
1 TTCC-TTCT-TCTTTCTTTCCTCTCCTTC
105 TT
1 TT
107 TCCCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 19 0.70
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (27 bp):
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Found at i:471 original size:10 final size:10
Alignment explanation
Indices: 449--473 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
439 TTAAATATAT
449 AAAAATTAAA
1 AAAAATTAAA
459 AAAAATTAAA
1 AAAAATTAAA
469 AAAAA
1 AAAAA
474 CACGTGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:874 original size:31 final size:30
Alignment explanation
Indices: 839--905 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
829 ATAATTTGTG
* *
839 AAAATTGA-ATCAAATTCAAAATTTTATGTAT
1 AAAATTGATA-CAAAATCAAAA-CTTATGTAT
870 AAAATT-ATACAAAATCAAAACTTATGTAT
1 AAAATTGATACAAAATCAAAACTTATGTAT
*
899 ACAATTG
1 AAAATTG
906 CTCATTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 13 0.42
30 11 0.35
31 7 0.23
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAATTGATACAAAATCAAAACTTATGTAT
Found at i:973 original size:7 final size:7
Alignment explanation
Indices: 963--992 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
953 TATAAATCAT
963 ATCTATA
1 ATCTATA
970 ATCTATA
1 ATCTATA
*
977 ATTTATA
1 ATCTATA
984 ATCTATA
1 ATCTATA
991 AT
1 AT
993 TAATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (7 bp):
ATCTATA
Found at i:985 original size:14 final size:14
Alignment explanation
Indices: 966--999 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
956 AAATCATATC
966 TATAATCTATAATT
1 TATAATCTATAATT
980 TATAATCTATAATT
1 TATAATCTATAATT
*
994 AATAAT
1 TATAAT
1000 TAAACCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAATCTATAATT
Found at i:1910 original size:22 final size:23
Alignment explanation
Indices: 1876--1918 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1866 GGTACGAGTT
*
1876 TATTGTATATATTTATTTAAATG
1 TATTGTATATATTAATTTAAATG
*
1899 TATT-TATTTATTAATTTAAA
1 TATTGTATATATTAATTTAAA
1919 AATAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (23 bp):
TATTGTATATATTAATTTAAATG
Found at i:7991 original size:3 final size:3
Alignment explanation
Indices: 7985--8016 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
7975 ATCATCGTCG
*
7985 TCC TCC TCC TCC TCC TCC TCC TCC ACC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
8017 ATCATCGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.66, G:0.00, T:0.31
Consensus pattern (3 bp):
TCC
Found at i:8902 original size:78 final size:78
Alignment explanation
Indices: 8809--8993 Score: 361
Period size: 78 Copynumber: 2.4 Consensus size: 78
8799 CGTAAATTTG
*
8809 GAATTTATTCCCTATACTTTTATTTTTATCAACCTGTTAAAATATGCCATATAAGTTTTTGTACT
1 GAATTTAGTCCCTATACTTTTATTTTTATCAACCTGTTAAAATATGCCATATAAGTTTTTGTACT
8874 ATTCACAAATTCA
66 ATTCACAAATTCA
8887 GAATTTAGTCCCTATACTTTTATTTTTATCAACCTGTTAAAATATGCCATATAAGTTTTTGTACT
1 GAATTTAGTCCCTATACTTTTATTTTTATCAACCTGTTAAAATATGCCATATAAGTTTTTGTACT
8952 ATTCACAAATTCA
66 ATTCACAAATTCA
8965 GAATTTAGTCCCTATACTTTTATTTTTAT
1 GAATTTAGTCCCTATACTTTTATTTTTAT
8994 GAATTTAATC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 106 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (78 bp):
GAATTTAGTCCCTATACTTTTATTTTTATCAACCTGTTAAAATATGCCATATAAGTTTTTGTACT
ATTCACAAATTCA
Found at i:12580 original size:31 final size:30
Alignment explanation
Indices: 12521--12601 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 30
12511 AATGTGTATG
*
12521 ATTAAATCAAAATTAAGAA-TTTAAGTATA-A
1 ATTAAA-CCAAATT-AGAATTTTAAGTATATA
*
12551 ATTTAAACCACAATTAGAATTTTACGTATATA
1 A-TTAAACCA-AATTAGAATTTTAAGTATATA
* *
12583 ATTATACCAAATTAAAATT
1 ATTAAACCAAATTAGAATT
12602 CATATACACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 16 0.37
31 25 0.58
32 2 0.05
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (30 bp):
ATTAAACCAAATTAGAATTTTAAGTATATA
Found at i:17091 original size:18 final size:20
Alignment explanation
Indices: 17055--17091 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
17045 AAAGAATGAA
*
17055 TAAACTATATATAATTTTAT
1 TAAACTATATATAAATTTAT
17075 TAAACTA-A-ATAAATTTA
1 TAAACTATATATAAATTTA
17092 CGTTTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAACTATATATAAATTTAT
Found at i:18107 original size:15 final size:17
Alignment explanation
Indices: 18078--18109 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
18068 ATTTGTCAAA
18078 TAATATTTTAGATTTTT
1 TAATATTTTAGATTTTT
18095 TAAT-TTTTA-ATTTTT
1 TAATATTTTAGATTTTT
18110 CGATAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TAATATTTTAGATTTTT
Found at i:19754 original size:17 final size:17
Alignment explanation
Indices: 19732--19794 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
19722 GGCCCAACAG
19732 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
19749 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** *
19766 ATTTAAATCCATTTGAA
1 ATTTAAATTTATTTTAA
19783 ATTTAAATTTAT
1 ATTTAAATTTAT
19795 CATAAATATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:19770 original size:34 final size:34
Alignment explanation
Indices: 19732--19811 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
19722 GGCCCAACAG
* *
19732 ATTTAAATTTATTTTAAATTTAAGTTTAT-ATTAA
1 ATTTAAATTTATTTGAAATTTAAATTTATCA-TAA
**
19766 ATTTAAATCCATTTGAAATTTAAATTTATCATAA
1 ATTTAAATTTATTTGAAATTTAAATTTATCATAA
*
19800 ATATTAAGTTTA
1 AT-TTAAATTTA
19812 AATTTATTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
34 30 0.81
35 7 0.19
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (34 bp):
ATTTAAATTTATTTGAAATTTAAATTTATCATAA
Found at i:19801 original size:17 final size:16
Alignment explanation
Indices: 19732--19811 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 16
19722 GGCCCAACAG
*
19732 ATTTAAATTTATTTTAA
1 ATTTAAATTTA-TATAA
*
19749 ATTTAAGTTTATATTAA
1 ATTTAAATTTATA-TAA
** *
19766 ATTTAAATCCATTTGAA
1 ATTTAAATTTATAT-AA
19783 ATTTAAATTTATCATAA
1 ATTTAAATTTAT-ATAA
*
19800 ATATTAAGTTTA
1 AT-TTAAATTTA
19812 AATTTATTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
16 2 0.04
17 38 0.78
18 9 0.18
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTTAAATTTATATAA
Found at i:21815 original size:58 final size:58
Alignment explanation
Indices: 21633--21907 Score: 317
Period size: 58 Copynumber: 4.7 Consensus size: 58
21623 AAAATTATAT
* * *
21633 TTTTACCCTTGAACTTTCCAAAATTCCATTTTAAACCCCGATTTCTCCAAAAAATTACCA
1 TTTTACCCTCGAACTTTCAAAAATTCCATTTT-GACCCCGATTTCTCC-AAAAATTACCA
* * * * *
21693 TTTTACCC-CTAAACTTCCAAAAATTCCATTTTCACCTC-ATTT-TCCCAAAATTACCA
1 TTTTACCCTC-GAACTTTCAAAAATTCCATTTTGACCCCGATTTCTCCAAAAATTACCA
* * *
21749 TTTTACCCTCGAACTTTCAAAAATTCTATATTGACCTCGATTTCTCCAAAAATTACCA
1 TTTTACCCTCGAACTTTCAAAAATTCCATTTTGACCCCGATTTCTCCAAAAATTACCA
* *
21807 TTTTACCCTCGAAC-TTCTAAAAATTCCATTTTGATCCCGATTTTTCCAAAAATTACCA
1 TTTTACCCTCGAACTTTC-AAAAATTCCATTTTGACCCCGATTTCTCCAAAAATTACCA
* * * *
21865 CTTTACCAT-AAACTTTCAAAAATTCAATTTTTGACCCCGATTT
1 TTTTACCCTCGAACTTTCAAAAATTCCA-TTTTGACCCCGATTT
21908 TTTTTTTTCC
Statistics
Matches: 185, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
56 41 0.22
57 23 0.12
58 90 0.49
59 4 0.02
60 27 0.15
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
TTTTACCCTCGAACTTTCAAAAATTCCATTTTGACCCCGATTTCTCCAAAAATTACCA
Found at i:21857 original size:29 final size:29
Alignment explanation
Indices: 21589--21871 Score: 151
Period size: 29 Copynumber: 9.8 Consensus size: 29
21579 CCCTTAAACA
* *
21589 TTTCC-AAAATTCCATTTTTAACCTCGAACT
1 TTTCCAAAAATTCCA-TTTTACCCTCG-ATT
** * **
21619 TTT--AAAAATTATATTTTTACCCTTGAAC
1 TTTCCAAAAATTCCA-TTTTACCCTCGATT
21647 TTTCC-AAAATTCCATTTTAAACCC-CGATT
1 TTTCCAAAAATTCCATTTT--ACCCTCGATT
* * **
21676 TCTCCAAAAAATTACCATTTTACCC-CTAAA
1 TTTCC-AAAAATT-CCATTTTACCCTCGATT
*
21706 CTTCCAAAAATTCCATTTT-CACCTC-A-T
1 TTTCCAAAAATTCCATTTTAC-CCTCGATT
* **
21733 TTTCCCAAAATTACCATTTTACCCTCGAAC
1 TTTCCAAAAATT-CCATTTTACCCTCGATT
* *
21763 TTT-CAAAAATTCTATATTGA-CCTCGATT
1 TTTCCAAAAATTCCAT-TTTACCCTCGATT
* *
21791 TCTCCAAAAATTACCATTTTACCCTCGA-A
1 TTTCCAAAAATT-CCATTTTACCCTCGATT
* * *
21820 CTTCTAAAAATTCCATTTTGATCC-CGATT
1 TTTCCAAAAATTCCATTTT-ACCCTCGATT
*
21849 TTTCCAAAAATTACCACTTTACC
1 TTTCCAAAAATT-CCATTTTACC
21872 ATAAACTTTC
Statistics
Matches: 193, Mismatches: 39, Indels: 43
0.70 0.14 0.16
Matches are distributed among these distances:
27 11 0.06
28 50 0.26
29 85 0.44
30 34 0.18
31 6 0.03
32 7 0.04
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTCCAAAAATTCCATTTTACCCTCGATT
Found at i:21908 original size:58 final size:58
Alignment explanation
Indices: 21572--21909 Score: 305
Period size: 58 Copynumber: 5.8 Consensus size: 58
21562 CCAAAATCAT
* * * * * *
21572 ATTTTGACCCTTAAACATTTCCAAAATTCCATTTTTAACCTCGAACTTTT--AAAAATTA-T
1 ATTTT-ACCCTCAAAC-TTTCAAAAATTCCA-TTTTGACCCCG-ATTTTTCCAAAAATTACC
** * * *
21631 ATTTTTACCCTTGAACTTTCCAAAATTCCATTTTAAACCCCGATTTCTCCAAAAAATTACC
1 A-TTTTACCCTCAAACTTTCAAAAATTCCATTTT-GACCCCGATTTTTCC-AAAAATTACC
* * * *
21692 ATTTTACCC-CTAAACTTCCAAAAATTCCATTTTCACCTC-A-TTTTCCCAAAATTACC
1 ATTTTACCCTC-AAACTTTCAAAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACC
* * * * *
21748 ATTTTACCCTCGAACTTTCAAAAATTCTATATTGACCTCGATTTCTCCAAAAATTACC
1 ATTTTACCCTCAAACTTTCAAAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACC
* *
21806 ATTTTACCCTCGAAC-TTCTAAAAATTCCATTTTGATCCCGATTTTTCCAAAAATTACC
1 ATTTTACCCTCAAACTTTC-AAAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACC
* * *
21864 ACTTTACCAT-AAACTTTCAAAAATTCAATTTTTGACCCCGATTTTT
1 ATTTTACCCTCAAACTTTCAAAAATTCCA-TTTTGACCCCGATTTTT
21910 TTTTTTCCAA
Statistics
Matches: 236, Mismatches: 30, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
56 41 0.17
57 30 0.13
58 111 0.47
59 14 0.06
60 39 0.17
61 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
ATTTTACCCTCAAACTTTCAAAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACC
Found at i:32378 original size:49 final size:50
Alignment explanation
Indices: 32325--32952 Score: 527
Period size: 49 Copynumber: 12.7 Consensus size: 50
32315 AAAGATATGG
* * * * *
32325 AGGGAAAGGTTTAAGTCGCAACGGTGAA-CTTTGTACCTCAG-AGACATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCTCAGAAGACATAA
* * * *
32374 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACA-AAGACACAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* * * * * *
32423 AGGGAAAGATTTAAGGCGCAACAGAGAATCCAGTACCAC-GAAGACATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* *
32472 AGGGAAAGATTTAAGCCGCAAACGGTGAATCCT-GTACCTC-GAAGACACAAA
1 AGGGAAAGATTTAAGCCGC-AACGGCGAAT-CTAGTACCTCAGAAGACA-TAA
* * ** * * *
32523 AGGGAAAGGTTTAAGTCGCAACAACGAACCTTA-TATCTCAGAAGACACAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCTCAGAAGACATAA
* * * *
32573 AGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACC-CCGAAGACATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* * *
32622 AGGGAAAGATTTAAGCCGCAACGACGAATCTTGTACCTC-GAAGACACAAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACA-TAA
* * * * * * *
32672 AGAGAAAGGTTTAAGTCGTAATGGTGAATCTAGTACCTTAG-AGACATAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* * * *
32721 AGAGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACA-AAGACAT-A
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* * * * *
32769 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG-AGACATGA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
* * * * *
32818 AGGGAAAGATTTAAGCCACAACGGCGAATCCACTACCGC-GAAGACACAAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACA-TAA
* * * * *
32868 AGGGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGAA-TCATGAA
1 AGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCTCAGAAGACAT-AA
*
32918 A-GGAAA-ATTTAAGCCGCAACGGCGAATTTAGTACC
1 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACC
32953 ATGCGAGTTG
Statistics
Matches: 461, Mismatches: 96, Indels: 45
0.77 0.16 0.07
Matches are distributed among these distances:
47 2 0.00
48 61 0.13
49 231 0.50
50 136 0.30
51 31 0.07
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (50 bp):
AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCTCAGAAGACATAA
Found at i:32666 original size:199 final size:197
Alignment explanation
Indices: 32325--32888 Score: 608
Period size: 199 Copynumber: 2.9 Consensus size: 197
32315 AAAGATATGG
* * *
32325 AGGGAAAGGTTTAAGTCGCAACGGTGAACTTTGTACCTCAG-AGACATGAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTATACCTCAGAAGACA-AAAGGGAAAGATTTAAG
* ** *
32389 CCGCAACGGCGAATCCAATACCACAAAGACACAAAGGGAAAGATTTAAGGCGCAACAGA-GAATC
65 CCGCAACGGCGAATCCAGTACCAC-AAGACATGAAGGGAAAGATTTAAGCCGCAAC-GACGAATC
** * *
32453 CAGTACCACGAAGACA-TGAAGGGAAAGATTTAAGCCGCAAACGGTGAATCCT-GTACCTCGA-A
128 CAGTACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGCAAACGGTGAAT-CTAGTACCT-GAGA
32515 GACACAAA
191 GACA-AAA
*** *
32523 AGGGAAAGGTTTAAGTCGCAACAACGAACCTTATATCTCAGAAGACACAAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTATACCTCAGAAGACA-AAAGGGAAAGATTTAAG
* * *
32588 CCGCAACGGTGAATCCAGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCT
65 CCGCAACGGCGAATCCAGTACCAC-AAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC
* * * * * *
32653 TGTACCTCGAAGACACAAAAGAGAAAGGTTTAAGTCG-TAATGGTGAATCTAGTACCTTAGAGAC
129 AGTACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGCAAACGGTGAATCTAGTACCTGAGAGAC
*
32717 ATAA
194 AAAA
* * * * * *
32721 AGAGAAAGATTTAAGCCGCAACGGTGAATCC--AGTACCACA-AAGACATAAGGGAAAGGTTTAA
1 AGGGAAAGGTTTAAGTCGCAACGGTGAA-CCTTA-TACCTCAGAAGACAAAAGGGAAAGATTTAA
* * * * *
32783 GTCGCAATGGCGAA-CCTAGTACCTCAGAGACATGAAGGGAAAGATTTAAGCCACAACGGCGAAT
64 GCCGCAACGGCGAATCC-AGTACCACA-AGACATGAAGGGAAAGATTTAAGCCGCAACGACGAAT
* *
32847 CCACTACCGCGAAGACACAAAAGGGAAAGGTTTAAGTCGCAA
127 CCAGTACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGCAA
32889 TGGCGAACCT
Statistics
Matches: 307, Mismatches: 49, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
195 3 0.01
196 101 0.33
197 8 0.03
198 69 0.22
199 110 0.36
200 16 0.05
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (197 bp):
AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTATACCTCAGAAGACAAAAGGGAAAGATTTAAGC
CGCAACGGCGAATCCAGTACCACAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAG
TACCACGAAGACACAAAAGGGAAAGGTTTAAGTCGCAAACGGTGAATCTAGTACCTGAGAGACAA
AA
Found at i:32679 original size:99 final size:99
Alignment explanation
Indices: 32307--32952 Score: 467
Period size: 99 Copynumber: 6.6 Consensus size: 99
32297 TACAGGTCTG
* * * * * * *
32307 AGTACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAA-CTTTGTACCTC-AGAGAC
1 AGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TTGTACCTCGA-AGAC
**
32370 A-TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
64 ACAAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * ** * * * ** *
32405 AATACCACAAAGACACAAAGGGAAAGATTTAAGGCGCAACAGAGAATCCAGTACCACGAAGACA-
1 AGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTCGAAGACAC
** *
32469 TGAAGGGAAAGATTTAAGCCGCAAACGGTGAATCC
66 AAAAGGGAAAGATTTAAGCCGC-AACGGCGAATCC
* * ** * * ** * * *
32504 TGTACCTCGAAGACACAAAAGGGAAAGGTTTAAGTCGCAACAACGAACCTTATATCTCAGAAGAC
1 AGTACCCCGAAGACA-TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTC-GAAGAC
*
32569 AC-AAAGGGAAAGATTTAAGCCGCAACGGTGAATCC
64 ACAAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
*
32604 AGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTTGTACCTCGAAGACAC
1 AGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTCGAAGACAC
* * * * * * *
32669 AAAAGAGAAAGGTTTAAGTCGTAATGGTGAATCT
66 AAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
** * * * ** * *
32703 AGTA-CCTTAGAGACATAAAGAGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCAC-AA-AGA
1 AGTACCCCGA-AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTCGAAGACA
* * * *
32765 CATAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CC
65 CAAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * *** *
32799 TAGTACCTC-AGAGACATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCACTACCGCGAAGAC
1 -AGTACCCCGA-AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTCGAAGAC
* * *
32863 ACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CC
64 ACAAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * *
32898 TTA-TACCTCAGAA-TCATGAAAGGAAA-ATTTAAGCCGCAACGGCGAAT-TTAGTACC
1 --AGTACC-CCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTT-GTACC
32953 ATGCGAGTTG
Statistics
Matches: 454, Mismatches: 78, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
96 1 0.00
97 77 0.17
98 110 0.24
99 179 0.39
100 59 0.13
101 28 0.06
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (99 bp):
AGTACCCCGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTTGTACCTCGAAGACAC
AAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
Found at i:33372 original size:17 final size:17
Alignment explanation
Indices: 33350--33440 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 17
33340 AGCCCAACAG
33350 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
*
33367 ATTTAAGTTTA---T--
1 ATTTAAATTTATTTTAA
33379 A-TTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
** **
33395 ATTTAAATCCATTTGGA
1 ATTTAAATTTATTTTAA
*
33412 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
*
33429 ATATTAAGTTTA
1 AT-TTAAATTTA
33441 AATTTATTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
11 8 0.15
12 1 0.02
14 2 0.04
16 1 0.02
17 35 0.64
18 8 0.15
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:33416 original size:28 final size:28
Alignment explanation
Indices: 33352--33406 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
33342 CCCAACAGAT
* **
33352 TTAAATTTATTTTAAATTTAAGTTTATA
1 TTAAATTTATTTTAAATTTAAATCCATA
33380 TTAAATTTATTTTAAATTTAAATCCAT
1 TTAAATTTATTTTAAATTTAAATCCAT
33407 TTGGAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
TTAAATTTATTTTAAATTTAAATCCATA
Found at i:34070 original size:29 final size:29
Alignment explanation
Indices: 34017--34464 Score: 301
Period size: 29 Copynumber: 15.2 Consensus size: 29
34007 GTAATTTTGG
* *
34017 GGAAGTTCAAGGATAAAAGATGAAATTTTT
1 GGAAGTTCGAGGGTAAAA-ATGAAATTTTT
*
34047 AGACA-TTCGAGGGTAAAAATGAAA-TTTT
1 GGA-AGTTCGAGGGTAAAAATGAAATTTTT
* * *
34075 -GCAGTTTCGA-GATCGAAAAT-ATAATTTTT
1 GGAAG-TTCGAGGGT-AAAAATGA-AATTTTT
* *
34104 GGACA--TCAGATGG-CAAAATGATAATTTTT
1 GGA-AGTTC-GAGGGTAAAAATGA-AATTTTT
* **
34133 GAAAGTTTCG-GGGTAAAAAATGTGATTTTT
1 GGAAG-TTCGAGGGT-AAAAATGAAATTTTT
*
34163 GGAAGTTCGAGGGTCAAAATGAAATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTT
* *
34192 GGAAGTTCAAGGGTAAAAATGAGATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTT
** * *
34221 GGAAGTTTTAGGGTCGAAAATGGAATTTTT
1 GGAAGTTCGAGGGT-AAAAATGAAATTTTT
*
34251 GGAAGTTCGAGGGTAAAAATAAAATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTT
** ** *
34280 GGAAGTTTTAGGGTAAAGTTGGAATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTT
* * * *
34309 AGAAGTTCGTGGGATAAAAATGGATTTTTT
1 GGAAGTTCGAGGG-TAAAAATGAAATTTTT
* *
34339 GGAAGTTTTG-GGGTCAAAAATGGAA-TTTT
1 GGAAG-TTCGAGGGT-AAAAATGAAATTTTT
*
34368 AGAAGTTCGAGGGGGTAAAAATG-AATTTTT
1 GGAAGTTCGA--GGGTAAAAATGAAATTTTT
* * * *
34398 GGAAATTTC-AAGGTCGAAAATGGAATTTTT
1 GG-AAGTTCGAGGGT-AAAAATGAAATTTTT
* *
34428 GGAAGTTCGGGGGTAAAAATGTAATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTT
34457 GGATAGTT
1 GGA-AGTT
34465 TAGGGACCCT
Statistics
Matches: 330, Mismatches: 58, Indels: 60
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 30 0.09
29 161 0.49
30 112 0.34
31 22 0.07
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
GGAAGTTCGAGGGTAAAAATGAAATTTTT
Found at i:34161 original size:59 final size:57
Alignment explanation
Indices: 34117--34459 Score: 209
Period size: 59 Copynumber: 5.8 Consensus size: 57
34107 CATCAGATGG
* *
34117 CAAAATGATAATTTTTGAAAGTTTC-GGGGTAAAAAATGTGATTTTTGGAAGTTCGAGGGT
1 CAAAATGA-AATTTTTGAAAG-TTCAAGGGT-AAAAATGAGATTTTTGGAAG-TCGAGGGT
* **
34177 CAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATGAGATTTTTGGAAGTTTTAGGGT
1 CAAAATGAAATTTTTGAAAGTTCAAGGGTAAAAATGAGATTTTTGGAAG-TCGAGGGT
* * * * * **
34235 CGAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGT
1 C-AAAATGAAATTTTTGAAAGTTCAAGGGTAAAAATGAGATTTTTGGAAG-TCGAGGGT
* * ** *
34294 -AAAGTTGGAATTTTT-AGAAGTTCGTGGGATAAAAATG-GATTTTTTGGAAGTTTTG-GGGT
1 CAAA-ATGAAATTTTTGA-AAGTTCAAGGG-TAAAAATGAGA-TTTTTGGAAG--TCGAGGGT
* * * * *
34353 CAAAAATGGAATTTTAG-AAGTTCGAGGGGGTAAAAATGA-ATTTTTGGAAATTTC-AAGGT
1 C-AAAATGAAATTTTTGAAAGTTC-A-AGGGTAAAAATGAGATTTTTGG-AA-GTCGAGGGT
* * **
34412 CGAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTA-ATTTTTGGA
1 C-AAAATGAAATTTTTGAAAGTTCAAGGGTAAAAATG-AGATTTTTGGA
34460 TAGTTTAGGG
Statistics
Matches: 240, Mismatches: 25, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
57 3 0.01
58 64 0.27
59 130 0.54
60 37 0.15
61 6 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (57 bp):
CAAAATGAAATTTTTGAAAGTTCAAGGGTAAAAATGAGATTTTTGGAAGTCGAGGGT
Found at i:34219 original size:88 final size:88
Alignment explanation
Indices: 34118--34464 Score: 316
Period size: 88 Copynumber: 3.9 Consensus size: 88
34108 ATCAGATGGC
* * *
34118 AAAATGATAATTTTTGAAAGTTTCGGGGTAAAAAATGTG-ATTTTTGGAAGTTCGAGGGTCAAAA
1 AAAATGA-GATTTTTGAAAGTTTCAGGGTAAAAAATG-GAATTTTTGGAAGTTCGAGGGTAAAAA
34182 TGAAATTTTTGGAAGTTCAAGGGTA
64 TGAAATTTTTGGAAGTTCAAGGGTA
* * ** *
34207 AAAATGAGATTTTTGGAAGTTTTAGGGTCGAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATA
1 AAAATGAGATTTTTGAAAGTTTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATG
**
34272 AAATTTTTGGAAGTTTTAGGGTA
66 AAATTTTTGGAAGTTCAAGGGTA
** * * *
34295 AAGTTG-GAATTTTT-AGAAG-TTC-GTGGGATAAAAATGGATTTTTTGGAAGTTTTG-GGGTCA
1 AAAATGAG-ATTTTTGA-AAGTTTCAG-GGTA-AAAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* * *
34355 AAAATGGAA-TTTTAGAAGTTCGAGGGGGTA
60 AAAATGAAATTTTTGGAAGTTC-A-AGGGTA
* ** *
34385 AAAATGA-ATTTTTGGAAA-TTTCAAGGTCGAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAAT
1 AAAATGAGATTTTT-GAAAGTTTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAT
*
34448 GTAATTTTTGGATAGTT
65 GAAATTTTTGGA-AGTT
34465 TAGGGACCCT
Statistics
Matches: 206, Mismatches: 35, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
86 1 0.00
87 6 0.03
88 126 0.61
89 52 0.25
90 20 0.10
91 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (88 bp):
AAAATGAGATTTTTGAAAGTTTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATG
AAATTTTTGGAAGTTCAAGGGTA
Found at i:35584 original size:27 final size:27
Alignment explanation
Indices: 35472--35594 Score: 115
Period size: 27 Copynumber: 4.5 Consensus size: 27
35462 ATAATAATAA
35472 TATTATTATTATTATCATTAAAACAGT
1 TATTATTATTATTATCATTAAAACAGT
* * * *
35499 TATTATTATTAATGATTATTAAAAAACT
1 TATTATTATT-ATTATCATTAAAACAGT
* * * *
35527 GT-TTATTATTAATGTCATTAATAATA-A
1 -TATTATTATTATTATCATTAA-AACAGT
*
35554 TATTATTATTATTATTATTAAAACAGT
1 TATTATTATTATTATCATTAAAACAGT
*
35581 TATTAATATTATTA
1 TATTATTATTATTA
35595 ATGGGATTAT
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
26 4 0.05
27 46 0.61
28 24 0.32
29 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (27 bp):
TATTATTATTATTATCATTAAAACAGT
Found at i:37149 original size:6 final size:6
Alignment explanation
Indices: 37117--37196 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
37107 CCCAATCAGC
* * * ** *
37117 TTAAAT TT-ATT TTAAAA TTAAGTT TTAAAT TTAAAT TT-GGT TGAAAT
1 TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT
37164 TTAAAT TT--AT TATAAAT TTAAAT TTAAAAT TTA
1 TTAAAT TTAAAT T-TAAAT TTAAAT TT-AAAT TTA
37197 TTTTAAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
4 3 0.05
5 7 0.13
6 32 0.58
7 13 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:37199 original size:17 final size:16
Alignment explanation
Indices: 37140--37189 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
37130 AAAATTAAGT
*
37140 TTTAAATTTAAATTTGG
1 TTTAAATTTAAATTT-A
*
37157 TTGAAATTTAAATTTA
1 TTTAAATTTAAATTTA
37173 TTATAAATTTAAATTTA
1 TT-TAAATTTAAATTTA
37190 AAATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.07
17 27 0.93
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:37883 original size:30 final size:31
Alignment explanation
Indices: 37847--37906 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
37837 TAAATGAGAT
* * *
37847 TTATTATTATTTAA-AATATTATTAAAAACA
1 TTATTATTAATTAATAATAATAATAAAAACA
37877 TTATTATTAATTAATAATAATAATAAAAAC
1 TTATTATTAATTAATAATAATAATAAAAAC
37907 GAAGAGTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (31 bp):
TTATTATTAATTAATAATAATAATAAAAACA
Done.