Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015340.1 Kokia drynarioides strain JFW-HI SEQ_130387, 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: 66875
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Warning! 228 characters in sequence are not A, C, G, or T
Found at i:7763 original size:18 final size:16
Alignment explanation
Indices: 7718--7760 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
7708 ACATCAATTT
7718 TAATATAAATATTCAA
1 TAATATAAATATTCAA
*
7734 TACATTTAAATATTTCAA
1 TA-ATATAAATA-TTCAA
7752 TAATATAAA
1 TAATATAAA
7761 ATAGTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATAAATATTCAA
Found at i:13015 original size:19 final size:18
Alignment explanation
Indices: 12975--13016 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12965 TTCTGGGACT
12975 AAAAACACAAAAAAAAAA
1 AAAAACACAAAAAAAAAA
*
12993 AAAAA-ACAAACAAACAAAG
1 AAAAACACAAA-AAA-AAAA
13012 AAAAA
1 AAAAA
13017 GCCCAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAACACAAAAAAAAAA
Found at i:14575 original size:9 final size:9
Alignment explanation
Indices: 14563--14587 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14553 AAAAATTTAA
14563 AAAAAAAAG
1 AAAAAAAAG
14572 AAAAAAAAG
1 AAAAAAAAG
14581 AAAAAAA
1 AAAAAAA
14588 CTGAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:14618 original size:23 final size:22
Alignment explanation
Indices: 14561--14614 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
14551 ATAAAAATTT
* *
14561 AAAAAA-AAAAGAAAAAAAAGA
1 AAAAAACAAAATATAAAAAAGA
**
14582 AAAAAACTGAATATAAAAAAGA
1 AAAAAACAAAATATAAAAAAGA
*
14604 AAGAAACAAAA
1 AAAAAACAAAA
14615 ATATCGATGA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.81, C:0.04, G:0.09, T:0.06
Consensus pattern (22 bp):
AAAAAACAAAATATAAAAAAGA
Found at i:17523 original size:2 final size:2
Alignment explanation
Indices: 17516--17546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17506 ATTTTAAAAT
17516 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 T
17547 TTGTAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20134 original size:21 final size:22
Alignment explanation
Indices: 20110--20152 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20100 GAAAATTAAT
20110 TAAAT-TTAATTA-TAAAATATA
1 TAAATATT-ATTATTAAAATATA
20131 TAAATATTATTATTAAAATATA
1 TAAATATTATTATTAAAATATA
20153 ACATAGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATTATTATTAAAATATA
Found at i:21843 original size:10 final size:10
Alignment explanation
Indices: 21828--21859 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
21818 TTTTTTTAAA
21828 TTATATATAT
1 TTATATATAT
21838 TTATATATAT
1 TTATATATAT
*
21848 ATATATATAT
1 TTATATATAT
21858 TT
1 TT
21860 TTTGTAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATAT
Found at i:31031 original size:57 final size:57
Alignment explanation
Indices: 30951--31059 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
30941 AGGAACAAAG
30951 AATTTCATGAATTACATGTTGATTAAGGAATCAAATCAAATGAATGAATGAACATAT
1 AATTTCATGAATTACATGTTGATTAAGGAATCAAATCAAATGAATGAATGAACATAT
* *
31008 AATTTCATGAATTACTTGTTGATTAAGGAATCATATCAAATGAATGAATGAA
1 AATTTCATGAATTACATGTTGATTAAGGAATCAAATCAAATGAATGAATGAA
31060 AGAACCAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (57 bp):
AATTTCATGAATTACATGTTGATTAAGGAATCAAATCAAATGAATGAATGAACATAT
Found at i:33199 original size:23 final size:21
Alignment explanation
Indices: 33161--33205 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
33151 AAAGAATTTA
*
33161 TAAAATCATTAAATATTAAATT
1 TAAAATAATTAAATA-TAAATT
33183 TAAAATAATATAAATATAAATT
1 TAAAATAAT-TAAATATAAATT
33205 T
1 T
33206 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATAATTAAATATAAATT
Found at i:39341 original size:27 final size:27
Alignment explanation
Indices: 39309--39372 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
39299 AGGTCCAACA
*
39309 CCAGGAGCTCCAGGTGGGGGTGGAGGT
1 CCAGGAGCTCCAGGTGGAGGTGGAGGT
39336 CCAGGAGCTCCAGGTGGAGGTGGAGGT
1 CCAGGAGCTCCAGGTGGAGGTGGAGGT
*
39363 CCCGGAGCTC
1 CCAGGAGCTC
39373 GACCTCCAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.23, G:0.47, T:0.14
Consensus pattern (27 bp):
CCAGGAGCTCCAGGTGGAGGTGGAGGT
Found at i:40743 original size:50 final size:49
Alignment explanation
Indices: 40624--41196 Score: 367
Period size: 50 Copynumber: 11.7 Consensus size: 49
40614 ACCAAGGAAA
* * *
40624 CATGAAGATGTAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
40673 CATGAAG--GTGAAGGGAAAGGTTGAAGCCGTAATGGCGAACCCGATAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
40720 CTTGAAAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACTCGGTAC
1 CATG-AAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * * *
40770 CATGAAGA--TGAAGGAAAAGGTTG-AGATCGTAACGGTGAACCCGATAC
1 CATGAAGATGTGATGGGAAAGGTTGAAG-CCGCAACGGCGAACCCGGTAC
* * * * * * * * *
40817 CTTGGAAGATGTGATAGGAAAGGTTGAGGTCGTAATGTCGAACTCGATAC
1 CAT-GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * **
40867 CATGAAGA--TGAAGAGAAAGGTT-AAGGCCGTAACGGTGAACCCAATAC
1 CATGAAGATGTGATGGGAAAGGTTGAA-GCCGCAACGGCGAACCCGGTAC
* * * * * *
40914 CTTGGAAGACGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCTGTAC
1 CAT-GAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
** * * * *
40964 CATGAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACTCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * ** * * *
41013 CTTAGAAGATGCGATGGG-AAGGATTGAAGCCACAATAGCAAATCTGGTAC
1 CAT-GAAGATGTGATGGGAAAGG-TTGAAGCCGCAACGGCGAACCCGGTAC
* * * * *
41063 CATGAAGATATGAAGGGAAAGGTTG-AGTCGCAATGGTGAACCCGGTAC
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
* * * * ** * *
41111 CTTAGAAGATGTAATGGG-AAGGATTGAGGCCACAACGAAGAATCTGGTAC
1 CAT-GAAGATGTGATGGGAAAGG-TTGAAGCCGCAACGGCGAACCCGGTAC
* * * *
41161 CATGAAGATATGAAGGGAAAGGTTGAGGCCACAACG
1 CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACG
41197 AGAACCTTGT
Statistics
Matches: 408, Mismatches: 96, Indels: 40
0.75 0.18 0.07
Matches are distributed among these distances:
46 2 0.00
47 97 0.24
48 35 0.09
49 114 0.28
50 158 0.39
51 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (49 bp):
CATGAAGATGTGATGGGAAAGGTTGAAGCCGCAACGGCGAACCCGGTAC
Found at i:40801 original size:97 final size:98
Alignment explanation
Indices: 40628--41187 Score: 548
Period size: 97 Copynumber: 5.7 Consensus size: 98
40618 AGGAAACATG
* * * *
40628 AAGATGTAATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGAAG-GTGAAGGGAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
*
40692 GTTGA-AGCCGTAATGGCGAACCCGATACCTTGA
66 GTTGAGA-CCGTAATGGTGAACCCGATACCTTGA
* *
40725 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACTCGGTACCATGAAG-ATGAAGGAAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
* * *
40789 GTTGAGATCGTAACGGTGAACCCGATACCTTGG
66 GTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * * * * *
40822 AAGATGTGATAGGAAAGGTTGAGGTCGTAATGTCGAACTCGATACCATGAAG-ATGAAGAGAAAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
* * * * *
40886 GTTAAGGCCGTAACGGTGAACCCAATACCTTGG
66 GTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * * *
40919 AAGACGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCTGTACCATGAAGACATGAAGGGAAA
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGA-ATGAAGGGAAA
* * * * *
40984 GGTTGAGGCCGCAATGGCGAACTCGGTACCTT-A
65 GGTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * * ** *
41017 GAAGATGCGATGGG-AAGGATTGAAGCCACAATAGC-AAATCTGGTACCATGAAGATATGAAGGG
1 -AAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACTC-GGTACCATGAAGA-ATGAAGGG
* * *
41080 AAAGGTTGAG-TCGCAATGGTGAACCCGGTACCTT-A
62 AAAGGTTGAGACCGTAATGGTGAACCCGATACCTTGA
* * **
41115 GAAGATGTAATGGG-AAGGATTGAGGCCACAACGAAGAA-TCTGGTACCATGAAGATATGAAGGG
1 -AAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACTC-GGTACCATGAAGA-ATGAAGGG
41178 AAAGGTTGAG
62 AAAGGTTGAG
41188 GCCACAACGA
Statistics
Matches: 395, Mismatches: 61, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
97 214 0.54
98 93 0.24
99 88 0.22
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.18
Consensus pattern (98 bp):
AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGGTACCATGAAGAATGAAGGGAAAG
GTTGAGACCGTAATGGTGAACCCGATACCTTGA
Found at i:41209 original size:98 final size:98
Alignment explanation
Indices: 40960--41209 Score: 317
Period size: 98 Copynumber: 2.5 Consensus size: 98
40950 GGTGAACCCT
* * *
40960 GTACCATGAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGCGAA-CTCGGTACCTTAGAAGATG
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAA-GGAGAACCT-GGTACCTTAGAAGATG
* *
41024 CGATGGGAAGGATTGAAGCCACAATAGCAAATCTG
64 CAATGGGAAGGATTGAAGCCACAATAGAAAATCTG
* * * * *
41059 GTACCATGAAGATATGAAGGGAAAGGTTGAGTCGCA-ATGGTGAACCCGGTACCTTAGAAGATGT
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGC-CACAAGGAGAACCTGGTACCTTAGAAGATGC
* *
41123 AATGGGAAGGATTGAGGCCACAA-CGAAGAATCTG
65 AATGGGAAGGATTGAAGCCACAATAGAA-AATCTG
* *
41157 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAACGAGAACCTTGTACC
1 GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAAGGAGAACCTGGTACC
41210 CTAAAAATGA
Statistics
Matches: 130, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
97 4 0.03
98 92 0.71
99 33 0.25
100 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (98 bp):
GTACCATGAAGATATGAAGGGAAAGGTTGAGGCCACAAGGAGAACCTGGTACCTTAGAAGATGCA
ATGGGAAGGATTGAAGCCACAATAGAAAATCTG
Found at i:41539 original size:39 final size:39
Alignment explanation
Indices: 41397--41745 Score: 286
Period size: 38 Copynumber: 9.0 Consensus size: 39
41387 GACACCATTT
* *
41397 AATCTCTTACCCCGATCATGGAGCAGATTGAAGACAT-C
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* *
41435 AATCTTTTACC-CGATCATGGGACAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* * ** * * **
41472 AATCTTTTAACTTAATCA-GAAGGTAGATTGAAGACATGT
1 AATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCC
*
41511 AATCTCTTACCTTGATCATGGGGCAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
** * *
41549 AATCTCTTACCTTAATCA-GAAGGCAGATTGAAGACATGC
1 AATCTCTTACCTCGATCATG-GGGCAGATTGAAGACATCC
*
41588 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
* * * *
41626 AATCT-TATACC-CTAATTA-GTGGGCAAATTGAAGACACACC
1 AATCTCT-TACCTC-GATCATG-GGGCAGATTGAAGACA-TCC
* *
41666 AATCTCTTACCTCGATCATGGGGTAGATTAAAGACATCAATC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATC---C
* * * * *
41708 AATCTCTTACCCCAATTATAGGGAAGATTGAAGACATC
1 AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATC
41746 ATCCAATCTT
Statistics
Matches: 250, Mismatches: 42, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
36 3 0.01
37 35 0.14
38 84 0.34
39 63 0.25
40 29 0.12
41 3 0.01
42 33 0.13
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (39 bp):
AATCTCTTACCTCGATCATGGGGCAGATTGAAGACATCC
Found at i:41542 original size:77 final size:77
Alignment explanation
Indices: 41419--41707 Score: 377
Period size: 77 Copynumber: 3.8 Consensus size: 77
41409 CGATCATGGA
* * *
41419 GCAGATTGAAGACAT-CAATCTTTTACC-CGATCATGGGACAGATTGAAGCATCCAATCTTTTAA
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
41482 CTTAATCAGAAG
66 CTTAATCAGAAG
* * * *
41494 GTAGATTGAAGACATGTAATCTCTTACCTTGATCATGGGGCAGATTGAAGCATCCAATCTCTTAC
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
41559 CTTAATCAGAAG
66 CTTAATCAGAAG
* *
41571 GCAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTATAC
1 GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
* * **
41636 CCTAATTAGTGG
66 CTTAATCAGAAG
* ** * *
41648 GCAAATTGAAGACACACCAATCTCTTACCTCGATCATGGGGTAGATTAAAGACAT-CAATC
1 GCAGATTGAAGACA-TGCAATCTCTTACCTCGATCATGGGGCAGATTGAAG-CATCCAATC
41708 AATCTCTTAC
Statistics
Matches: 187, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
75 14 0.07
76 10 0.05
77 124 0.66
78 36 0.19
79 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (77 bp):
GCAGATTGAAGACATGCAATCTCTTACCTCGATCATGGGGCAGATTGAAGCATCCAATCTTTTAC
CTTAATCAGAAG
Found at i:41711 original size:42 final size:42
Alignment explanation
Indices: 41544--41754 Score: 115
Period size: 42 Copynumber: 5.2 Consensus size: 42
41534 CAGATTGAAG
** * * * *
41544 CATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAG--A-
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* * * * *
41583 CATGCAATCTCTTACCCCGATCATGGGGCAGATT---GA-AG
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* * *
41621 CATCCAATCT-TATACCCTAATTAGT-GGGCAA-ATTGAAGACA-
1 CATCCAATCTCT-TACCCCAATCA-TAGGG-AAGATTAAAGACAT
* * * *
41662 CA-CCAATCTCTTACCTCGATCATGGGGTAGATTAAAGACAT
1 CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
* *
41703 CAAT-CAATCTCTTACCCCAATTATAGGGAAGATTGAAGACAT
1 C-ATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
41745 CATCCAATCT
1 CATCCAATCT
41755 TATACCCTTA
Statistics
Matches: 132, Mismatches: 24, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 23 0.17
39 31 0.23
40 26 0.20
41 8 0.06
42 41 0.31
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
CATCCAATCTCTTACCCCAATCATAGGGAAGATTAAAGACAT
Found at i:41761 original size:42 final size:41
Alignment explanation
Indices: 41587--41754 Score: 129
Period size: 42 Copynumber: 4.1 Consensus size: 41
41577 TGAAGACATG
* * *
41587 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG----CATC
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATCATC
*
41625 CAATCT-TATACCCTAATTAGTGGGCAA-ATTGAAGACA-CA-C
1 CAATCTCT-TACCCCAATTA-TGGG-AAGATTGAAGACATCATC
* * * * *
41665 CAATCTCTTACCTCGATCATGGGGTAGATTAAAGACATCAAT-
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATC-ATC
41707 CAATCTCTTACCCCAATTATAGGGAAGATTGAAGACATCATC
1 CAATCTCTTACCCCAATTAT-GGGAAGATTGAAGACATCATC
41749 CAATCT
1 CAATCT
41755 TATACCCTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
37 1 0.01
38 24 0.24
39 4 0.04
40 26 0.26
41 6 0.06
42 40 0.40
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
CAATCTCTTACCCCAATTATGGGAAGATTGAAGACATCATC
Found at i:42580 original size:14 final size:13
Alignment explanation
Indices: 42534--42582 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
42524 AAAAACACAG
42534 AGACAAAAGCAAA
1 AGACAAAAGCAAA
* *
42547 AGATAAAGAGTAACA
1 AGACAAA-AGCAA-A
42562 AGACAAAAGCAAGA
1 AGACAAAAGCAA-A
42576 AGACAAA
1 AGACAAA
42583 TGTAATCGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.21
14 16 0.55
15 7 0.24
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.04
Consensus pattern (13 bp):
AGACAAAAGCAAA
Found at i:46941 original size:21 final size:21
Alignment explanation
Indices: 46898--46951 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
46888 GGAGTTTTTA
* * *
46898 GTATTGGTAGAAGCATGATTT
1 GTATCGGTAGAAGCATCACTT
* *
46919 GTTTCGGTAGAAGCTTCACTT
1 GTATCGGTAGAAGCATCACTT
*
46940 GTATCAGTAGAA
1 GTATCGGTAGAA
46952 CTGTTATAGG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACTT
Found at i:55952 original size:16 final size:16
Alignment explanation
Indices: 55923--55972 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
55913 ACCACTTAAC
55923 ATATATTTTAATATTT
1 ATATATTTTAATATTT
55939 ATATAGTTTT-ATA-TT
1 ATATA-TTTTAATATTT
55954 ATTATATATTTAA-ATTT
1 A-TATAT-TTTAATATTT
55971 AT
1 AT
55973 GTTATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 4 0.14
16 17 0.59
17 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATATATTTTAATATTT
Found at i:55994 original size:16 final size:15
Alignment explanation
Indices: 55955--55998 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
55945 TTTTATATTA
*
55955 TTAT-ATATTTAAAT
1 TTATGATATATAAAT
*
55969 TTATGTTATATAAAT
1 TTATGATATATAAAT
55984 TATATGATATATAAA
1 T-TATGATATATAAA
55999 AGTTTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
TTATGATATATAAAT
Found at i:56635 original size:11 final size:12
Alignment explanation
Indices: 56619--56649 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
56609 TAGAGATGGT
56619 GAAAAAAAAAA-
1 GAAAAAAAAAAG
56630 GAAAAAAAAAAG
1 GAAAAAAAAAAG
56642 GAAAAAAA
1 GAAAAAAA
56650 TTGCAGCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:56637 original size:12 final size:12
Alignment explanation
Indices: 56620--56649 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
56610 AGAGATGGTG
56620 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
56632 AAAAAAAAAGGA
1 AAAAAAAAAAGA
56644 AAAAAA
1 AAAAAA
56650 TTGCAGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:57614 original size:22 final size:22
Alignment explanation
Indices: 57586--57628 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57576 AAACAAAATT
57586 TATTTAAT-TGATTTATTTAATA
1 TATTTAATAT-ATTTATTTAATA
*
57608 TATTTAATATTTTTATTTAAT
1 TATTTAATATATTTATTTAAT
57629 TAATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTTAATATATTTATTTAATA
Found at i:64805 original size:11 final size:11
Alignment explanation
Indices: 64789--64814 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
64779 CATGCATGTT
64789 AAATTTAATAC
1 AAATTTAATAC
64800 AAATTTAATAC
1 AAATTTAATAC
64811 AAAT
1 AAAT
64815 GTAAAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTTAATAC
Done.