Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013871.1 Kokia drynarioides strain JFW-HI SEQ_128899, 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: 33744
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:482 original size:30 final size:30
Alignment explanation
Indices: 410--686 Score: 171
Period size: 29 Copynumber: 9.4 Consensus size: 30
400 GGAGGTCCCT
* *
410 AAACTGTCCAAAAATCCTA-TTTCTACCCCTG
1 AAACT-TCCAAAAATCCCACTTTCGACCCC-G
441 -AACTTCCAAAAATCCCACTTTCGACCCCG
1 AAACTTCCAAAAATCCCACTTTCGACCCCG
* * * * **
470 AAATTTCTAAAAAT-TCAGTTTTTACCCTCG
1 AAACTTCCAAAAATCCCACTTTCGACCC-CG
* *
500 -AACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACTTCCAAAAATCCCACTTTCGACCCCG
**
529 AAACTTCCAAAAATCCCA-TTTTTACCCTCG
1 AAACTTCCAAAAATCCCACTTTCGACCC-CG
* * *
559 -AACTTCCAAAAGTCCC-GTTTTGACCCCG
1 AAACTTCCAAAAATCCCACTTTCGACCCCG
* * *
587 AAACTTCCAAAAATTACCA-TTT-TACCCCA
1 AAACTTCCAAAAA-TCCCACTTTCGACCCCG
* * * ** *
616 AAACTTCCCAAAGTCCCATTTTTTACCTCG
1 AAACTTCCAAAAATCCCACTTTCGACCCCG
* * * *
646 AAACTTCAAAAAATTACCA-TTT-TACCCCC
1 AAACTTCCAAAAA-TCCCACTTTCGACCCCG
675 AAACTTCCAAAA
1 AAACTTCCAAAA
687 GTCTCATTTT
Statistics
Matches: 197, Mismatches: 36, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.03
29 110 0.56
30 77 0.39
31 4 0.02
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.28
Consensus pattern (30 bp):
AAACTTCCAAAAATCCCACTTTCGACCCCG
Found at i:511 original size:59 final size:59
Alignment explanation
Indices: 410--790 Score: 364
Period size: 59 Copynumber: 6.5 Consensus size: 59
400 GGAGGTCCCT
* * *
410 AAACTGTCCAAAAA-TCCTATTTCTACCC-CTGAACTTCCAAAAATCCCACTTTCGACCCCG
1 AAACT-TCCAAAAATTCC-ATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
470 AAATTTCTAAAAATT-CAGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
529 AAACTTCCAAAAATCCCATTTTTACCCTCGAACTTCCAAAAGTCCC-GTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
587 AAACTTCCAAAAATTACCA-TTTTACCC-CAAAACTTCCCAAAGTCCCATTTTTTACCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * * **
646 AAACTTCAAAAAATTACCA-TTTTACCCCCAAACTTCCAAAAGTCTCATTTTTAACCTTG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * *
705 AAACTTCTAAAAATTCCATTTTTAGCCTCGAACTTCCCAAAATTCCATTTTTGACTCTG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
764 AAACTTCCTAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATT-CCATTTTTACCC
791 CAAAAAGTCC
Statistics
Matches: 274, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.00
58 50 0.18
59 211 0.77
60 12 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:709 original size:30 final size:30
Alignment explanation
Indices: 441--777 Score: 180
Period size: 29 Copynumber: 11.4 Consensus size: 30
431 TCTACCCCTG
* * ** *
441 AACTTCCAAAAATCCCACTTTCGACCCCGA
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* * *
471 AATTTCTAAAAAT-TCAGTTTTTACCCTCG-
1 AACTTCCAAAAATCTCA-TTTTTAACCTCGA
* ** * *
500 AACTTCCAAAAATCCCATTTTCGACCCCAA
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* *
530 AACTTCCAAAAATCCCATTTTTACCCTCG-
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* ** * *
559 AACTTCCAAAAGTC-CCGTTTTGACCCCGA
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* *
588 AACTTCCAAAAAT-TACCA-TTTT-ACCCCAA
1 AACTTCCAAAAATCT--CATTTTTAACCTCGA
* * * *
617 AACTTCCCAAAGTCCCATTTTTTACCTCGA
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* * *
647 AACTTCAAAAAAT-TACCA-TTTT-ACCCCCA
1 AACTTCCAAAAATCT--CATTTTTAACCTCGA
* *
676 AACTTCCAAAAGTCTCATTTTTAACCTTGA
1 AACTTCCAAAAATCTCATTTTTAACCTCGA
* *
706 AACTTCTAAAAAT-TCCATTTTTAGCCTCG-
1 AACTTCCAAAAATCT-CATTTTTAACCTCGA
* *
735 AACTTCCCAAAAT-TCCATTTTTGA-CTCTGA
1 AACTTCCAAAAATCT-CATTTTTAACCTC-GA
*
765 AACTTCCTAAAAT
1 AACTTCCAAAAAT
778 TACCATTTTA
Statistics
Matches: 234, Mismatches: 55, Indels: 36
0.72 0.17 0.11
Matches are distributed among these distances:
28 16 0.07
29 108 0.46
30 107 0.46
31 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATCTCATTTTTAACCTCGA
Found at i:778 original size:30 final size:30
Alignment explanation
Indices: 410--786 Score: 264
Period size: 30 Copynumber: 12.7 Consensus size: 30
400 GGAGGTCCCT
*
410 AAACTGTCCAAAAA-TCCTATTTCT-ACCCCTG
1 AAACT-TCCAAAAATTCC-ATTTTTGACCCC-G
* * *
441 -AACTTCCAAAAATCCCACTTTCGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
470 AAATTTCTAAAAATT-CAGTTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCA-TTTTTGACCC-CG
* * *
500 -AACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
529 AAACTTCCAAAAATCCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* **
559 -AACTTCC-AAAAGTCCCGTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
587 AAACTTCCAAAAATTACCA-TTTT-ACCCCA
1 AAACTTCCAAAAATT-CCATTTTTGACCCCG
* * * * *
616 AAACTTCCCAAAGTCCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
646 AAACTTCAAAAAATTACCA-TTTT-ACCCCC
1 AAACTTCCAAAAATT-CCATTTTTGACCCCG
* * **
675 AAACTTCC-AAAAGTCTCATTTTTAACCTTG
1 AAACTTCCAAAAATTC-CATTTTTGACCCCG
* *
705 AAACTTCTAAAAATTCCATTTTT-AGCCTCG
1 AAACTTCCAAAAATTCCATTTTTGA-CCCCG
* * *
735 -AACTTCCCAAAATTCCATTTTTGACTCTG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
764 AAACTTCCTAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
787 ACCCCAAAAA
Statistics
Matches: 274, Mismatches: 48, Indels: 48
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.00
28 22 0.08
29 115 0.42
30 118 0.43
31 18 0.07
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.31
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:856 original size:29 final size:29
Alignment explanation
Indices: 821--885 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
811 TCAAATTTTC
821 CCAAAATTATC-GTTTTGCCCCCTGAGAAT
1 CCAAAATTATCAGTTTTGCCCCC-GAGAAT
*
850 CCAAAATTATCATTTTTGCCCCCGAGAAT
1 CCAAAATTATCAGTTTTGCCCCCGAGAAT
879 CCGAAAA
1 CC-AAAA
886 GTCTCATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (29 bp):
CCAAAATTATCAGTTTTGCCCCCGAGAAT
Found at i:869 original size:30 final size:29
Alignment explanation
Indices: 821--895 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
811 TCAAATTTTC
*
821 CCAAAATTATC-GTTTTGCCCCCTGAGAAT
1 CCAAAATTATCATTTTTGCCCCC-GAGAAT
850 CCAAAATTATCATTTTTGCCCCCGAGAAT
1 CCAAAATTATCATTTTTGCCCCCGAGAAT
* *
879 CCGAAAAGTCTCATTTT
1 CC-AAAATTATCATTTT
896 GAACTCCGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (29 bp):
CCAAAATTATCATTTTTGCCCCCGAGAAT
Found at i:1239 original size:96 final size:96
Alignment explanation
Indices: 1101--1292 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 96
1091 AAAACTTTAA
* * *
1101 AATCGAGGCAATATTCTTTCATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCAA-T
1 AATCGAGGCAATATTCCTTCATTTCGAGTTCCGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
*
1165 TTCTCTTCAAATCGAAATAATCGAATACCCTT
66 TT-TCTTCAAATCGAAATAATCAAATACCCTT
* *
1197 AATCGAGGCAATGTTTCCTT-ATCTTCGA-TTCCG-AAATATTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAAT-ATTCCTTCAT-TTCGAGTTCCGAAAAT-TTGCGCCTTAACTCACTAGGTGCA
* *
1259 ACCTTTCTTCAAATCGAGATAATCAAATATCCTT
63 ACCTTTCTTCAAATCGAAATAATCAAATACCCTT
1293 TTCGTAAAGA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 4 0.05
96 68 0.81
97 12 0.14
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (96 bp):
AATCGAGGCAATATTCCTTCATTTCGAGTTCCGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCAAATACCCTT
Found at i:1855 original size:22 final size:22
Alignment explanation
Indices: 1827--1869 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1817 GCAACAGTAG
1827 GCACACAAAGTGCTAAACAGAA
1 GCACACAAAGTGCTAAACAGAA
* *
1849 GCACACACAGTGCTGAACAGA
1 GCACACAAAGTGCTAAACAGA
1870 GGGCACGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.09
Consensus pattern (22 bp):
GCACACAAAGTGCTAAACAGAA
Found at i:5133 original size:22 final size:23
Alignment explanation
Indices: 5086--5136 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
5076 CTTTATTTGA
5086 TAAAATATTTTGATATAATAAAT
1 TAAAATATTTTGATATAATAAAT
*
5109 TAAAATATTTTTGA-AT-ATAAGT
1 TAAAATA-TTTTGATATAATAAAT
5131 TAAAAT
1 TAAAAT
5137 TGACAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.42
23 9 0.35
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAAATATTTTGATATAATAAAT
Found at i:6076 original size:31 final size:31
Alignment explanation
Indices: 6041--6102 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6031 TAAATGATTG
*
6041 TAAGGTTAAATCTTGTCTTCAAATGTTATAT
1 TAAGGTTAAATCTTGCCTTCAAATGTTATAT
6072 TAAGGTTAAATCTTGCCTTCAAATGTTATAT
1 TAAGGTTAAATCTTGCCTTCAAATGTTATAT
6103 AATCTAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (31 bp):
TAAGGTTAAATCTTGCCTTCAAATGTTATAT
Found at i:11504 original size:10 final size:10
Alignment explanation
Indices: 11489--11557 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
11479 TTAATTCTTT
11489 TATATATTTA
1 TATATATTTA
*
11499 TATATATTTT
1 TATATATTTA
*
11509 TATAAATTTA
1 TATATATTTA
*
11519 TA-ATTGTTTA
1 TATA-TATTTA
* *
11529 TTTGT-TTTA
1 TATATATTTA
11538 TATATATTTA
1 TATATATTTA
11548 TA-A-ATTTA
1 TATATATTTA
11556 TA
1 TA
11558 AAATTTTAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
8 7 0.15
9 9 0.19
10 31 0.66
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TATATATTTA
Found at i:11586 original size:37 final size:38
Alignment explanation
Indices: 11499--11595 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 38
11489 TATATATTTA
* * *
11499 TATATATTTTTATAAATTTAT-AATTGTTTATTTGTTT
1 TATATATATTTATAAATTTATAAAATGTTTAATTGTTT
11536 TATATATATTTATAAATTTATAAAAT-TTTAATT-TTT
1 TATATATATTTATAAATTTATAAAATGTTTAATTGTTT
*
11572 TAGT-TATATATTATATATTT-TAAA
1 TA-TATATAT-TTATAAATTTATAAA
11596 TCTTTATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
36 14 0.26
37 36 0.68
38 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (38 bp):
TATATATATTTATAAATTTATAAAATGTTTAATTGTTT
Found at i:11587 original size:45 final size:46
Alignment explanation
Indices: 11488--11605 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 46
11478 TTTAATTCTT
* * * *
11488 TTATATATTTATATATATTTTTATAAATTTATAATTGTTTATTTGTTT
1 TTATATATTTATA-A-ATTTATATAAATTTATAATTGTTTAGTTATTA
*
11536 TATATATATTTATAAATTTATA-AAATTT-TAATTTTTTAGTTATATA
1 T-TATATATTTATAAATTTATATAAATTTATAATTGTTTAGTTAT-TA
11582 TTATATATTT-TAAATCTTTATATA
1 TTATATATTTATAAA--TTTATATA
11606 TCTTTCAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
44 4 0.07
45 21 0.35
46 14 0.23
47 7 0.12
48 2 0.03
49 12 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (46 bp):
TTATATATTTATAAATTTATATAAATTTATAATTGTTTAGTTATTA
Found at i:12802 original size:21 final size:21
Alignment explanation
Indices: 12763--12819 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
12753 AAAAATATAA
* *
12763 ATTTCGAATTTTTTATAAA-T
1 ATTTTGAATTTTTTTTAAATT
12783 ATTTTGAATTCTTTTTTAAATT
1 ATTTTGAATT-TTTTTTAAATT
*
12805 ATTTTG-ATTATTTTT
1 ATTTTGAATTTTTTTT
12820 GTATTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 11 0.34
22 7 0.22
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTTTGAATTTTTTTTAAATT
Found at i:12819 original size:22 final size:23
Alignment explanation
Indices: 12770--12819 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
12760 TAAATTTCGA
12770 ATTTTTTATAAATATTTTGAATT
1 ATTTTTTATAAATATTTTGAATT
* *
12793 CTTTTTTA-AATTATTTTG-ATT
1 ATTTTTTATAAATATTTTGAATT
12814 ATTTTT
1 ATTTTT
12820 GTATTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (23 bp):
ATTTTTTATAAATATTTTGAATT
Found at i:16993 original size:41 final size:41
Alignment explanation
Indices: 16907--17061 Score: 240
Period size: 41 Copynumber: 3.7 Consensus size: 41
16897 TTGTCTCGGG
* *
16907 ATGAGCATGAGATTATG-TAAAGTAGAAGACTCGTGACTCGGA
1 ATGAGCATGAGATTATGTTTAAG--GAAGACTCGTGACTCGAA
16949 ATGAGCATGAGATTATGTTTAAGGAAGACTCGTGACTCGAA
1 ATGAGCATGAGATTATGTTTAAGGAAGACTCGTGACTCGAA
*
16990 ATGAGCATGAGATTATGTTTAAGGAAGACTTGTGACTCGAA
1 ATGAGCATGAGATTATGTTTAAGGAAGACTCGTGACTCGAA
*
17031 ATGACCATGAGATTATGTTTAAAGGAAGACT
1 ATGAGCATGAGATTATGTTT-AAGGAAGACT
17062 TATGAATCGG
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
41 76 0.71
42 27 0.25
43 4 0.04
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.27
Consensus pattern (41 bp):
ATGAGCATGAGATTATGTTTAAGGAAGACTCGTGACTCGAA
Found at i:17085 original size:41 final size:38
Alignment explanation
Indices: 16910--17085 Score: 165
Period size: 41 Copynumber: 4.3 Consensus size: 38
16900 TCTCGGGATG
* *
16910 AGCATGAGATTATG-TAAAGTAGAAGACTCGTGACTCGGAA
1 AGCATGAGATTATGTTTAAG--GAAGACTTGTGACTC-GAA
*
16950 TGAGCATGAGATTATGTTTAAGGAAGACTCGTGACTCGAAA
1 --AGCATGAGATTATGTTTAAGGAAGACTTGTGACTCG-AA
16991 TGAGCATGAGATTATGTTTAAGGAAGACTTGTGACTCGAA
1 --AGCATGAGATTATGTTTAAGGAAGACTTGTGACTCGAA
* *
17031 ATGACCATGAGATTATGTTTAAAGGAAGACTTATGAATCGGTAA
1 A-G--CATGAGATTATGTTT-AAGGAAGACTTGTGACTC-G-AA
*
17075 AGCATAAGATT
1 AGCATGAGATT
17086 GTTTAGAAAG
Statistics
Matches: 121, Mismatches: 5, Indels: 17
0.85 0.03 0.12
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 3 0.02
41 77 0.64
42 30 0.25
43 6 0.05
44 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (38 bp):
AGCATGAGATTATGTTTAAGGAAGACTTGTGACTCGAA
Found at i:17085 original size:82 final size:81
Alignment explanation
Indices: 16909--17085 Score: 205
Period size: 82 Copynumber: 2.1 Consensus size: 81
16899 GTCTCGGGAT
* * * *
16909 GAGCATGAGATTATG-TAAAGTAGAAGACTCGTGACTCGGAATGAGCATGAGATTATGTTTAAGG
1 GAGCATAAGATTATGTTTAAG--GAAGACTCGTGACTCGAAATGACCATGAGATTATGTTTAAGG
* *
16973 AAGACTCGTGACTCGAAA
64 AAGACTCATGAATCGAAA
* *
16991 TGAGCATGAGATTATGTTTAAGGAAGACTTGTGACTCGAAATGACCATGAGATTATGTTTAAAGG
1 -GAGCATAAGATTATGTTTAAGGAAGACTCGTGACTCGAAATGACCATGAGATTATGTTT-AAGG
* *
17056 AAGACTTATGAATCGGTAA
64 AAGACTCATGAATC-GAAA
17075 -AGCATAAGATT
1 GAGCATAAGATT
17086 GTTTAGAAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
82 45 0.55
83 30 0.37
84 7 0.09
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (81 bp):
GAGCATAAGATTATGTTTAAGGAAGACTCGTGACTCGAAATGACCATGAGATTATGTTTAAGGAA
GACTCATGAATCGAAA
Found at i:21431 original size:6 final size:6
Alignment explanation
Indices: 21406--21450 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
21396 ACAATTCATA
* * *
21406 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
21451 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:25047 original size:29 final size:31
Alignment explanation
Indices: 24967--25036 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
24957 AAGAAAAATT
* *
24967 GTCAAA-TTAACTATCAAATTAAAAAATAAA
1 GTCAAATTTAAATACCAAATTAAAAAATAAA
24997 GTGTCAAATTTAAATACCAAATTAAAAAA-AAA
1 --GTCAAATTTAAATACCAAATTAAAAAATAAA
25029 -TCAAATTT
1 GTCAAATTT
25037 TGATACGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 8 0.23
32 9 0.26
33 18 0.51
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (31 bp):
GTCAAATTTAAATACCAAATTAAAAAATAAA
Found at i:25552 original size:66 final size:66
Alignment explanation
Indices: 25470--25599 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
25460 GTAAATTCGT
* *
25470 ATCACCATGAAGGCGAACTCAGATCTAGGAAACACATGTTAACTCTAGAATAGGGTACATGTTGG
1 ATCACCATGAAGGCGAACTCAGATCTAGGAAACACATGTTAACTCTAAAATAAGGTACATGTTGG
25535 C
66 C
* * * *
25536 ATCACTATGAAGGCGAACTCAGATCTAGGAAATATATGTTAACTCTAAAATAAGGTACGTGTTG
1 ATCACCATGAAGGCGAACTCAGATCTAGGAAACACATGTTAACTCTAAAATAAGGTACATGTTG
25600 ATATACATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (66 bp):
ATCACCATGAAGGCGAACTCAGATCTAGGAAACACATGTTAACTCTAAAATAAGGTACATGTTGG
C
Found at i:26753 original size:40 final size:39
Alignment explanation
Indices: 26709--26822 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 39
26699 GGCGTTTGGA
26709 CCAAAAACGCCGCAAATGGTAAAGCAATAGTGGGGTTTTT
1 CCAAAAACGCCGCAAA-GGTAAAGCAATAGTGGGGTTTTT
* * * * *
26749 CCAAAAACGTCGTAAAAAGTAAAGCAATAGCGGTGTTTTT
1 CCAAAAACGCCG-CAAAGGTAAAGCAATAGTGGGGTTTTT
*
26789 CCAAAAACACCGCCAAAGGTATAGAGCAATAGTG
1 CCAAAAACGCCG-CAAAGGTA-A-AGCAATAGTG
26823 ATGTTTATGG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 47 0.78
41 4 0.07
42 9 0.15
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (39 bp):
CCAAAAACGCCGCAAAGGTAAAGCAATAGTGGGGTTTTT
Found at i:26838 original size:42 final size:42
Alignment explanation
Indices: 26792--26905 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
26782 TGTTTTTCCA
* * * * *
26792 AAAACACCGCCAAAGGTATAGAGCAATAGTGATGTTTATGGG
1 AAAACGCCGCAAAAGGTAAAGAGCAATAGTGACGTTTATAGG
* * * *
26834 AAAACGCCGCAAAAAGTAAAGAGCATTAGCGGCGTTTATAGG
1 AAAACGCCGCAAAAGGTAAAGAGCAATAGTGACGTTTATAGG
* *
26876 AAAACGCCACAAAAGGTAAAGAGCTATAGT
1 AAAACGCCGCAAAAGGTAAAGAGCAATAGT
26906 CAATTTACAC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (42 bp):
AAAACGCCGCAAAAGGTAAAGAGCAATAGTGACGTTTATAGG
Found at i:28727 original size:43 final size:43
Alignment explanation
Indices: 28669--28784 Score: 160
Period size: 43 Copynumber: 2.7 Consensus size: 43
28659 ATGACATTTG
** * * *
28669 TGGGAAAAATACCGCTAAATAACATGTTCTATAGCGGCGTTTA
1 TGGGAAAAACGCCGCTAAAGAACATGCTCTATAGCGGCGTTAA
*
28712 TGGGAAAAACGCCGCTAAAGAACGTGCTCTATAGCGGCGTTAA
1 TGGGAAAAACGCCGCTAAAGAACATGCTCTATAGCGGCGTTAA
* *
28755 TGGTAAAAACGCTGCTAAAGAACATGCTCT
1 TGGGAAAAACGCCGCTAAAGAACATGCTCT
28785 TTAATGGTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (43 bp):
TGGGAAAAACGCCGCTAAAGAACATGCTCTATAGCGGCGTTAA
Found at i:28809 original size:17 final size:17
Alignment explanation
Indices: 28783--28815 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28773 AGAACATGCT
28783 CTTTAATGGTGTTTGTG
1 CTTTAATGGTGTTTGTG
*
28800 CTTTAGTGGTGTTTGT
1 CTTTAATGGTGTTTGT
28816 AGGAAAAGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.30, T:0.55
Consensus pattern (17 bp):
CTTTAATGGTGTTTGTG
Found at i:28900 original size:43 final size:43
Alignment explanation
Indices: 28810--28941 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 43
28800 CTTTAGTGGT
* * * *
28810 GTTTGTAGGAAAAGCGTCGCTAAAGAACATGTTCTT-TAGTGGA
1 GTTTGTAAGAAAAGCGCCGCTAAAGAACATGTT-TTATAGCGGC
* * *
28853 GTTTGTAAGAAAAGCGCCGCTAAAGACCTTGTTTTATAGCAGC
1 GTTTGTAAGAAAAGCGCCGCTAAAGAACATGTTTTATAGCGGC
* * * * * *
28896 GTTTGT-TGGAAAGCTCTGCTAAAGATCATGTTCTATAGCGGC
1 GTTTGTAAGAAAAGCGCCGCTAAAGAACATGTTTTATAGCGGC
28938 GTTT
1 GTTT
28942 TTACGAATAA
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
42 34 0.47
43 39 0.53
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (43 bp):
GTTTGTAAGAAAAGCGCCGCTAAAGAACATGTTTTATAGCGGC
Done.