Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011469.1 Kokia drynarioides strain JFW-HI SEQ_126453, 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: 74366
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:756 original size:23 final size:23
Alignment explanation
Indices: 730--877 Score: 199
Period size: 23 Copynumber: 6.3 Consensus size: 23
720 ACACTAGCAC
730 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
753 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
776 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
801 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
824 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
847 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
870 GCTCTCTG
1 GCTCTCTG
878 TTGCCCAGCA
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
22 3 0.03
23 87 0.79
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:798 original size:46 final size:44
Alignment explanation
Indices: 730--904 Score: 172
Period size: 48 Copynumber: 3.7 Consensus size: 44
720 ACACTAGCAC
730 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACT-TGTGTGCTCTCTGTTTAGCACGTCT-GT
* * *
776 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGTGCTCTCTGTTTAGCAC-GTCTGT
* * *
824 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCAC-TTGTGTGCTCTCTGTTTAGCAC-GTCTGT
*
870 GCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTT
1 GCTCTCTGATT----AGCACTTGTGTGCTCTCTGTT
905 AGTACTTTGG
Statistics
Matches: 111, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
45 2 0.02
46 48 0.43
47 1 0.01
48 54 0.49
49 6 0.05
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.42
Consensus pattern (44 bp):
GCTCTCTGATTAGCACTTGTGTGCTCTCTGTTTAGCACGTCTGT
Found at i:852 original size:71 final size:68
Alignment explanation
Indices: 730--922 Score: 225
Period size: 71 Copynumber: 2.8 Consensus size: 68
720 ACACTAGCAC
* * *
730 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTG--CTCTCTGTTATTAGCA
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGTAC-T-TTGTGTACTCTCTG-T-TTAGCA
793 CTGTGTGT
61 CTGTGTGT
801 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGT
1 GCTCTCTGATTAGCACTTTGTGTGCTCTCTG-TTAGTACTTTGTGTACTCTCTGTTTAGCACTGT
866 GTGT
65 GTGT
*
870 GCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTGTTAGTACTTTG-GTACTCTCT
1 GCTCTCTGATT----AGCACTTTGTGTGCTCTCTGTTAGTACTTTGTGTACTCTCT
923 ATTTGTTCCG
Statistics
Matches: 111, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
68 2 0.02
69 35 0.32
70 13 0.12
71 56 0.50
72 5 0.05
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (68 bp):
GCTCTCTGATTAGCACTTTGTGTGCTCTCTGTTAGTACTTTGTGTACTCTCTGTTTAGCACTGTG
TGT
Found at i:7480 original size:26 final size:26
Alignment explanation
Indices: 7444--7494 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
7434 ATTACCATAC
*
7444 TGGCTCGTAAGAGCGATACACTGTAT
1 TGGCTCGTAAGAGCAATACACTGTAT
*
7470 TGGCTCGTAAGAGCAATATACTGTA
1 TGGCTCGTAAGAGCAATACACTGTA
7495 CCGGATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (26 bp):
TGGCTCGTAAGAGCAATACACTGTAT
Found at i:7625 original size:26 final size:25
Alignment explanation
Indices: 7596--7685 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 25
7586 TATTGTACTA
*
7596 GCTCGAAAGAGCGATAAACTGAACTG
1 GCTC-AAAGAGCGATATACTGAACTG
*
7622 GCTCAAGAGAGCGATATATTGAACTG
1 GCTCAA-AGAGCGATATACTGAACTG
* * * *
7648 GATCTTAAGAGCGATATACTGTATTG
1 GCTC-AAAGAGCGATATACTGAACTG
7674 GCTCATAAGAGC
1 GCTCA-AAGAGC
7686 AATTTAACTT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.04
26 49 0.94
27 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (25 bp):
GCTCAAAGAGCGATATACTGAACTG
Found at i:8161 original size:26 final size:27
Alignment explanation
Indices: 8106--8164 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
8096 ACACTAGCGC
*
8106 GCTCTCCATTAATTTAGCACGTATTAT
1 GCTCTCCATTAATTTAGCACGTATAAT
8133 GCTCTCCGATT-A-TTAGCACGTA-AAGT
1 GCTCTCC-ATTAATTTAGCACGTATAA-T
8159 GCTCTC
1 GCTCTC
8165 TATTTAGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 17 0.59
27 8 0.28
28 3 0.10
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (27 bp):
GCTCTCCATTAATTTAGCACGTATAAT
Found at i:9711 original size:85 final size:84
Alignment explanation
Indices: 9568--9737 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 84
9558 CGTGTGGGGT
*
9568 ATTTCGCATGTTCACACGGCTTGTCACACAGTTTGTGACACGACCATGTAAGGATACTTCGTGTA
1 ATTTCGCATGTTCACACGGCTTGTCACACAGTTTGTGACACGACCATGTAAGAATACTTCGTGTA
9633 ACACCCAAAACCCGTTACC
66 ACACCCAAAACCCGTTACC
9652 NATTTCGCATGTTCACACGGCTTGTCACACAGTTTGTGACACGACCATGTAAGAATACTTCGTGT
1 -ATTTCGCATGTTCACACGGCTTGTCACACAGTTTGTGACACGACCATGTAAGAATACTTCGTGT
9717 AACACCCAAAACCCGTTACC
65 AACACCCAAAACCCGTTACC
9737 A
1 A
9738 CTGCCGGGTA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 1 0.01
85 83 0.99
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (84 bp):
ATTTCGCATGTTCACACGGCTTGTCACACAGTTTGTGACACGACCATGTAAGAATACTTCGTGTA
ACACCCAAAACCCGTTACC
Found at i:11076 original size:107 final size:107
Alignment explanation
Indices: 10887--11124 Score: 352
Period size: 107 Copynumber: 2.2 Consensus size: 107
10877 TCAAATGTTG
* * * **
10887 CTGCTCACACAAGCTATAGAGAATATACGAATCAAGCATAAATCTCAGCCATTGTAAGGCCTATA
1 CTGCTCACACAAGCTGTAGAGAATATACGAATCAAGCATAAATCTCAACCATCGTAAGAACTATA
* *
10952 ATCCATTATTGGATTCATTTCACATTTTCTC-GACTCACGATA
66 ATCCATTATCGAATTCATTTCACATTTT-TCAGACTCACGATA
* **
10994 CTTCTCACACAAGCTGTAGAGAATATGTGAATCAAGCATAAATCTCAACCATCGTAAGAACTATA
1 CTGCTCACACAAGCTGTAGAGAATATACGAATCAAGCATAAATCTCAACCATCGTAAGAACTATA
* *
11059 ATCCATTCTCGAATTCATTTCACATTTTTCAGACTCACGATG
66 ATCCATTATCGAATTCATTTCACATTTTTCAGACTCACGATA
11101 CTGCTCACACAAGCTGTAGAGAAT
1 CTGCTCACACAAGCTGTAGAGAAT
11125 CCGTAACAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
106 2 0.02
107 115 0.98
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (107 bp):
CTGCTCACACAAGCTGTAGAGAATATACGAATCAAGCATAAATCTCAACCATCGTAAGAACTATA
ATCCATTATCGAATTCATTTCACATTTTTCAGACTCACGATA
Found at i:16218 original size:14 final size:14
Alignment explanation
Indices: 16199--16227 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16189 GAACTCTCAA
16199 AATCTCTTCTCTCT
1 AATCTCTTCTCTCT
16213 AATCTCTTCTCTCT
1 AATCTCTTCTCTCT
16227 A
1 A
16228 TGTCTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (14 bp):
AATCTCTTCTCTCT
Found at i:20646 original size:21 final size:19
Alignment explanation
Indices: 20596--20648 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
20586 CTGTACTAGT
20596 TCTACCGATACAAGTATAA
1 TCTACCGATACAAGTATAA
* *
20615 TCCCTATCGATACATGTCATACA
1 T--CTACCGATACAAGT-ATA-A
20638 TCTACCGATAC
1 TCTACCGATAC
20649 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.04
21 21 0.78
22 3 0.11
23 2 0.07
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.28
Consensus pattern (19 bp):
TCTACCGATACAAGTATAA
Found at i:21426 original size:53 final size:51
Alignment explanation
Indices: 21346--21584 Score: 239
Period size: 51 Copynumber: 4.6 Consensus size: 51
21336 ATTTCGTTTA
* * * *
21346 ATACTCAGGATGACA-TATAGTTATCGGACATCTTATTCCATATAGGAATTCAT
1 ATACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATATAGG-ATTCAT
* * *
21399 ATACTCATGATGACACTGAGTCATCGGACCTTTAATCCATCAT-GGATTCAG
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCAT-ATAGGATTCAT
* * *
21450 GTACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATATAGGATTCAT
* * * * * * * *
21501 TTACTCACGATGAAACTTAATCATCGAACCTTTAATACGTAAAGGATTCTT
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATATAGGATTCAT
* * *
21552 TTACTCACGATGAAACTTAATCATCGGACCTTT
1 ATACTCACGATGACACTTAGTCATCGGACCTTT
21585 TCATTTATAG
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.01
51 125 0.76
52 10 0.06
53 27 0.16
54 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (51 bp):
ATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATATAGGATTCAT
Found at i:21462 original size:51 final size:51
Alignment explanation
Indices: 21382--21584 Score: 244
Period size: 51 Copynumber: 4.0 Consensus size: 51
21372 GACATCTTAT
* * * * * * *
21382 TCCATATAGGAATTCATATACTCATGATGACACTGAGTCATCGGACCTTTAA
1 TCCATAAAGG-ATTCATTTACTCACGATGAAACTTAATCATCGAACCTTTAA
* * ** * *
21434 TCCATCATGGATTCAGGTACTCACGATGACACTTAGTCATCGAACCTTTAA
1 TCCATAAAGGATTCATTTACTCACGATGAAACTTAATCATCGAACCTTTAA
21485 TCCATAAAGGATTCATTTACTCACGATGAAACTTAATCATCGAACCTTTAA
1 TCCATAAAGGATTCATTTACTCACGATGAAACTTAATCATCGAACCTTTAA
* * * *
21536 TACGTAAAGGATTCTTTTACTCACGATGAAACTTAATCATCGGACCTTT
1 TCCATAAAGGATTCATTTACTCACGATGAAACTTAATCATCGAACCTTT
21585 TCATTTATAG
Statistics
Matches: 133, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
51 126 0.95
52 7 0.05
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (51 bp):
TCCATAAAGGATTCATTTACTCACGATGAAACTTAATCATCGAACCTTTAA
Found at i:27781 original size:26 final size:26
Alignment explanation
Indices: 27752--27802 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
27742 TTGTAAAAAC
*
27752 GATATAGTATACTGGTTCGTAAGAGT
1 GATATAGTATACTGGCTCGTAAGAGT
* *
27778 GATATATTTTACTGGCTCGTAAGAG
1 GATATAGTATACTGGCTCGTAAGAG
27803 CGATTTACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (26 bp):
GATATAGTATACTGGCTCGTAAGAGT
Found at i:27970 original size:26 final size:26
Alignment explanation
Indices: 27912--27967 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
27902 AAAATACTAA
* *
27912 ACTGGCTCGTGAGAGCGATATATTGT
1 ACTGGCTCGTAAGAGCGATATACTGT
* *
27938 ACTGGCTCGTAAGAGTGATTTACTG-
1 ACTGGCTCGTAAGAGCGATATACTGT
27963 ACTGG
1 ACTGG
27968 GCTTGTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (26 bp):
ACTGGCTCGTAAGAGCGATATACTGT
Found at i:31322 original size:21 final size:21
Alignment explanation
Indices: 31291--31342 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
31281 ATTGAATATT
*
31291 TTTTTTCATTT-TTTTATTGAG
1 TTTTTT-ATTTATTTTATTGAA
*
31312 TTTATTTATTTATTTTTTTGAA
1 TTT-TTTATTTATTTTATTGAA
31334 TTTTTTATT
1 TTTTTTATT
31343 GTGGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (21 bp):
TTTTTTATTTATTTTATTGAA
Found at i:31938 original size:110 final size:110
Alignment explanation
Indices: 31799--32007 Score: 285
Period size: 110 Copynumber: 1.9 Consensus size: 110
31789 AAATAAAGAA
* * * *
31799 CATTTATCGATTTTAAATAGGATATTCAATTACTCAGGTTCAAAGAAAAAATCATACCCAGCACA
1 CATTTATCGATTTTAAATAAGATACTCAATTACTCAGGTTCAAAG-AAAAATCACACCCAACACA
*
31864 TAAGGACACAATTTCTTGA-GCCCCTAAAATAAAAAAAACATCGAG
65 TAAGGACACAATTTCTCGAGGCCCCTAAAATAAAAAAAACATCGAG
* * * * *
31909 CATTTATTGATTTTAAATAAGATACTCAATTATTTAGGTTCAAAGAAAAATCACACCCAACTCGT
1 CATTTATCGATTTTAAATAAGATACTCAATTACTCAGGTTCAAAGAAAAATCACACCCAACACAT
* * *
31974 TAGGGCACAATTTCTCGAGGTCCCTAAAATAAAA
66 AAGGACACAATTTCTCGAGGCCCCTAAAATAAAA
32008 GGACATTGCC
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 31 0.36
110 54 0.64
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (110 bp):
CATTTATCGATTTTAAATAAGATACTCAATTACTCAGGTTCAAAGAAAAATCACACCCAACACAT
AAGGACACAATTTCTCGAGGCCCCTAAAATAAAAAAAACATCGAG
Found at i:40053 original size:16 final size:16
Alignment explanation
Indices: 40028--40078 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
40018 TTTAGTGGAC
*
40028 TTTGGTTTTTAAATTTA
1 TTTGG-TTTTATATTTA
*
40045 TTTTGTTTTATATTT-
1 TTTGGTTTTATATTTA
*
40060 TTTGGTTTTTTATTTA
1 TTTGGTTTTATATTTA
40076 TTT
1 TTT
40079 AGTCTAGGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.45
16 12 0.41
17 4 0.14
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.75
Consensus pattern (16 bp):
TTTGGTTTTATATTTA
Found at i:42629 original size:4 final size:4
Alignment explanation
Indices: 42620--42675 Score: 69
Period size: 4 Copynumber: 14.2 Consensus size: 4
42610 AATATGATAC
* * *
42620 GTAT GTAT GTAT GTAC G-AT GTAC GTAT GTAT GTAT ATAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
42667 ATAT GTAT G
1 GTAT GTAT G
42676 AACATGCACA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 2 0.05
4 41 0.95
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:42642 original size:7 final size:8
Alignment explanation
Indices: 42612--42665 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
42602 GGTCTAAGAA
42612 TATGATACG
1 TATG-TACG
*
42621 TATGTATG
1 TATGTACG
42629 TATGTACG
1 TATGTACG
42637 -ATGTACG
1 TATGTACG
*
42644 TATGTATG
1 TATGTACG
* *
42652 TATATATG
1 TATGTACG
42660 TATGTA
1 TATGTA
42666 TATATGTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.18
8 28 0.72
9 4 0.10
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.43
Consensus pattern (8 bp):
TATGTACG
Found at i:45085 original size:27 final size:27
Alignment explanation
Indices: 45051--45106 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
45041 CGCCAAAATG
*
45051 TTTACAAAAGATAGGAATGGA-AAACTA
1 TTTACAAAAGAAAGGAAT-GACAAACTA
*
45078 TTTACAAAATAAAGGAATGACAAACTA
1 TTTACAAAAGAAAGGAATGACAAACTA
45105 TT
1 TT
45107 GCCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (27 bp):
TTTACAAAAGAAAGGAATGACAAACTA
Found at i:47722 original size:31 final size:31
Alignment explanation
Indices: 47684--47753 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
47674 AGACAATAAC
47684 CAAACAATTTTACTCTAAACCTAGGTAATGG
1 CAAACAATTTTACTCTAAACCTAGGTAATGG
47715 CAAACAATTTTACTCTAAACCTAGGTAATGG
1 CAAACAATTTTACTCTAAACCTAGGTAATGG
47746 CAAACAAT
1 CAAACAAT
47754 AAACAAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (31 bp):
CAAACAATTTTACTCTAAACCTAGGTAATGG
Found at i:47792 original size:21 final size:21
Alignment explanation
Indices: 47767--47813 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
47757 CAAATCTTCA
47767 AGTTGTGTATCTAACAAGAGC
1 AGTTGTGTATCTAACAAGAGC
47788 AGTTGTGTATCTAACAAGAGC
1 AGTTGTGTATCTAACAAGAGC
47809 AGTTG
1 AGTTG
47814 AAACTATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (21 bp):
AGTTGTGTATCTAACAAGAGC
Found at i:48244 original size:14 final size:14
Alignment explanation
Indices: 48225--48251 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48215 AATAACCCTA
48225 AACCAAAATATGTT
1 AACCAAAATATGTT
48239 AACCAAAATATGT
1 AACCAAAATATGT
48252 GAATAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AACCAAAATATGTT
Found at i:49751 original size:26 final size:26
Alignment explanation
Indices: 49689--49742 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
49679 AACGATGAAA
49689 GAAAGGTTTTTGATAAATGGATTTGT
1 GAAAGGTTTTTGATAAATGGATTTGT
49715 GAAAGGTTTTTGATAAATGGATTTGT
1 GAAAGGTTTTTGATAAATGGATTTGT
49741 GA
1 GA
49743 CTTTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (26 bp):
GAAAGGTTTTTGATAAATGGATTTGT
Found at i:50359 original size:30 final size:31
Alignment explanation
Indices: 50325--50400 Score: 127
Period size: 32 Copynumber: 2.5 Consensus size: 31
50315 CTATTTAATT
50325 TTGAGTTGCATTTTTTGTT-AAAAAAAAAAA
1 TTGAGTTGCATTTTTTGTTAAAAAAAAAAAA
*
50355 TTGAGTTGCATTATTTGTTCAAAAAAAAAAAA
1 TTGAGTTGCATTTTTTGTT-AAAAAAAAAAAA
50387 TTGAGTTGCATTTT
1 TTGAGTTGCATTTT
50401 GTAATACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 18 0.43
32 24 0.57
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (31 bp):
TTGAGTTGCATTTTTTGTTAAAAAAAAAAAA
Found at i:51834 original size:41 final size:42
Alignment explanation
Indices: 51787--51953 Score: 267
Period size: 41 Copynumber: 4.1 Consensus size: 42
51777 AAATCTACCT
51787 TTTTTTTTTTTAATTATACATGTAAG-CTTTCTTTATTTTTAC
1 TTTTTTTTTTTAATTATACATGT-AGTCTTTCTTTATTTTTAC
51829 -TTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
1 TTTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
*
51870 TTTTTTTTTTTAATTATACATGTA----ATCTTT-TTTTTAC
1 TTTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
51907 TTTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
1 TTTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
51949 TTTTT
1 TTTTT
51954 GAAAAAGAAG
Statistics
Matches: 116, Mismatches: 2, Indels: 14
0.88 0.02 0.11
Matches are distributed among these distances:
37 31 0.27
38 5 0.04
40 2 0.02
41 43 0.37
42 35 0.30
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (42 bp):
TTTTTTTTTTTAATTATACATGTAGTCTTTCTTTATTTTTAC
Found at i:51923 original size:79 final size:80
Alignment explanation
Indices: 51787--51953 Score: 284
Period size: 79 Copynumber: 2.1 Consensus size: 80
51777 AAATCTACCT
51787 TTTTTTTTTTTAATTATACATGTAAGCTTTCTTTATTTTTACTTTTTTTTTTAATTATACATGTA
1 TTTTTTTTTTTAATTATACATGTAA---TTCTTTATTTTTACTTTTTTTTTTAATTATACATGTA
51852 GTCTTTCTTTATTTTTAC
63 GTCTTTCTTTATTTTTAC
51870 TTTTTTTTTTTAATTATACATGTAA-TCTTT-TTTTTACTTTTTTTTTTTAATTATACATGTAGT
1 TTTTTTTTTTTAATTATACATGTAATTCTTTATTTTTAC-TTTTTTTTTTAATTATACATGTAGT
51933 CTTTCTTTATTTTTAC
65 CTTTCTTTATTTTTAC
51949 TTTTT
1 TTTTT
51954 GAAAAAGAAG
Statistics
Matches: 83, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
78 7 0.08
79 51 0.61
83 25 0.30
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (80 bp):
TTTTTTTTTTTAATTATACATGTAATTCTTTATTTTTACTTTTTTTTTTAATTATACATGTAGTC
TTTCTTTATTTTTAC
Found at i:64617 original size:75 final size:75
Alignment explanation
Indices: 64494--64650 Score: 314
Period size: 75 Copynumber: 2.1 Consensus size: 75
64484 TAAATTGAGA
64494 TTACCTGTCATATGATCCGTAGCACCAGAATCAATAACCCATTTTGAAAAGGAGGAAACAAGACA
1 TTACCTGTCATATGATCCGTAGCACCAGAATCAATAACCCATTTTGAAAAGGAGGAAACAAGACA
64559 TGTATTGGGT
66 TGTATTGGGT
64569 TTACCTGTCATATGATCCGTAGCACCAGAATCAATAACCCATTTTGAAAAGGAGGAAACAAGACA
1 TTACCTGTCATATGATCCGTAGCACCAGAATCAATAACCCATTTTGAAAAGGAGGAAACAAGACA
64634 TGTATTGGGT
66 TGTATTGGGT
64644 TTACCTG
1 TTACCTG
64651 ACTCAATAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (75 bp):
TTACCTGTCATATGATCCGTAGCACCAGAATCAATAACCCATTTTGAAAAGGAGGAAACAAGACA
TGTATTGGGT
Found at i:65119 original size:22 final size:23
Alignment explanation
Indices: 65092--65145 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
65082 TACAAATCAG
*
65092 CCTACATATCAA-CTATCCAATC
1 CCTACAAATCAATCTATCCAATC
*
65114 CCTACAAATCAATCTATCTAATC
1 CCTACAAATCAATCTATCCAATC
65137 CCTACAAAT
1 CCTACAAAT
65146 GAGCCTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (23 bp):
CCTACAAATCAATCTATCCAATC
Found at i:72142 original size:29 final size:31
Alignment explanation
Indices: 72097--72156 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
72087 TCACAAATTT
72097 AGAATTTAATCATTTTA-CTTTTAT-TTTTA
1 AGAATTTAATCATTTTATCTTTTATATTTTA
*
72126 AGAATTTAATC-TCTTTATTTTTTATATTTTA
1 AGAATTTAATCAT-TTTATCTTTTATATTTTA
72157 TAATTTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 15 0.56
30 6 0.22
31 5 0.19
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (31 bp):
AGAATTTAATCATTTTATCTTTTATATTTTA
Found at i:72162 original size:30 final size:28
Alignment explanation
Indices: 72094--72163 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
72084 TCTTCACAAA
72094 TTTAGAATTTAATCATTTTACTTTTATT
1 TTTAGAATTTAATCATTTTACTTTTATT
*
72122 TTTAAGAATTTAATC-TCTTTATTTTTTATAT
1 TTT-AGAATTTAATCAT-TTTA-CTTTTAT-T
*
72153 TTTATAATTTA
1 TTTAGAATTTA
72164 GGTTCAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 4 0.11
29 15 0.42
30 13 0.36
31 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTAGAATTTAATCATTTTACTTTTATT
Found at i:73643 original size:2 final size:2
Alignment explanation
Indices: 73636--73664 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73626 CAAAAAGAAC
73636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73665 ATTTCAGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74341 original size:2 final size:2
Alignment explanation
Indices: 74336--74366 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74326 TAAAAAAAGC
74336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.