Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005402.1 Kokia drynarioides strain JFW-HI SEQ_119409, 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: 48993
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2003 original size:17 final size:18
Alignment explanation
Indices: 1975--2009 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1965 CTAGAACCGA
1975 TTAAATTAATTTATAATT
1 TTAAATTAATTTATAATT
*
1993 TTAAA-TAATTTTTAATT
1 TTAAATTAATTTATAATT
2010 ATTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTAATTTATAATT
Found at i:3522 original size:18 final size:18
Alignment explanation
Indices: 3480--3515 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3470 TCTCTCTCTC
3480 AACAAAAATTTCAAAAAA
1 AACAAAAATTTCAAAAAA
*
3498 AAAAAAAATTTCCAAAAA
1 AACAAAAATTT-CAAAAA
3516 TTCAAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (18 bp):
AACAAAAATTTCAAAAAA
Found at i:6138 original size:6 final size:6
Alignment explanation
Indices: 6109--6149 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
6099 ATGACCCGGG
* * *
6109 GCCTGA GGCTGT GCCTGA GTCTGA GCCTGA GCCTGA GCCTG
1 GCCTGA GCCTGA GCCTGA GCCTGA GCCTGA GCCTGA GCCTG
6150 GTGAGAGGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.12, C:0.29, G:0.37, T:0.22
Consensus pattern (6 bp):
GCCTGA
Found at i:8089 original size:16 final size:16
Alignment explanation
Indices: 8047--8090 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 16
8037 CCACCTTATC
8047 ATGTCTTATGATTAAT
1 ATGTCTTATGATTAAT
*
8063 ATATC-TATGATTAAT
1 ATGTCTTATGATTAAT
8078 ATGTCTTATGATT
1 ATGTCTTATGATT
8091 TTTATACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (16 bp):
ATGTCTTATGATTAAT
Found at i:9409 original size:21 final size:19
Alignment explanation
Indices: 9375--9417 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
9365 TTTATATAAG
9375 TTTATATTTTTTTTGTTAT
1 TTTATATTTTTTTTGTTAT
*
9394 TTTACTATTATTTTTTTTTAT
1 TTTA-TATT-TTTTTTGTTAT
9415 TTT
1 TTT
9418 TTTTGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTATATTTTTTTTGTTAT
Found at i:9458 original size:18 final size:18
Alignment explanation
Indices: 9437--9512 Score: 50
Period size: 18 Copynumber: 4.2 Consensus size: 18
9427 TTTTAATAGT
9437 TTTTATTATTTATATATA
1 TTTTATTATTTATATATA
*
9455 TTTT-TTCATTTATAATAAA
1 TTTTATT-ATTTAT-ATATA
* * *
9474 TTTAATAATTT-TCTATA
1 TTTTATTATTTATATATA
* *
9491 TTTTTTTGTATTAT-TATA
1 TTTTATTAT-TTATATATA
9509 TTTT
1 TTTT
9513 TTAATTTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
17 10 0.23
18 21 0.48
19 12 0.27
20 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTTATTATTTATATATA
Found at i:13163 original size:10 final size:11
Alignment explanation
Indices: 13144--13181 Score: 62
Period size: 10 Copynumber: 3.6 Consensus size: 11
13134 TTTGAAAATT
13144 TTATTTTATTA
1 TTATTTTATTA
13155 TTA-TTTATTA
1 TTATTTTATTA
13165 TTATTTTATTA
1 TTATTTTATTA
13176 TT-TTTT
1 TTATTTT
13182 GGGTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 14 0.54
11 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:13831 original size:49 final size:49
Alignment explanation
Indices: 13665--14100 Score: 162
Period size: 50 Copynumber: 8.9 Consensus size: 49
13655 CGTGGCTATA
* * * *
13665 ATGTCTTCGTGGTACTAGATTCGCCGTTGTAGCTTAAAT-ATTTCCTTCC
1 ATGTCTTTGAGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTTCC-TCC
* *
13714 ATG-CTTTGAGGTACGAGGTTCGCCGTTGC-GACTTAAA-CTTTTCC-CC
1 ATGTCTTTGAGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTTTCCTCC
* * * *
13760 ATATATCTTCT-CGGTATTAGATTCGCCATTGCAGCTTAAATCTTTTCCTCC
1 --ATGTCTT-TGAGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTTCCTCC
* * ** * * *
13811 ATGTCTTTGGGGTACAAGATTCATCGTTGC-GACTTAAACCTTTCCCTTCG
1 ATGTCTTTGAGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTTTCC-TCC
* * * * * * * *
13861 TTATCTTCGTGGTACTGGATTCGCCGTTAC-GACTTAAATCTTTCCCTTC
1 ATGTCTTTGAGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTTTCCTCC
* * * * * *
13910 ATG-CTTCTGAGATACAAGGTTTGTCGTTGC-GACTTAAATCTTTCCCTCC
1 ATGTCTT-TGAGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTTTCCTCC
* * * * * ** ** * *
13959 ATTATCTTCGTGGTACTGGATTTGTTGTCACGGCTTAAAAT-TTTCCCTCC
1 A-TGTCTTTGAGGTACTAGATTCGCCGTTGCAGCTT-AAATCTTTTCCTCC
* * * * * *
14009 ATG-CTTCT-TGGTATTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTC
1 ATGTCTT-TGAGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTTCCTCC
* * * **
14057 ATTATCTTCGTGGTACTAGATTTACCGTTGC-GACTTAAATCTTT
1 A-TGTCTTTGAGGTACTAGATTCGCCGTTGCAG-CTTAAATCTTT
14101 CCTTTCATGT
Statistics
Matches: 292, Mismatches: 72, Indels: 45
0.71 0.18 0.11
Matches are distributed among these distances:
46 2 0.01
47 5 0.02
48 69 0.24
49 99 0.34
50 107 0.37
51 10 0.03
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (49 bp):
ATGTCTTTGAGGTACTAGATTCGCCGTTGCAGCTTAAATCTTTTCCTCC
Found at i:13882 original size:50 final size:49
Alignment explanation
Indices: 13828--14119 Score: 215
Period size: 50 Copynumber: 5.9 Consensus size: 49
13818 TGGGGTACAA
* *
13828 GATTCATCGTTGCGACTTAAACCTTTCCCTTCGTTATCTTCGTGGTACTG
1 GATTCACCGTTGCGACTTAAATCTTTCCCTTC-TTATCTTCGTGGTACTG
* * *
13878 GATTCGCCGTTACGACTTAAATCTTTCCCTTC--ATGCTTC-TGAGATACAAG
1 GATTCACCGTTGCGACTTAAATCTTTCCCTTCTTAT-CTTCGTG-G-TAC-TG
*** *
13928 G-TTTGTCGTTGCGACTTAAATCTTTCCCTCCATTATCTTCGTGGTACTG
1 GATTCACCGTTGCGACTTAAATCTTTCCCTTC-TTATCTTCGTGGTACTG
**** ** * * * *
13977 GATTTGTTGTCACGGCTTAAAAT-TTTCCC-TC-CATGCTTCTTGGTATTG
1 GATTCACCGTTGCGACTT-AAATCTTTCCCTTCTTAT-CTTCGTGGTACTG
*
14025 GATTCACCGTTGC-AGCTTAAATCTTTCCCTTCATTATCTTCGTGGTACTA
1 GATTCACCGTTGCGA-CTTAAATCTTTCCCTTC-TTATCTTCGTGGTACTG
* * * *
14075 GATTTACCGTTGCGACTTAAATCTTTCCTTTCATGT-TTCGTGGTA
1 GATTCACCGTTGCGACTTAAATCTTTCCCTTCTTATCTTCGTGGTA
14120 ATGAAACTTG
Statistics
Matches: 192, Mismatches: 33, Indels: 36
0.74 0.13 0.14
Matches are distributed among these distances:
47 10 0.05
48 41 0.21
49 36 0.19
50 89 0.46
51 12 0.06
52 4 0.02
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (49 bp):
GATTCACCGTTGCGACTTAAATCTTTCCCTTCTTATCTTCGTGGTACTG
Found at i:13926 original size:99 final size:98
Alignment explanation
Indices: 13668--14109 Score: 382
Period size: 99 Copynumber: 4.5 Consensus size: 98
13658 GGCTATAATG
* *
13668 TCTTCGTGGTACTAGATTCGCCGTT--GTAGCTTAAATATTT-CCTTCCATGCTTTGAGGTACGA
1 TCTTCGTGGTACTAGATTCGCCGTTACG-A-CTTAAATCTTTCCCTT-CATGCTTTGAGGTACAA
* * *
13730 GGTTCGCCGTTGCGACTTAAACTTTTCCC--CATATA
63 GATTCACCGTTGCGACTTAAACCTTTCCCTTCAT-TA
* * * * * *
13765 TCTTC-TCGGTATTAGATTCGCCATTGC-AGCTTAAATCTTTTCCTCCATGTCTTTGGGGTACAA
1 TCTTCGT-GGTACTAGATTCGCCGTTACGA-CTTAAATCTTTCCCTTCATG-CTTTGAGGTACAA
* *
13828 GATTCATCGTTGCGACTTAAACCTTTCCCTTCGTTA
63 GATTCACCGTTGCGACTTAAACCTTTCCCTTCATTA
* * *
13864 TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTTCATGCTTCTGAGATACAAGG
1 TCTTCGTGGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATGCTT-TGAGGTACAAGA
*** * *
13929 TTTGTCGTTGCGACTTAAATCTTTCCCTCCATTA
65 TTCACCGTTGCGACTTAAACCTTTCCCTTCATTA
* * ** * * * * ***
13963 TCTTCGTGGTACTGGATTTGTTGTCACGGCTTAAAAT-TTTCCCTCCATGCTTCT-TGGTATTGG
1 TCTTCGTGGTACTAGATTCGCCGTTACGACTT-AAATCTTTCCCTTCATGCTT-TGAGGTACAAG
*
14026 ATTCACCGTTGC-AGCTTAAATCTTTCCCTTCATTA
64 ATTCACCGTTGCGA-CTTAAACCTTTCCCTTCATTA
** * *
14061 TCTTCGTGGTACTAGATTTACCGTTGCGACTTAAATCTTTCCTTTCATG
1 TCTTCGTGGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATG
14110 TTTCGTGGTA
Statistics
Matches: 282, Mismatches: 50, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
96 1 0.00
97 42 0.15
98 109 0.39
99 122 0.43
100 8 0.03
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (98 bp):
TCTTCGTGGTACTAGATTCGCCGTTACGACTTAAATCTTTCCCTTCATGCTTTGAGGTACAAGAT
TCACCGTTGCGACTTAAACCTTTCCCTTCATTA
Found at i:14071 original size:197 final size:193
Alignment explanation
Indices: 13668--14109 Score: 479
Period size: 197 Copynumber: 2.2 Consensus size: 193
13658 GGCTATAATG
* * *
13668 TCTTCGTGGTACTAGATTCGCCGTT-GTAGCTTAAATATTT-CCTTCCATGCTTTGAGGTACGAG
1 TCTTCGTGGTACTAGATTCGCCGTTCG-A-CTTAAATCTTTCCCTT-CATGCTTTGAGATACAAG
* *
13731 GTTCGCCGTTGCGACTTAAACTTTTCCCCATATATCTTCTCGGTATTAGATTCGCCATTGCAGCT
63 GTTCGCCGTTGCGACTTAAACTTTCCCCCATATATCTTCTCGGTACTAGATTCG-C-TTGCAGCT
* * *
13796 TAAATCTTTTCCTCCATGTCTTTGGGGTACAAGATTCATCGTTGCGACTTAAACCTTTCCCTTCG
126 TAAATCTTTCCCTCCATGTCTTTGGGGTACAAGATTCACCGTTGCGACTTAAACCTTTCCCTTCA
13861 TTA
191 TTA
*
13864 TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTTCATGCTTCTGAGATACAAGG
1 TCTTCGTGGTACTAGATTCGCCGTT-CGACTTAAATCTTTCCCTTCATGCTT-TGAGATACAAGG
* * * *
13929 TTTGTCGTTGCGACTTAAATCTTTCCCTCCAT-TATCTTCGT-GGTACTGGATTTG-TTGTCACG
64 TTCGCCGTTGCGACTTAAA-CTTTCCC-CCATATATCTTC-TCGGTACTAGATTCGCTTG-CA--
* *** *
13991 GCTTAAAAT-TTTCCCTCCATG-CTTCT-TGGTATTGGATTCACCGTTGC-AGCTTAAATCTTTC
123 GCTT-AAATCTTTCCCTCCATGTCTT-TGGGGTACAAGATTCACCGTTGCGA-CTTAAACCTTTC
14052 CCTTCATTA
185 CCTTCATTA
** *
14061 TCTTCGTGGTACTAGATTTACCGTTGCGACTTAAATCTTTCCTTTCATG
1 TCTTCGTGGTACTAGATTCGCCGTT-CGACTTAAATCTTTCCCTTCATG
14110 TTTCGTGGTA
Statistics
Matches: 210, Mismatches: 23, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
195 3 0.01
196 44 0.21
197 114 0.54
198 40 0.19
199 9 0.04
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (193 bp):
TCTTCGTGGTACTAGATTCGCCGTTCGACTTAAATCTTTCCCTTCATGCTTTGAGATACAAGGTT
CGCCGTTGCGACTTAAACTTTCCCCCATATATCTTCTCGGTACTAGATTCGCTTGCAGCTTAAAT
CTTTCCCTCCATGTCTTTGGGGTACAAGATTCACCGTTGCGACTTAAACCTTTCCCTTCATTA
Found at i:14568 original size:18 final size:18
Alignment explanation
Indices: 14541--14577 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
14531 AACAATTGCC
*
14541 AAATACTTACAAGGAACA
1 AAATAATTACAAGGAACA
14559 AAATAATTACAAGGAACA
1 AAATAATTACAAGGAACA
14577 A
1 A
14578 TATTAGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (18 bp):
AAATAATTACAAGGAACA
Found at i:19366 original size:15 final size:15
Alignment explanation
Indices: 19346--19383 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
19336 CAGACTTATG
19346 TCTTCTTTGGATCGC
1 TCTTCTTTGGATCGC
19361 TCTTCTTTGGATCGC
1 TCTTCTTTGGATCGC
19376 TCTTCTTT
1 TCTTCTTT
19384 AGGCGCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.26, G:0.16, T:0.53
Consensus pattern (15 bp):
TCTTCTTTGGATCGC
Found at i:27236 original size:13 final size:13
Alignment explanation
Indices: 27220--27253 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27210 AAATTTTATT
27220 TTATTTTTATTTA
1 TTATTTTTATTTA
* *
27233 TTATTATTATTTT
1 TTATTTTTATTTA
27246 TTATTTTT
1 TTATTTTT
27254 TGGGTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTTATTTA
Found at i:27657 original size:20 final size:21
Alignment explanation
Indices: 27619--27657 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
27609 ATTAGAAAAT
*
27619 AAAACAATTTGAATTTATTTA
1 AAAACAATTTGAATATATTTA
*
27640 AAAAC-ATTTTAATATATT
1 AAAACAATTTGAATATATT
27658 AATATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (21 bp):
AAAACAATTTGAATATATTTA
Found at i:40590 original size:191 final size:192
Alignment explanation
Indices: 40258--40608 Score: 542
Period size: 191 Copynumber: 1.8 Consensus size: 192
40248 TTCTCCAAAG
* * *
40258 GCACCAAAATAAAACGTAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCTACAAAAAGCATTGC
1 GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
* * * * * *
40323 ACACAATGTTTTTGAGTAGATGCTTTCAAATATATTCTTTAATTCAAGAATGAAGTAATTACATA
66 ACACAATGTGTTTGAGTAAATACTCTCAAATATATTCTTTAATTCAAGAATAAAGTAATTACAAA
*
40388 TGAAATGCGAAGGTTCTATTTATAGTTAAGCTCTCTCGGAAGATGATAATTCTCATGAAAAT
131 TGAAATGCGAAGGCTCTATTTATAGTTAAGCTCTCTCGGAAGATGATAATTCTCATGAAAAT
* * * *
40450 GCACCAAAATAAAATGAAAGCAAGCTCAAAGCGAAAGAACT-AAAAAAGCCACAAAAAGTAATGC
1 GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
* *
40514 ACACAATGTGTTTGAGTAAATACTCTCAAATATTTTCTTTAATTCAAGAATAAAGTGATTACAAA
66 ACACAATGTGTTTGAGTAAATACTCTCAAATATATTCTTTAATTCAAGAATAAAGTAATTACAAA
*
40579 TGAAGTGCGAAGGCTCTATTTATAGTTAAG
131 TGAAATGCGAAGGCTCTATTTATAGTTAAG
40609 TTCACTCAGA
Statistics
Matches: 142, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
191 105 0.74
192 37 0.26
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (192 bp):
GCACCAAAATAAAACGAAAGCAAACTCAAAACGAAAGAACTAAAAAAAGCCACAAAAAGCAATGC
ACACAATGTGTTTGAGTAAATACTCTCAAATATATTCTTTAATTCAAGAATAAAGTAATTACAAA
TGAAATGCGAAGGCTCTATTTATAGTTAAGCTCTCTCGGAAGATGATAATTCTCATGAAAAT
Found at i:40988 original size:16 final size:16
Alignment explanation
Indices: 40967--41005 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40957 TTTTGGTTCC
40967 TAATCTAAATTTGGGT
1 TAATCTAAATTTGGGT
40983 TAATCTAAATTTGGGT
1 TAATCTAAATTTGGGT
40999 TAATCTA
1 TAATCTA
41006 TTTGCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (16 bp):
TAATCTAAATTTGGGT
Found at i:43681 original size:18 final size:18
Alignment explanation
Indices: 43656--43698 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
43646 TTATATTCAG
*
43656 TTTT-TTTTTCTTTTA-T
1 TTTTATTTTTCTTCTAGT
43672 ATTTTATTTTTCTTCTAGT
1 -TTTTATTTTTCTTCTAGT
43691 TTTTATTT
1 TTTTATTT
43699 GCCTTTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTCTTCTAGT
Found at i:44234 original size:2 final size:2
Alignment explanation
Indices: 44229--44267 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44219 TAGCCATCAA
44229 AT AT AT AT 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 AT AT AT AT A
44268 AAAAGTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48843 original size:54 final size:53
Alignment explanation
Indices: 48784--48888 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 53
48774 TGAACTTGAT
*
48784 ATTTTTCCTAATTTGTTATCTAAATTTGTTTTTACCCAATTTGGTACCTTGACA
1 ATTTTTCCTAATTTGTTACCTAAATTTGTTTTTACCCAATTTGGTA-CTTGACA
* * *
48838 ATTTTTCTTAATTTGTTACCTAAATTTTTTTTTATCCAATTTGGTACTTGA
1 ATTTTTCCTAATTTGTTACCTAAATTTGTTTTTACCCAATTTGGTACTTGA
48889 ACTTGGTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.24, C:0.14, G:0.09, T:0.53
Consensus pattern (53 bp):
ATTTTTCCTAATTTGTTACCTAAATTTGTTTTTACCCAATTTGGTACTTGACA
Found at i:48868 original size:26 final size:26
Alignment explanation
Indices: 48785--48869 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
48775 GAACTTGATA
*
48785 TTTTTCCTAATTTGTTATCTAAATTT
1 TTTTTCCTAATTTGTTACCTAAATTT
* * ** ***
48811 GTTTTTACCCAATTTGGTACCTTGACAA
1 -TTTTT-CCTAATTTGTTACCTAAATTT
*
48839 TTTTTCTTAATTTGTTACCTAAATTT
1 TTTTTCCTAATTTGTTACCTAAATTT
48865 TTTTT
1 TTTTT
48870 TATCCAATTT
Statistics
Matches: 41, Mismatches: 16, Indels: 3
0.68 0.27 0.05
Matches are distributed among these distances:
26 18 0.44
27 10 0.24
28 13 0.32
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.56
Consensus pattern (26 bp):
TTTTTCCTAATTTGTTACCTAAATTT
Found at i:48879 original size:28 final size:27
Alignment explanation
Indices: 48785--48880 Score: 65
Period size: 28 Copynumber: 3.5 Consensus size: 27
48775 GAACTTGATA
*
48785 TTTTTCCTAATTTGTTATCTAAATTTGTT
1 TTTTTCC-AATTTGTTACCTAAATTT-TT
** *
48814 TTTACCCAATTTGGTACCTTGACAA--TTT
1 TTTTTCCAATTTGTTACC-T-A-AATTTTT
*
48842 TTCTT--AATTTGTTACCTAAATTTTT
1 TTTTTCCAATTTGTTACCTAAATTTTT
48867 TTTTATCCAATTTG
1 TTTT-TCCAATTTG
48881 GTACTTGAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 17
0.66 0.12 0.22
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 7 0.14
26 11 0.22
28 19 0.38
29 7 0.14
30 1 0.02
31 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (27 bp):
TTTTTCCAATTTGTTACCTAAATTTTT
Done.