Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006807.1 Kokia drynarioides strain JFW-HI SEQ_121406, 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: 15962
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:64 original size:17 final size:17
Alignment explanation
Indices: 44--128 Score: 82
Period size: 17 Copynumber: 4.8 Consensus size: 17
34 TTCATTTTGG
44 GTTTAAATTTAATTTAA
1 GTTTAAATTTAATTTAA
**
61 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
* *
81 GTTTAAATTTAAATCAA
1 GTTTAAATTTAATTTAA
*
98 GTTTAAATTTAAATTGAA
1 GTTTAAATTT-AATTTAA
116 -TTTAAATTTAATT
1 GTTTAAATTTAATT
129 AAAAGGTCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.07
17 28 0.50
18 9 0.16
19 6 0.11
20 9 0.16
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:65 original size:11 final size:11
Alignment explanation
Indices: 45--128 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
35 TCATTTTGGG
45 TTTAAATTTAA
1 TTTAAATTTAA
*
56 TTTAAGTTTAAA
1 TTTAAATTT-AA
***
68 CTTTTCTTTTAAA
1 -TTTAAATTT-AA
81 GTTTAAATTTAA
1 -TTTAAATTTAA
* * *
93 ATCAAGTTTAAA
1 TTTAAATTT-AA
*
105 TTTAAATTGAA
1 TTTAAATTTAA
116 TTTAAATTTAA
1 TTTAAATTTAA
127 TT
1 TT
129 AAAAGGTCCA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
11 28 0.52
12 11 0.20
13 15 0.28
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:128 original size:5 final size:6
Alignment explanation
Indices: 45--126 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
35 TCATTTTGGG
* ***
45 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTCT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
* * *
94 -TCAAG TTTAAA TTTAAA -TTGAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
127 TTAAAAGGTC
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
5 12 0.21
6 36 0.63
7 9 0.16
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:2132 original size:29 final size:29
Alignment explanation
Indices: 2094--2293 Score: 152
Period size: 30 Copynumber: 6.8 Consensus size: 29
2084 TTTGAGCCCT
* *
2094 AACTTCTCCAAAATTATATTTTTAATCACG
1 AACTT-TCCAAAATTACATTTTTAACCACG
* *
2124 AACTTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCC-AAAATTACATTTTTAACCACG
* * * *
2154 AACTTTCCAAAATTCCATTTTTGACCTCA
1 AACTTTCCAAAATTACATTTTTAACCACG
* * * *
2183 AACCTTCAAAAAATTACATTTTTACCCCCG
1 AACTTTC-CAAAATTACATTTTTAACCACG
* * *
2213 AACTTTCCAAGATT-CTATTTTTGACCTCG
1 AACTTTCCAAAATTAC-ATTTTTAACCACG
** * *
2242 ATTTTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCC-AAAATTACATTTTTAACCACG
* *
2272 AAC-TTCAAAAATTACGTTTTTA
1 AACTTTCCAAAATTACATTTTTA
2294 CCCTCAAACT
Statistics
Matches: 135, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
28 15 0.11
29 50 0.37
30 69 0.51
31 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTTAACCACG
Found at i:2163 original size:59 final size:59
Alignment explanation
Indices: 2065--2285 Score: 250
Period size: 59 Copynumber: 3.8 Consensus size: 59
2055 GTGGTCCCTA
* * * * * *
2065 AACTGTCCAAAAATTATATTTTGAGCCCT--AACTTCTCCAAAATTATATTTTTAATCACG
1 AACTTTCCAAAAATTACATTTTTA-CCCTCGAACTT-TCCAAAATTATATTTTTGACCTCG
** *
2124 AACTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCA
1 AACTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTATATTTTTGACCTCG
* * * * *
2183 AACCTTCAAAAAATTACATTTTTACCCCCGAACTTTCCAAGATTCTATTTTTGACCTCG
1 AACTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTATATTTTTGACCTCG
** *
2242 ATTTTTCCAAAAATTACATTTTTACCCTCGAAC-TTCAAAAATTA
1 AACTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTA
2286 CGTTTTTACC
Statistics
Matches: 137, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
58 12 0.09
59 120 0.88
60 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
AACTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTATATTTTTGACCTCG
Found at i:2383 original size:85 final size:86
Alignment explanation
Indices: 2157--2439 Score: 283
Period size: 85 Copynumber: 3.3 Consensus size: 86
2147 ACCCTCGAAC
* * * *
2157 TTTCC-AAAATTCCATTTTTGA-CCTCAAACCTTCAAAAAATTACATTTTTACCCCCGAACTT-T
1 TTTCCAAAAATTACATTTTT-ACCCTCAAA-CTTC-AAAAATTACGTTTTTACCCTCAAACTTCT
* * * *
2219 CCAAGATTCTATTTTTGACCTCGATT
63 -TAAAATTCCA-TTTTGACCTCCATT
* *
2245 TTTCCAAAAATTACATTTTTACCCTCGAACTTCAAAAATTACGTTTTTACCCTCAAACTTCTTAC
1 TTTCCAAAAATTACATTTTTACCCTCAAACTTCAAAAATTACGTTTTTACCCTCAAACTTCTTAA
2310 AATTCCATTTTGACC-CCATT
66 AATTCCATTTTGACCTCCATT
* * * * *
2330 TTT-TAAAAATTACCTTTTTACCCTCAAACTTTCGAAAATTATGTTTTTACCCTCGAACTTCTTA
1 TTTCCAAAAATTACATTTTTACCCTCAAAC-TTCAAAAATTACGTTTTTACCCTCAAACTTCTTA
* *
2394 AAATTCCATTTTTTACC-CTGATT
65 AAATTCCA-TTTTGACCTC-CATT
*
2417 TTTCCCAAAATTACA-TTTTACCC
1 TTTCCAAAAATTACATTTTTACCC
2440 CCGAATGTCT
Statistics
Matches: 166, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
84 23 0.14
85 45 0.27
86 16 0.10
87 44 0.27
88 19 0.11
89 19 0.11
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (86 bp):
TTTCCAAAAATTACATTTTTACCCTCAAACTTCAAAAATTACGTTTTTACCCTCAAACTTCTTAA
AATTCCATTTTGACCTCCATT
Found at i:2409 original size:30 final size:29
Alignment explanation
Indices: 2122--2412 Score: 168
Period size: 29 Copynumber: 10.0 Consensus size: 29
2112 TTTTTAATCA
* *
2122 CGAACTTTCCAAAAATTACATTTTTACCCT
1 CGAAC-TTCTAAAAATTCCATTTTTACCCT
*
2152 CGAACTT-TCCAAAATTCCATTTTTGA-CCT
1 CGAACTTCT-AAAAATTCCATTTTT-ACCCT
* * * *
2181 CAAACCTTCAAAAAATTACATTTTTACCCC
1 CGAA-CTTCTAAAAATTCCATTTTTACCCT
* * *
2211 CGAACTT-TCCAAGATTCTATTTTTGA-CCT
1 CGAACTTCT-AAAAATTCCATTTTT-ACCCT
** * *
2240 CGATTTTTCCAAAAATTACATTTTTACCCT
1 CGA-ACTTCTAAAAATTCCATTTTTACCCT
* *
2270 CGAACTTC-AAAAATTACGTTTTTACCCT
1 CGAACTTCTAAAAATTCCATTTTTACCCT
* * * *
2298 CAAACTTCTTACAATTCCATTTTGACCC-
1 CGAACTTCTAAAAATTCCATTTTTACCCT
** *
2326 C-ATTTTTTAAAAATTACC-TTTTTACCCT
1 CGAACTTCTAAAAATT-CCATTTTTACCCT
* * ***
2354 CAAACTT-TCGAAAATTATGTTTTTACCCT
1 CGAACTTCT-AAAAATTCCATTTTTACCCT
*
2383 CGAACTTCTTAAAATTCCATTTTTTACCCT
1 CGAACTTCTAAAAATTCCA-TTTTTACCCT
2413 GATTTTTCCC
Statistics
Matches: 196, Mismatches: 47, Indels: 36
0.70 0.17 0.13
Matches are distributed among these distances:
27 17 0.09
28 31 0.16
29 90 0.46
30 58 0.30
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (29 bp):
CGAACTTCTAAAAATTCCATTTTTACCCT
Found at i:2454 original size:85 final size:86
Alignment explanation
Indices: 2133--2444 Score: 280
Period size: 87 Copynumber: 3.6 Consensus size: 86
2123 GAACTTTCCA
* ** * *
2133 AAAATTACATTTTT-ACCCTCGAACTTTCC-AAAATTCCATTTTTGA-CCTCAAACCTTCAAAAA
1 AAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACA-TTTT-ACCCTCGAA-CTTC-AAAA
** * *
2195 ATTACATTTTTACCCCCGAACTT-TCC
61 ATTATGTTTTTACCCTCGAACTTCT-T
* *
2221 AAGATTCTATTTTTGA-CCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTCAAAAATT
1 AAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACA-TTTTACCCTCGAACTTCAAAAATT
* *
2285 ACGTTTTTACCCTCAAACTTCTT
64 ATGTTTTTACCCTCGAACTTCTT
* * * * * *
2308 ACAATTCCA-TTTTGACCC-CATTTTT-TAAAAATTACCTTTTTACCCTCAAACTTTCGAAAATT
1 AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTA-CATTTTACCCTCGAAC-TTCAAAAATT
2370 ATGTTTTTACCCTCGAACTTCTT
64 ATGTTTTTACCCTCGAACTTCTT
* * *
2393 AAAATTCCATTTTTTACCCTGATTTTTCCCAAAATTACATTTTACCCCCGAA
1 AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACATTTTACCCTCGAA
2445 TGTCTAAATT
Statistics
Matches: 185, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
84 21 0.11
85 45 0.24
86 14 0.08
87 50 0.27
88 35 0.19
89 20 0.11
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (86 bp):
AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACATTTTACCCTCGAACTTCAAAAATTAT
GTTTTTACCCTCGAACTTCTT
Found at i:2462 original size:85 final size:86
Alignment explanation
Indices: 2133--2463 Score: 254
Period size: 85 Copynumber: 3.8 Consensus size: 86
2123 GAACTTTCCA
* ** * *
2133 AAAATTACATTTTT-ACCCTCGAACTTTCC-AAAATTCCATTTTTGA-CCTCAAACCTTCAAAAA
1 AAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACA-TTTT-ACCCTCGAA-CTTC-AAAA
* *
2195 ATTAC-ATTTTTACCCCCGAACTT-TCC
61 ATT-CTATTTTTACCCTCGAACTTCT-T
* *
2221 AAGATTCTATTTTTGA-CCTCGATTTTTCCAAAAATTACATTTTTACCCTCGAACTTCAAAAATT
1 AAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACA-TTTTACCCTCGAACTTCAAAAATT
* *
2285 AC-GTTTTTACCCTCAAACTTCTT
64 -CTATTTTTACCCTCGAACTTCTT
* * * * * *
2308 ACAATTCCA-TTTTGACCC-CATTTTT-TAAAAATTACCTTTTTACCCTCAAACTTTCGAAAATT
1 AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTA-CATTTTACCCTCGAAC-TTCAAAAATT
* *
2370 ATGTTTTTACCCTCGAACTTCTT
64 CTATTTTTACCCTCGAACTTCTT
* * * *
2393 AAAATTCCATTTTTTACCCTGATTTTTCCCAAAATTACATTTTACCCCCGAA-TGTC-TAAATTC
1 AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACATTTTACCCTCGAACT-TCAAAAATTC
2456 TATTTTTA
65 TATTTTTA
2464 ACTCGAAACT
Statistics
Matches: 199, Mismatches: 32, Indels: 27
0.77 0.12 0.10
Matches are distributed among these distances:
84 21 0.11
85 57 0.29
86 16 0.08
87 50 0.25
88 35 0.18
89 20 0.10
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (86 bp):
AAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACATTTTACCCTCGAACTTCAAAAATTCT
ATTTTTACCCTCGAACTTCTT
Found at i:2862 original size:97 final size:98
Alignment explanation
Indices: 2756--2950 Score: 236
Period size: 97 Copynumber: 2.0 Consensus size: 98
2746 AAAAACTTTA
* * * * *
2756 AAATCGAGGCAATA-TTCTTTTAT-TTCGAGTTTTGACAATTTGTGCCTTAACTTACTAGGCACG
1 AAATCGAGGCAATATTTC-TTTATCTTCGA-TTCTGAAAATTTCTACCTAAACTTACTAGGCACG
*
2819 A-TTTTTCTTCAAATCG-GAATAATCGAATATCCTT
64 ACTTTTTCTTCAAATCGAG-ATAATCGAACATCCTT
* * **
2853 AAATCGAGGCAATGTTTCTTTATCTTTGATTCTGAAAATTTCTACCTAAACTTACTAGGTGCGAC
1 AAATCGAGGCAATATTTCTTTATCTTCGATTCTGAAAATTTCTACCTAAACTTACTAGGCACGAC
*
2918 TTTTTCTTTAAATCGAGATAATCGAACATCCTT
66 TTTTTCTTCAAATCGAGATAATCGAACATCCTT
2951 TTCAAAAGTG
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
97 46 0.55
98 36 0.43
99 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (98 bp):
AAATCGAGGCAATATTTCTTTATCTTCGATTCTGAAAATTTCTACCTAAACTTACTAGGCACGAC
TTTTTCTTCAAATCGAGATAATCGAACATCCTT
Found at i:14227 original size:49 final size:49
Alignment explanation
Indices: 14152--14715 Score: 489
Period size: 49 Copynumber: 11.5 Consensus size: 49
14142 CTATAGGTCT
*
14152 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* **
14201 CAGTACCACGAAGACATGAAGCGAAAGATCTAAGCTGCAACAACGGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* * ** *
14250 CAGTACCAC-AAGGACATGAAGGGAAATATTTAAGCCACAACGACGGATC
1 CAGTACCACGAA-GACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* * *
14299 CAGTACCACGAGGACATGAAGGGAAAGATCTAAG-TCGTAACTGCGGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCT-GCAACGGCGGATC
** * * * ** *
14348 CAGTACCACGAAGACACAAAGGGAAAGATTTCAG-TCGCAATGATGAATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCT-GCAACGGCGGATC
* * * * *
14397 CAGTACCACGAGGACATGAAGGGAAATATCTAAGCCGCAATGGCAGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* ** * * * *
14446 CAATACCACGAAGACACAAAGGGAAAGATTTAAGCTGCAACAGCGAATT
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* * * *
14495 GAGTACCACGAGGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* * * * * *
14544 TAGTACCACGAAAACACG-AGGGAAAGGT-TAAG-TCGCAATGGC-GAAC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCT-GCAACGGCGGATC
* * *
14590 CTAGTACCTCAC-AGAGACATGAAGGGAAAGATCTAAGCCGTAATGGCGGATC
1 C-AGTA-C-CACGA-AGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* ** * ** * *
14642 CAGTACCACAAAGACATGAAAAGAAAGATTTAAGCCACAACGGTGAATC
1 CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
* * *
14691 TAGTACCGCGAAGACA-CAAGGGAAA
1 CAGTACCACGAAGACATGAAGGGAAA
14716 AGATTAAAGA
Statistics
Matches: 408, Mismatches: 93, Indels: 29
0.77 0.18 0.05
Matches are distributed among these distances:
46 3 0.01
47 14 0.03
48 19 0.05
49 341 0.84
50 12 0.03
51 15 0.04
52 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (49 bp):
CAGTACCACGAAGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATC
Found at i:14325 original size:98 final size:98
Alignment explanation
Indices: 14152--14683 Score: 554
Period size: 98 Copynumber: 5.4 Consensus size: 98
14142 CTATAGGTCT
* * * * * *
14152 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCACGAAGACA
1 CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACGACGGATCCAGTACCACGAGGACA
* * **
14217 TGAAGCGAAAGATCTAAGCTGCAACAACGGATC
66 TGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* * *
14250 CAGTACCAC-AAGGACATGAAGGGAAATATTTAAGCCACAACGACGGATCCAGTACCACGAGGAC
1 CAGTACCACGAA-GACACGAAGGGAAAGATTTAAGCCGCAACGACGGATCCAGTACCACGAGGAC
* * *
14314 ATGAAGGGAAAGATCTAAGTCGTAACTGCGGATC
65 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* * * * * *
14348 CAGTACCACGAAGACACAAAGGGAAAGATTTCAGTCGCAATGATGAATCCAGTACCACGAGGACA
1 CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACGACGGATCCAGTACCACGAGGACA
* * *
14413 TGAAGGGAAATATCTAAGCCGCAATGGCAGATC
66 TGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* * * * **
14446 CAATACCACGAAGACACAAAGGGAAAGATTTAAGCTGCAAC-AGCGAATTGAGTACCACGAGGAC
1 CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACGA-CGGATCCAGTACCACGAGGAC
*
14510 ATGAAGGGAAAGATCTAAGCCGCAACGACGGATC
65 ATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* * * * * * *
14544 TAGTACCACGAAAACACG-AGGGAAAG-GTTAAGTCGCAATGGC-GAACCTAGTACCTCAC-AGA
1 CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACGACGGATCC-AGTA-C-CACGAG-
* *
14605 GACATGAAGGGAAAGATCTAAGCCGTAATGGCGGATC
62 GACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* * ** *
14642 CAGTACCACAAAGACATGAAAAGAAAGATTTAAGCCACAACG
1 CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACG
14684 GTGAATCTAG
Statistics
Matches: 358, Mismatches: 66, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
95 1 0.00
96 14 0.04
97 13 0.04
98 312 0.87
99 8 0.02
100 10 0.03
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (98 bp):
CAGTACCACGAAGACACGAAGGGAAAGATTTAAGCCGCAACGACGGATCCAGTACCACGAGGACA
TGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
Found at i:14419 original size:147 final size:145
Alignment explanation
Indices: 14152--14676 Score: 556
Period size: 147 Copynumber: 3.6 Consensus size: 145
14142 CTATAGGTCT
*
14152 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCACGAAGACA
1 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACTGCGGATCCAGTACCACGAAGACA
* * *
14217 TGAAGCGAAAGATCTAAGCTGCAACAACGGATCCAGTACCACAAGGACATGAAGGGAAATATTTA
66 TGAAGGGAAAGATCTAAGC-GCAACGACGGATCCAGTACCACGAGGACATGAAGGGAAATATTTA
* * *
14282 AGCCACAACGACGGATC
130 AGCCGCAATGGC-GATC
*
14299 CAGTACCACGAGGACATGAAGGGAAAGATCTAAG-TCGTAACTGCGGATCCAGTACCACGAAGAC
1 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCT-GCAACTGCGGATCCAGTACCACGAAGAC
** * * * * * *
14363 ACAAAGGGAAAGATTTCAGTCGCAATGATGAATCCAGTACCACGAGGACATGAAGGGAAATATCT
65 ATGAAGGGAAAGATCTAAG-CGCAACGACGGATCCAGTACCACGAGGACATGAAGGGAAATATTT
14428 AAGCCGCAATGGCAGATC
129 AAGCCGCAATGGC-GATC
* * ** * * * ** *
14446 CAATACCACGAAGACACAAAGGGAAAGATTTAAGCTGCAACAGCGAATTGAGTACCACGAGGACA
1 CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACTGCGGATCCAGTACCACGAAGACA
* ** * **
14511 TGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGAAAACACG-AGGGAAA-GGTTA
66 TGAAGGGAAAGATCTAAG-CGCAACGACGGATCCAGTACCACGAGGACATGAAGGGAAATATTTA
* *
14574 AGTCGCAATGGCGAAC
130 AGCCGCAATGGCGATC
* * *
14590 CTAGTACCTCAC-AGAGACATGAAGGGAAAGATCTAAGCCGTAA-TGGCGGATCCAGTACCACAA
1 C-AGTA-C-CACGAG-GACATGAAGGGAAAGATCTAAGCTGCAACT-GCGGATCCAGTACCACGA
** *
14653 AGACATGAAAAGAAAGATTTAAGC
61 AGACATGAAGGGAAAGATCTAAGC
14677 CACAACGGTG
Statistics
Matches: 309, Mismatches: 61, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
144 4 0.01
145 16 0.05
146 11 0.04
147 276 0.89
148 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (145 bp):
CAGTACCACGAGGACATGAAGGGAAAGATCTAAGCTGCAACTGCGGATCCAGTACCACGAAGACA
TGAAGGGAAAGATCTAAGCGCAACGACGGATCCAGTACCACGAGGACATGAAGGGAAATATTTAA
GCCGCAATGGCGATC
Found at i:15120 original size:17 final size:17
Alignment explanation
Indices: 15100--15184 Score: 82
Period size: 17 Copynumber: 4.8 Consensus size: 17
15090 TTCATTTTGG
15100 GTTTAAATTTAATTTAA
1 GTTTAAATTTAATTTAA
**
15117 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
* *
15137 GTTTAAATTTAAATCAA
1 GTTTAAATTTAATTTAA
*
15154 GTTTAAATTTAAATTGAA
1 GTTTAAATTT-AATTTAA
15172 -TTTAAATTTAATT
1 GTTTAAATTTAATT
15185 AAAAGGTCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.07
17 28 0.50
18 9 0.16
19 6 0.11
20 9 0.16
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:15121 original size:11 final size:11
Alignment explanation
Indices: 15101--15184 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
15091 TCATTTTGGG
15101 TTTAAATTTAA
1 TTTAAATTTAA
*
15112 TTTAAGTTTAAA
1 TTTAAATTT-AA
***
15124 CTTTTCTTTTAAA
1 -TTTAAATTT-AA
15137 GTTTAAATTTAA
1 -TTTAAATTTAA
* * *
15149 ATCAAGTTTAAA
1 TTTAAATTT-AA
*
15161 TTTAAATTGAA
1 TTTAAATTTAA
15172 TTTAAATTTAA
1 TTTAAATTTAA
15183 TT
1 TT
15185 AAAAGGTCCA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
11 28 0.52
12 11 0.20
13 15 0.28
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:15184 original size:5 final size:6
Alignment explanation
Indices: 15101--15182 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
15091 TCATTTTGGG
* ***
15101 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTCT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
* * *
15150 -TCAAG TTTAAA TTTAAA -TTGAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15183 TTAAAAGGTC
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
5 12 0.21
6 36 0.63
7 9 0.16
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Done.