Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001569.1 Kokia drynarioides strain JFW-HI SEQ_113169, 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: 19180
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:1976 original size:24 final size:24
Alignment explanation
Indices: 1949--1994 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1939 TCTTATAATT
*
1949 CATAAAAAAAAAACTTTCTTTTTG
1 CATAAAAAAAAAACTATCTTTTTG
*
1973 CATAAAAAGAAAACTATCTTTT
1 CATAAAAAAAAAACTATCTTTT
1995 ATTTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (24 bp):
CATAAAAAAAAAACTATCTTTTTG
Found at i:3201 original size:30 final size:30
Alignment explanation
Indices: 3167--3231 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
3157 ACTTATTTTA
** *
3167 TTGTTAATTTTGTTTTTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
3197 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
3227 TTGTT
1 TTGTT
3232 TGTTAAGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGACAT
Found at i:3242 original size:30 final size:30
Alignment explanation
Indices: 3183--3246 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
3173 ATTTTGTTTT
* **
3183 TATTTTAGAGGCATTTGTTAATTTTGTTAC
1 TATTTTAGAGACATTTGTTAATTAAGTTAC
**
3213 TATTTTAGAGACATTTGTTTGTTAAGTTAC
1 TATTTTAGAGACATTTGTTAATTAAGTTAC
3243 -ATTT
1 TATTT
3247 ATCTTAGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (30 bp):
TATTTTAGAGACATTTGTTAATTAAGTTAC
Found at i:3826 original size:40 final size:40
Alignment explanation
Indices: 3782--3860 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
3772 AAAGCAATGG
* *
3782 CGGCGTTTTTTCA-AATATGCCACAAAAGGTAAAGAAATAA
1 CGGCGTTTTCTCATAA-ACGCCACAAAAGGTAAAGAAATAA
* *
3822 CGGCGTTTTCTCATAAACGTCACAAAAGGTAAAGCAATA
1 CGGCGTTTTCTCATAAACGCCACAAAAGGTAAAGAAATA
3861 GCAGCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (40 bp):
CGGCGTTTTCTCATAAACGCCACAAAAGGTAAAGAAATAA
Found at i:3916 original size:21 final size:21
Alignment explanation
Indices: 3890--3931 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3880 GCCGCAAAAA
3890 GTAAGAGCATTAGCGGCGTTT
1 GTAAGAGCATTAGCGGCGTTT
3911 GTAAGAGCATTAGCGGCGTTT
1 GTAAGAGCATTAGCGGCGTTT
3932 ATGACAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (21 bp):
GTAAGAGCATTAGCGGCGTTT
Found at i:3964 original size:62 final size:61
Alignment explanation
Indices: 3850--3972 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 61
3840 GTCACAAAAG
*
3850 GTAAAGCAATAGCAGCATTTATGAGAAAACGCCGCAAAAAGTAAGAGCATTAGCGGCGTTT
1 GTAAAGCAATAGCAGCATTTATGACAAAACGCCGCAAAAAGTAAGAGCATTAGCGGCGTTT
* * * * *
3911 GTAAGAGCATTAGCGGCGTTTATGACAAAACGCCGCAAAAGGTAAGAGTATTAGCGGCGTTT
1 GTAA-AGCAATAGCAGCATTTATGACAAAACGCCGCAAAAAGTAAGAGCATTAGCGGCGTTT
3973 ATGATAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
61 4 0.07
62 51 0.93
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (61 bp):
GTAAAGCAATAGCAGCATTTATGACAAAACGCCGCAAAAAGTAAGAGCATTAGCGGCGTTT
Found at i:3968 original size:41 final size:41
Alignment explanation
Indices: 3911--4003 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
3901 AGCGGCGTTT
*
3911 GTAAGAGCATTAGCGGCGTTTATGACAAAACGCCGCAAAAG
1 GTAAGAGTATTAGCGGCGTTTATGACAAAACGCCGCAAAAG
*
3952 GTAAGAGTATTAGCGGCGTTTATGATAAAACGCCGCAAAAG
1 GTAAGAGTATTAGCGGCGTTTATGACAAAACGCCGCAAAAG
*
3993 GTAATAGTATT
1 GTAAGAGTATT
4004 GCTTCATCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (41 bp):
GTAAGAGTATTAGCGGCGTTTATGACAAAACGCCGCAAAAG
Found at i:4469 original size:13 final size:13
Alignment explanation
Indices: 4449--4481 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4439 GGTTAACAAA
4449 ATAATAAAATTAAG
1 ATAATAAAA-TAAG
4463 A-AATAAAATAAG
1 ATAATAAAATAAG
4475 ATAATAA
1 ATAATAA
4482 TTAATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 12 0.67
14 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
ATAATAAAATAAG
Found at i:5284 original size:83 final size:84
Alignment explanation
Indices: 5150--5317 Score: 232
Period size: 83 Copynumber: 2.0 Consensus size: 84
5140 TAACCTTTAG
* ** *
5150 CGGTGTTTATGAGAAAAACACTGCAATAGGTAAAGAGCATTAGCGGTGTTTTACCCATAAACGCT
1 CGGTGTTTATGAGAAAAACACTGCAATAGGTAAAGAGCATAAGCGACGTTTTACCCATAAACGCC
*
5215 ACTAAAGGTTAAGCAATAA
66 ACTAAAAGTTAAGCAATAA
* ** *
5234 CGGTGTTTATGAGAAAATGC-C-GCAATAGGTAAAGAGCATAAGCGACGTTTTTTCCATAAATGC
1 CGGTGTTTATGAGAAAA-ACACTGCAATAGGTAAAGAGCATAAGCGACGTTTTACCCATAAACGC
5297 CACTAAAAGTTAAGCAATAA
65 CACTAAAAGTTAAGCAATAA
5317 C
1 C
5318 AGCGTTTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
83 55 0.74
84 18 0.24
85 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (84 bp):
CGGTGTTTATGAGAAAAACACTGCAATAGGTAAAGAGCATAAGCGACGTTTTACCCATAAACGCC
ACTAAAAGTTAAGCAATAA
Found at i:6908 original size:56 final size:55
Alignment explanation
Indices: 6846--7033 Score: 198
Period size: 56 Copynumber: 3.4 Consensus size: 55
6836 GATTTTGAAG
* *
6846 AAAAAAATTTGGTGTTGGCCAATGCTTGGTTGACACCACCTTTTTGATCAGATAAA
1 AAAAAAATTTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTAATCAGAT-AA
* ** * * ** * *
6902 AAAAAAACTTGGTGTTGGCC-ATGCATTAATCAACACTAGTATTTTTTATCTGATAA
1 AAAAAAATTTGGTGTTGGCCAATGC-TTGGTCGACACCA-CCTTTTTAATCAGATAA
* * **
6958 AAAAAATTTTGGTATTGGTTAATGCTTGGTCGACACCACCTTTTTAATCAGATAA
1 AAAAAAATTTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTAATCAGATAA
*
7013 AAAAAATTTTGGTGTTGGCCA
1 AAAAAAATTTGGTGTTGGCCA
7034 TCTATTGGCC
Statistics
Matches: 103, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
55 35 0.34
56 53 0.51
57 15 0.15
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (55 bp):
AAAAAAATTTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTAATCAGATAA
Found at i:8808 original size:20 final size:20
Alignment explanation
Indices: 8785--8829 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8775 ATTTTCGAAT
*
8785 TTTTTAAAATATTTTTTCTA
1 TTTTTAAAATATTTTTTATA
** *
8805 TTTTCGAAATGTTTTTTATA
1 TTTTTAAAATATTTTTTATA
8825 TTTTT
1 TTTTT
8830 GAATTTTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTAAAATATTTTTTATA
Found at i:8873 original size:24 final size:23
Alignment explanation
Indices: 8821--8877 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
8811 AAATGTTTTT
8821 TATATTTTTGAATTTTTTAACAA
1 TATATTTTTGAATTTTTTAACAA
8844 TAATATTTTTGAAATACTTTTT-AC-A
1 T-ATATTTTTG-AAT--TTTTTAACAA
8869 TATATTTTT
1 TATATTTTT
8878 TATATTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 17 0.57
25 5 0.17
26 2 0.07
27 5 0.17
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATTTTTGAATTTTTTAACAA
Found at i:8896 original size:20 final size:20
Alignment explanation
Indices: 8873--8915 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
8863 TTTACATATA
*
8873 TTTTTTATATTTTCGAATTT
1 TTTTTTAGATTTTCGAATTT
*
8893 TTTTTTAGCTTTTCGAATTT
1 TTTTTTAGATTTTCGAATTT
8913 TTT
1 TTT
8916 AAAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTTTTAGATTTTCGAATTT
Found at i:8950 original size:35 final size:36
Alignment explanation
Indices: 8908--8977 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
8898 TAGCTTTTCG
8908 AATTTTTTAAA-AT-TATTTTTATATCTTCGAAATGA
1 AATTTTTTAAATATAT-TTTTTATATCTTCGAAATGA
* *
8943 AATTTTTTACATATATTTTTTATATTTTCGAAATG
1 AATTTTTTAAATATATTTTTTATATCTTCGAAATG
8978 GTTTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 10 0.32
36 20 0.65
37 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (36 bp):
AATTTTTTAAATATATTTTTTATATCTTCGAAATGA
Found at i:10104 original size:7 final size:6
Alignment explanation
Indices: 10074--10236 Score: 80
Period size: 6 Copynumber: 27.7 Consensus size: 6
10064 GGATCTACTC
*
10074 AATTTT GATTTCT AA-TTT AA-TTT ATATTTT AA-TTT AATTTCT AATTTT
1 AATTTT AATTT-T AATTTT AATTTT A-ATTTT AATTTT AATTT-T AATTTT
* *
10122 --GTTT ATATTTT AA-TTT AATTTCT AA-TTT CA-TTT ATATTTT AA-TTT
1 AATTTT A-ATTTT AATTTT AATTT-T AATTTT AATTTT A-ATTTT AATTTT
* * *
10167 AATTTCT AA-TTT CATTTT TATTTT AA-TTT AATTTCT AA-TTT CATTTT
1 AATTT-T AATTTT AATTTT AATTTT AATTTT AATTT-T AATTTT AATTTT
* * *
10214 TATTTT AAATTT CATTTCT AATT
1 AATTTT AATTTT AATTT-T AATT
10237 ATTATTTTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
4 3 0.02
5 36 0.30
6 50 0.41
7 33 0.27
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:10117 original size:29 final size:29
Alignment explanation
Indices: 10081--10236 Score: 249
Period size: 29 Copynumber: 5.3 Consensus size: 29
10071 CTCAATTTTG
*
10081 ATTTCTAATTTAATTTATATTTTAATTTA
1 ATTTCTAATTTCATTTATATTTTAATTTA
**
10110 ATTTCTAATTTTGTTTATATTTTAATTTA
1 ATTTCTAATTTCATTTATATTTTAATTTA
10139 ATTTCTAATTTCATTTATATTTTAATTTA
1 ATTTCTAATTTCATTTATATTTTAATTTA
*
10168 ATTTCTAATTTCATTTTTATTTTAATTTA
1 ATTTCTAATTTCATTTATATTTTAATTTA
* *
10197 ATTTCTAATTTCATTTTTATTTTAAATTTC
1 ATTTCTAATTTCATTTATATTTT-AATTTA
10227 ATTTCTAATT
1 ATTTCTAATT
10237 ATTATTTTTT
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 105 0.88
30 15 0.12
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTCTAATTTCATTTATATTTTAATTTA
Found at i:10236 original size:12 final size:11
Alignment explanation
Indices: 10128--10218 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
10118 TTTTGTTTAT
*
10128 ATTTTAATTTA
1 ATTTTAATTTC
10139 ATTTCTAATTTC
1 ATTT-TAATTTC
*
10151 A-TTTATATTTT
1 ATTTTA-ATTTC
*
10162 AATTTAATTTC
1 ATTTTAATTTC
* * *
10173 TAATTTCATTTTT
1 --ATTTTAATTTC
*
10186 ATTTTAATTTA
1 ATTTTAATTTC
10197 ATTTCTAATTTC
1 ATTT-TAATTTC
*
10209 ATTTTTATTT
1 ATTTTAATTT
10219 TAAATTTCAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
10 2 0.03
11 32 0.52
12 21 0.34
13 7 0.11
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTAATTTC
Found at i:10869 original size:31 final size:31
Alignment explanation
Indices: 10831--10919 Score: 151
Period size: 31 Copynumber: 2.9 Consensus size: 31
10821 TTGTCGCTTC
10831 ACATGACAGTATATAATTCAACTCCGACAAT
1 ACATGACAGTATATAATTCAACTCCGACAAT
* *
10862 ACATGACAATATATAATTCAACTCCGGCAAT
1 ACATGACAGTATATAATTCAACTCCGACAAT
*
10893 ACATGAAAGTATATAATTCAACTCCGA
1 ACATGACAGTATATAATTCAACTCCGA
10920 AATTCGATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (31 bp):
ACATGACAGTATATAATTCAACTCCGACAAT
Found at i:11209 original size:60 final size:58
Alignment explanation
Indices: 11075--11464 Score: 407
Period size: 59 Copynumber: 6.6 Consensus size: 58
11065 GAAAAGAGAG
* * *
11075 AAAGTTGGTGTC-AGCCAATGCATGACCAACACAAAAAAAAATTATTTTTTTATCTGATTAAA
1 AAAGGTGGTGTCGA-CCAATGCATGACCAACAC-CAAAAAAATT-TTTTTTTATCAGA-T-AA
* * * * * *
11137 AAAGGTGATGTCGGCCAATGCATGGCTAACACCAAAAAAATTGTTTTTTTTTCTGATAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATT-TTTTTTTATCAGATAA
* * * **
11196 AAAGGGTGGTGTCGATCAATACATGACCAATA-CAAAAAAATTCATTTTTATCAGATAAA
1 AAA-GGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTTTTTTTATCAGAT-AA
*
11255 AAAGGTGGTGTCG-CCAATGCATGGCCAACACCAAAAAAATTTATTTTTTTATCAGATAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAA-TT-TTTTTTTATCAGATAA
*
11314 AAAGGTGGTGTCGACCAATGCATGGCCAACACC---AAAATTTTTTTTTATCAGATAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTTTTTTTATCAGATAA
* * * * * *
11369 ATAAAGTGGTGTCGATCAA-GTATTGACCAACACCAAAAAAAATATTTTTTATCTGATAA
1 A-AAGGTGGTGTCGACCAATGCA-TGACCAACACCAAAAAAATTTTTTTTTATCAGATAA
* *
11428 AAAGGTGGTGTCAACCAATGCATGACCAACACTAAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAA
11465 TTTGAGGAGG
Statistics
Matches: 278, Mismatches: 37, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
55 19 0.07
56 27 0.10
57 17 0.06
58 56 0.20
59 59 0.21
60 53 0.19
61 21 0.08
62 26 0.09
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (58 bp):
AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTTTTTTTATCAGATAA
Found at i:11262 original size:58 final size:60
Alignment explanation
Indices: 11075--11464 Score: 412
Period size: 58 Copynumber: 6.6 Consensus size: 60
11065 GAAAAGAGAG
* * * *
11075 AAAGTTGGTGTC-AGCCAATGCATGACCAACACAAAAAAAAATTATTTTTTTATCTGATTAAA
1 AAAGGTGGTGTCGA-CCAATGCATGACCAACACCAAAAAAATTTA-TTTTTTATCAGA-TAAA
* * * * * *
11137 AAAGGTGATGTCGGCCAATGCATGGCTAACACCAAAAAAATTGT-TTTTTTTTCTGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATT-TATTTTTTATCAGATAAA
* * * * *
11197 AAGGGTGGTGTCGATCAATACATGACCAATA-CAAAAAAATTCA-TTTTTATCAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTATTTTTTATCAGATAAA
*
11255 AAAGGTGGTGTCG-CCAATGCATGGCCAACACCAAAAAAATTTATTTTTTTATCAGAT-AA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTA-TTTTTTATCAGATAAA
*
11314 AAAGGTGGTGTCGACCAATGCATGGCCAACACC---AAAATTT-TTTTTTATCAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTATTTTTTATCAGATAAA
* * * *
11370 TAAA-GTGGTGTCGATCAA-GTATTGACCAACACCAAAAAAA-ATATTTTTTATCTGAT-AA
1 -AAAGGTGGTGTCGACCAATGCA-TGACCAACACCAAAAAAATTTATTTTTTATCAGATAAA
* *
11428 AAAGGTGGTGTCAACCAATGCATGACCAACACTAAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAA
11465 TTTGAGGAGG
Statistics
Matches: 278, Mismatches: 34, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
55 15 0.05
56 25 0.09
57 26 0.09
58 65 0.23
59 43 0.15
60 58 0.21
61 11 0.04
62 34 0.12
63 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (60 bp):
AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAAAAATTTATTTTTTATCAGATAAA
Found at i:11291 original size:117 final size:113
Alignment explanation
Indices: 11075--11456 Score: 412
Period size: 117 Copynumber: 3.3 Consensus size: 113
11065 GAAAAGAGAG
* *
11075 AAAGTTGGTGTC-AGCCAATGCATGACCAACACAAAAAAAAATTATTTTTTTATCTGATTAAAAA
1 AAAGGTGGTGTCGA-CCAATGCATGACCAA-AC--AAAAAAATTA--TTTTTATCAGA-TAAAAA
* *
11139 AGGTGATGTCGGCCAATGCATGGCTAACACCAAAAAAATTGTTTTTTTTTCTGATAA
59 AGGTGGTGTC-GCCAATGCATGGCCAACACCAAAAAAATT-TTTTTTTTTCTGATAA
* *
11196 AAAGGGTGGTGTCGATCAATACATGACCAATACAAAAAAATTCATTTTTATCAGATAAAAAAGGT
1 AAA-GGTGGTGTCGACCAATGCATGACCAA-ACAAAAAAATT-ATTTTTATCAGATAAAAAAGGT
*
11261 GGTGTCGCCAATGCATGGCCAACACCAAAAAAATTTATTTTTTTATCAGATAA
63 GGTGTCGCCAATGCATGGCCAACACCAAAAAAATTT-TTTTTTT-TCTGATAA
* * * *
11314 AAAGGTGGTGTCGACCAATGCATGGCC-AACACCAAAATTTTTTTTTATCAGATAAATAAA-GTG
1 AAAGGTGGTGTCGACCAATGCATGACCAAACA-AAAAAATTATTTTTATCAGATAAA-AAAGGTG
* * * * * *
11377 GTGTCGATCAA-GTATTGACCAACACCAAAAAAAATATTTTTTATCTGATAA
64 GTGTCG-CCAATGCA-TGGCCAACACCAAAAAAATTTTTTTTTTTCTGATAA
*
11428 AAAGGTGGTGTCAACCAATGCATGACCAA
1 AAAGGTGGTGTCGACCAATGCATGACCAA
11457 CACTAAAATT
Statistics
Matches: 228, Mismatches: 23, Indels: 26
0.82 0.08 0.09
Matches are distributed among these distances:
114 32 0.14
115 36 0.16
116 32 0.14
117 56 0.25
118 25 0.11
119 10 0.04
120 9 0.04
121 4 0.02
122 23 0.10
123 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (113 bp):
AAAGGTGGTGTCGACCAATGCATGACCAAACAAAAAAATTATTTTTATCAGATAAAAAAGGTGGT
GTCGCCAATGCATGGCCAACACCAAAAAAATTTTTTTTTTTCTGATAA
Found at i:13373 original size:20 final size:20
Alignment explanation
Indices: 13348--13398 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
13338 TGATATGGTC
*
13348 AGATTGCATTAAACAAAATG
1 AGATTGAATTAAACAAAATG
*
13368 AGATTGAATCAAACAAAATG
1 AGATTGAATTAAACAAAATG
13388 AGATTGAATTA
1 AGATTGAATTA
13399 TTTATGGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.25
Consensus pattern (20 bp):
AGATTGAATTAAACAAAATG
Found at i:13486 original size:22 final size:22
Alignment explanation
Indices: 13461--13506 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
13451 TATCTGACAC
*
13461 ATTGTTTGATTACAAGAAAATT
1 ATTGTTTAATTACAAGAAAATT
*
13483 ATTGTTTAATTACAAGAACATT
1 ATTGTTTAATTACAAGAAAATT
13505 AT
1 AT
13507 GAAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
ATTGTTTAATTACAAGAAAATT
Found at i:13769 original size:8 final size:8
Alignment explanation
Indices: 13756--13791 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
13746 ATAACCCAAA
13756 TATTTAAT
1 TATTTAAT
13764 TATTTAAT
1 TATTTAAT
*
13772 TATTTAAA
1 TATTTAAT
13780 TATTTAAT
1 TATTTAAT
13788 TATT
1 TATT
13792 AAAATCAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:13777 original size:16 final size:16
Alignment explanation
Indices: 13756--13796 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
13746 ATAACCCAAA
*
13756 TATTTAATTATTTAAT
1 TATTTAAATATTTAAT
13772 TATTTAAATATTTAAT
1 TATTTAAATATTTAAT
*
13788 TATTAAAAT
1 TATTTAAAT
13797 CAACCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAAATATTTAAT
Found at i:13812 original size:42 final size:42
Alignment explanation
Indices: 13764--13972 Score: 160
Period size: 42 Copynumber: 5.1 Consensus size: 42
13754 AATATTTAAT
13764 TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAA
1 TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAA
**
13806 TATTTAATTCA---AAATATTTAATTATT----T-AA---TTA
1 TATTTAATT-ATTTAAATATTTAATTATTAAAATCAACCCAAA
* * *
13838 TATTTAATTAAATTAAAT-TTTAATTATTAAAAACAACCCAAG
1 TATTTAATT-ATTTAAATATTTAATTATTAAAATCAACCCAAA
13880 TATTTAATTATTT-AATAATTTAATTATTAAAAAT-AACCCAAAA
1 TATTTAATTATTTAAAT-ATTTAATTATT-AAAATCAACCC-AAA
* * *
13923 TTTAATTTAAAATATTTAATTATTTAATTATTAAAAACAACCCAAA
1 --T-ATTT-AATTATTTAAATATTTAATTATTAAAATCAACCCAAA
13969 -ATTT
1 TATTT
13973 TTTCCTAATA
Statistics
Matches: 132, Mismatches: 13, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
32 11 0.08
34 10 0.08
35 6 0.05
36 1 0.01
39 2 0.02
40 18 0.14
41 3 0.02
42 37 0.28
43 7 0.05
45 1 0.01
46 11 0.08
47 23 0.17
48 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (42 bp):
TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAA
Found at i:13924 original size:25 final size:25
Alignment explanation
Indices: 13896--13972 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
13886 ATTATTTAAT
13896 AATTTAATTATTAAAAATAACCCAA
1 AATTTAATTATTAAAAATAACCCAA
***
13921 AATTTAA-T-TT-AAAAT-ATTTAA
1 AATTTAATTATTAAAAATAACCCAA
* *
13942 TTATTTAATTATTAAAAACAACCCAA
1 -AATTTAATTATTAAAAATAACCCAA
13968 AATTT
1 AATTT
13973 TTTCCTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
21 3 0.08
22 11 0.29
23 3 0.08
24 3 0.08
25 15 0.39
26 3 0.08
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTTAATTATTAAAAATAACCCAA
Found at i:13942 original size:47 final size:45
Alignment explanation
Indices: 13856--13972 Score: 159
Period size: 47 Copynumber: 2.6 Consensus size: 45
13846 TAAATTAAAT
* *
13856 TTTAATTATTAAAAACAACCC--AA-GTATTTAATTATTTAATAA
1 TTTAATTATTAAAAACAACCCAAAATTTATTTAAATATTTAATAA
* *
13898 TTTAATTATTAAAAATAACCCAAAATTTAATTTAAAATATTTAATTA
1 TTTAATTATTAAAAACAACCCAAAATTT-ATTT-AAATATTTAATAA
13945 TTTAATTATTAAAAACAACCCAAAATTT
1 TTTAATTATTAAAAACAACCCAAAATTT
13973 TTTCCTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
42 20 0.31
44 2 0.03
45 1 0.02
46 4 0.06
47 38 0.58
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (45 bp):
TTTAATTATTAAAAACAACCCAAAATTTATTTAAATATTTAATAA
Found at i:13973 original size:115 final size:116
Alignment explanation
Indices: 13764--13973 Score: 293
Period size: 115 Copynumber: 1.8 Consensus size: 116
13754 AATATTTAAT
13764 TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAATATTTAATTCAAAATATTTAATT
1 TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAATATTTAATTCAAAATATTTAATT
** ** **
13829 ATTTAATTATATTTAATTAAATTAAATTTTAATTATTAAAAACAACCCAAG
66 ATTTAATTATATAAAAACAAACAAAATTTTAATTATTAAAAACAACCCAAG
*
13880 TATTTAATTATTT-AATAATTTAATTATTAAAAAT-AACCCAAA-ATTTAATTTAAAATATTTAA
1 TATTTAATTATTTAAAT-ATTTAATTATT-AAAATCAACCCAAATATTTAATTCAAAATATTTAA
*
13942 TTATTTAATTAT-TAAAAACAACCCAAAATTTT
64 TTATTTAATTATATAAAAACAA-ACAAAATTTT
13974 TTCCTAATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
114 5 0.06
115 41 0.49
116 32 0.39
117 5 0.06
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (116 bp):
TATTTAATTATTTAAATATTTAATTATTAAAATCAACCCAAATATTTAATTCAAAATATTTAATT
ATTTAATTATATAAAAACAAACAAAATTTTAATTATTAAAAACAACCCAAG
Found at i:16368 original size:27 final size:27
Alignment explanation
Indices: 16324--16421 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
16314 TGAGGAGTAA
* * *
16324 TCTGATTTTGGGTCGAAAGAGCGTTAT
1 TCTGATTCTGGCTCGAAAGAGCATTAT
*
16351 TCTGATTCTGGCTTGAAAGAGCATTAT
1 TCTGATTCTGGCTCGAAAGAGCATTAT
*
16378 TCTGATTCTGGGCTCGTAAGAGCATTAT
1 TCTGATTCT-GGCTCGAAAGAGCATTAT
16406 TCTGATTCTGGGCTCG
1 TCTGATTCT-GGCTCG
16422 CAATAGCTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
27 32 0.50
28 32 0.50
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (27 bp):
TCTGATTCTGGCTCGAAAGAGCATTAT
Found at i:16400 original size:28 final size:28
Alignment explanation
Indices: 16324--16421 Score: 146
Period size: 28 Copynumber: 3.6 Consensus size: 28
16314 TGAGGAGTAA
* *
16324 TCTGATTTTGGG-TCGAAAGAGCGTTAT
1 TCTGATTCTGGGCTCGAAAGAGCATTAT
*
16351 TCTGATTCT-GGCTTGAAAGAGCATTAT
1 TCTGATTCTGGGCTCGAAAGAGCATTAT
*
16378 TCTGATTCTGGGCTCGTAAGAGCATTAT
1 TCTGATTCTGGGCTCGAAAGAGCATTAT
16406 TCTGATTCTGGGCTCG
1 TCTGATTCTGGGCTCG
16422 CAATAGCTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.03
27 30 0.47
28 32 0.50
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (28 bp):
TCTGATTCTGGGCTCGAAAGAGCATTAT
Found at i:18445 original size:14 final size:15
Alignment explanation
Indices: 18423--18456 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18413 AACATTCAAC
18423 ACAAAGTCCAA-ATT
1 ACAAAGTCCAAGATT
*
18437 ACAATGTCCAAGATT
1 ACAAAGTCCAAGATT
18452 ACAAA
1 ACAAA
18457 ATAGCCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (15 bp):
ACAAAGTCCAAGATT
Done.