Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013660.1 Kokia drynarioides strain JFW-HI SEQ_128688, 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: 90146
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:1934 original size:20 final size:20
Alignment explanation
Indices: 1909--1948 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1899 ATTCCACTAC
1909 TAAACCAATTAACAATCGAA
1 TAAACCAATTAACAATCGAA
1929 TAAACCAATTAACAATCGAA
1 TAAACCAATTAACAATCGAA
1949 ATTATATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAACCAATTAACAATCGAA
Found at i:2056 original size:39 final size:39
Alignment explanation
Indices: 2012--2149 Score: 128
Period size: 39 Copynumber: 3.6 Consensus size: 39
2002 ATTATTATTA
2012 ATTTATATTATTTGTTATTAATATTAAGTAATTAATAAT
1 ATTTATATTATTTGTTATTAATATTAAGTAATTAATAAT
* * *
2051 CTTTATATTA--AGTAATTAATATATTAAGTAATTAATAAT
1 ATTTATATTATTTGTTATT-A-ATATTAAGTAATTAATAAT
* *
2090 ATTTATATTAATATT-ATATTTATATTAA-TAATTAAT-AT
1 ATTTATATT-AT-TTGTTATTAATATTAAGTAATTAATAAT
* *
2128 ATTTTTA-TATTT-ATATTAATAT
1 ATTTATATTATTTGTTATTAATAT
2150 ATTTCGATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
35 11 0.13
36 2 0.02
37 6 0.07
38 9 0.11
39 44 0.53
40 8 0.10
42 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (39 bp):
ATTTATATTATTTGTTATTAATATTAAGTAATTAATAAT
Found at i:2076 original size:8 final size:8
Alignment explanation
Indices: 2054--2152 Score: 70
Period size: 8 Copynumber: 12.8 Consensus size: 8
2044 TAATAATCTT
2054 TATATTAA
1 TATATTAA
2062 GTA-ATTAA
1 -TATATTAA
2070 TATATTAA
1 TATATTAA
2078 GTA-ATTAA
1 -TATATTAA
2086 TAATATT--
1 T-ATATTAA
2093 TATATTAA
1 TATATTAA
*
2101 TAT-TATATT
1 TATAT-TA-A
2110 TATATTAA
1 TATATTAA
2118 TA-ATTAA
1 TATATTAA
**
2125 TATATTTT
1 TATATTAA
2133 TATATT--
1 TATATTAA
2139 TATATTAA
1 TATATTAA
2147 TATATT
1 TATATT
2153 TCGATTTAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
6 11 0.15
7 12 0.16
8 38 0.51
9 12 0.16
10 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (8 bp):
TATATTAA
Found at i:2089 original size:23 final size:21
Alignment explanation
Indices: 2027--2148 Score: 69
Period size: 23 Copynumber: 5.7 Consensus size: 21
2017 TATTATTTGT
2027 TATTAAT-ATTAAGTAATTAATAA
1 TATTAATAATTAA-TAATT-AT-A
* *
2050 TCTTTAT-ATTAAGTAATTAATA
1 TATTAATAATTAA-TAATT-ATA
*
2072 TATTAAGTAATTAATAATATTTA
1 TATTAA-TAATTAATAAT-TATA
2095 TATTAAT-ATT-AT-ATT-TA
1 TATTAATAATTAATAATTATA
*
2112 TATTAATAATTAATATATTTTTA
1 TATTAATAATTAATA-A-TTATA
*
2135 TATTTAT-ATTAATA
1 TATTAATAATTAATA
2149 TATTTCGATT
Statistics
Matches: 84, Mismatches: 6, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.11
18 4 0.05
19 4 0.05
20 2 0.02
21 4 0.05
22 15 0.18
23 40 0.48
24 6 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTAATAATTAATAATTATA
Found at i:2103 original size:6 final size:6
Alignment explanation
Indices: 2086--2149 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
2076 AAGTAATTAA
* * *
2086 TAATAT TTATAT TAATAT T-ATAT TTATAT TAATAAT TAATA- T-ATTT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAAT-AT TAATAT TAATAT
* *
2132 TTATAT TTATAT TAATAT
1 TAATAT TAATAT TAATAT
2150 ATTTCGATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.15
6 33 0.69
7 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TAATAT
Found at i:2108 original size:17 final size:17
Alignment explanation
Indices: 2088--2149 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
2078 GTAATTAATA
2088 ATATTTATATTAATATT
1 ATATTTATATTAATATT
2105 ATATTTATATTAATAATT
1 ATATTTATATTAAT-ATT
2123 A-A--TATATT--T-TT
1 ATATTTATATTAATATT
2134 ATATTTATATTAATAT
1 ATATTTATATTAATAT
2150 ATTTCGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 1 0.03
14 6 0.16
15 6 0.16
16 1 0.03
17 16 0.42
18 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATATTAATATT
Found at i:2118 original size:29 final size:29
Alignment explanation
Indices: 2086--2149 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2076 AAGTAATTAA
2086 TAATATTT-ATATTAATATTATATTTATAT
1 TAATATTTAATA-TAATATTATATTTATAT
* * *
2115 TAATAATTAATATATTTTTATATTTATAT
1 TAATATTTAATATAATATTATATTTATAT
2144 TAATAT
1 TAATAT
2150 ATTTCGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATATTTAATATAATATTATATTTATAT
Found at i:2194 original size:12 final size:12
Alignment explanation
Indices: 2177--2310 Score: 51
Period size: 12 Copynumber: 10.3 Consensus size: 12
2167 TATATTTCTA
2177 TATTATTTATTT
1 TATTATTTATTT
2189 TATTATTCTATCTAT
1 TATTATT-TAT-T-T
2204 TATTATATTATCTAT
1 TATTAT-TTAT-T-T
2219 TATTATATTATTCT
1 TATTAT-TTATT-T
* *
2233 TATAATATTATTA
1 TATTAT-TTATTT
2246 TA-TATATTATTAT
1 TATTAT-TTATT-T
**
2259 T-TTATTTA-AA
1 TATTATTTATTT
**
2269 TATTATTTAAAT
1 TATTATTTATTT
*
2281 TATTATTTCTATT
1 TATTATTTAT-TT
2294 TAGTTA-TTATTT
1 TA-TTATTTATTT
2306 ATATT
1 -TATT
2311 TAGTCTATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
10 1 0.01
11 7 0.07
12 31 0.31
13 17 0.17
14 17 0.17
15 25 0.25
16 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:2195 original size:15 final size:15
Alignment explanation
Indices: 2177--2312 Score: 61
Period size: 15 Copynumber: 8.9 Consensus size: 15
2167 TATATTTCTA
2177 TATTATTTATTTTAT
1 TATTATTTATTTTAT
* *
2192 TA-T-TCTA-TCTAT
1 TATTATTTATTTTAT
*
2204 TATTATATTA-TCTAT
1 TATTAT-TTATTTTAT
2219 TATTATATTATTCTTAT
1 TATTAT-TTATT-TTAT
*
2236 AATATTA-TTATATATAT
1 --TATTATTTAT-TTTAT
* *
2253 TATTATTTTATTTAAA
1 TATTA-TTTATTTTAT
**
2269 TATTATTTAAATTAT
1 TATTATTTATTTTAT
*
2284 TATT-TCTA-TTTAGT
1 TATTATTTATTTTA-T
2298 TATTATTTATATTTA
1 TATTATTTAT-TTTA
2313 GTCTATTTAG
Statistics
Matches: 92, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
12 6 0.07
13 7 0.08
14 10 0.11
15 37 0.40
16 8 0.09
17 18 0.20
18 1 0.01
19 5 0.05
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (15 bp):
TATTATTTATTTTAT
Found at i:2274 original size:11 final size:12
Alignment explanation
Indices: 2260--2288 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2250 TATTATTATT
2260 TTATTTAAA-TA
1 TTATTTAAATTA
2271 TTATTTAAATTA
1 TTATTTAAATTA
2283 TTATTT
1 TTATTT
2289 CTATTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTAAATTA
Found at i:2275 original size:3 final size:3
Alignment explanation
Indices: 2177--2264 Score: 64
Period size: 3 Copynumber: 30.3 Consensus size: 3
2167 TATATTTCTA
*
2177 TAT TATT TAT T-T TAT TAT T-C TAT CTAT TAT TA- TAT TAT CTAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT
* *
2222 TA- TAT TAT TCT TA- TAA TAT TAT TA- TAT ATAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
2264 T
1 T
2265 TAAATATTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
2 13 0.19
3 44 0.64
4 12 0.17
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2302 original size:17 final size:17
Alignment explanation
Indices: 2238--2319 Score: 63
Period size: 17 Copynumber: 5.2 Consensus size: 17
2228 ATTCTTATAA
*
2238 TATTA-TTATATATA-T
1 TATTATTTATATTTAGT
**
2253 TATTATTT-TATTTAAA
1 TATTATTTATATTTAGT
2269 TATTATTTA-A---A-T
1 TATTATTTATATTTAGT
*
2281 TATTATTTCTATTTAGT
1 TATTATTTATATTTAGT
2298 TATTATTTATATTTAGT
1 TATTATTTATATTTAGT
2315 CTATT
1 -TATT
2320 TAGAATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
12 8 0.15
13 2 0.04
15 10 0.19
16 12 0.23
17 17 0.32
18 4 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTTATATTTAGT
Found at i:3519 original size:94 final size:94
Alignment explanation
Indices: 3344--3660 Score: 374
Period size: 94 Copynumber: 3.4 Consensus size: 94
3334 TTTGTATATT
* * *
3344 CTCGTCAGCTTAGTGTGAGCAACATCGT-TA--GAG-AATAGTTATATGCACAAATATCGTATCG
1 CTCGTCAGCTTAGTGTGAGCAACATCATATACTG-GTAATAGTTATATGCACAGATACCGTATCG
** * *
3405 ATGACTGATGTA-TCGTATATGTTGCGAATC
65 ATGGTTGAGGTACT-GCATATGTTGCGAATC
* * *
3435 CTCGTCAGCTTAGTGTGAGCAGCATCATATACTGGTAATAGTTATATGCATAGATACCGTATTGA
1 CTCGTCAGCTTAGTGTGAGCAACATCATATACTGGTAATAGTTATATGCACAGATACCGTATCGA
3500 TGGTTGAGGTACTGCATATGTTGCGAATC
66 TGGTTGAGGTACTGCATATGTTGCGAATC
* * * * **
3529 CTCGTCAGCTTAGTGTGAGCAACATCGTATACTGGTAACATTTATATGTACAGATACAATATCGA
1 CTCGTCAGCTTAGTGTGAGCAACATCATATACTGGTAATAGTTATATGCACAGATACCGTATCGA
* * * *
3594 TGGTTAAGGCACCGCATATGTTGCGAGTC
66 TGGTTGAGGTACTGCATATGTTGCGAATC
* * *
3623 CTCATCAGCTTAGTGTGAGCAATATCATATACTAGTAA
1 CTCGTCAGCTTAGTGTGAGCAACATCATATACTGGTAA
3661 CAGAAATGAC
Statistics
Matches: 194, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
91 26 0.13
92 2 0.01
93 1 0.01
94 164 0.85
95 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (94 bp):
CTCGTCAGCTTAGTGTGAGCAACATCATATACTGGTAATAGTTATATGCACAGATACCGTATCGA
TGGTTGAGGTACTGCATATGTTGCGAATC
Found at i:4454 original size:21 final size:21
Alignment explanation
Indices: 4428--4483 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
4418 TTGGAGTTTG
*
4428 TTGTATCGGTAGAAGTGATAA
1 TTGTATCGGTAGAAGTCATAA
* * * *
4449 TTGTATCGATGGTAGTCATAC
1 TTGTATCGGTAGAAGTCATAA
4470 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
4484 CCTTCCCAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAA
Found at i:4862 original size:21 final size:20
Alignment explanation
Indices: 4829--4867 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4819 GTATATGGTT
4829 TGATATGGAATATAGATGTCA
1 TGATATGGAATATA-ATGTCA
4850 TGATATGTG-ATATAATGT
1 TGATATG-GAATATAATGT
4868 TGATTCCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (20 bp):
TGATATGGAATATAATGTCA
Found at i:5845 original size:16 final size:16
Alignment explanation
Indices: 5824--5865 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5814 AGAACTTGCC
5824 ATTGTTGAAATTCCTT
1 ATTGTTGAAATTCCTT
5840 ATTGTTGAAATTCCTT
1 ATTGTTGAAATTCCTT
* *
5856 GTTCTTGAAA
1 ATTGTTGAAA
5866 ACTTTTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (16 bp):
ATTGTTGAAATTCCTT
Found at i:24947 original size:12 final size:12
Alignment explanation
Indices: 24930--24954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24920 AATGAATAGC
24930 ACCAAAATAGAT
1 ACCAAAATAGAT
24942 ACCAAAATAGAT
1 ACCAAAATAGAT
24954 A
1 A
24955 TGAGAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
ACCAAAATAGAT
Found at i:29757 original size:41 final size:41
Alignment explanation
Indices: 29706--29816 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
29696 AAGAAAAATT
* * *
29706 CCGCTAAAGGTCAGAGCATTAGCGGCTTTTATGAGAAAACG
1 CCGCTAAAGGTAAGAGCATTAGCGGCGTTTATGAAAAAACG
*
29747 CCGCTAAAGGTAAGAGCATTAACGGCGTTTATGAAAAAACG
1 CCGCTAAAGGTAAGAGCATTAGCGGCGTTTATGAAAAAACG
* *
29788 CCGCTAAAGATAAGAGCATTAGCAGCGTT
1 CCGCTAAAGGTAAGAGCATTAGCGGCGTT
29817 AATAGGAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (41 bp):
CCGCTAAAGGTAAGAGCATTAGCGGCGTTTATGAAAAAACG
Found at i:30682 original size:23 final size:23
Alignment explanation
Indices: 30656--30704 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
30646 TAAAAGATTT
*
30656 TATCAATTATAACATCCACGTCA
1 TATCAATTATAACATCAACGTCA
30679 TATCAATTATAACATCAACGTCA
1 TATCAATTATAACATCAACGTCA
30702 TAT
1 TAT
30705 AAACTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (23 bp):
TATCAATTATAACATCAACGTCA
Found at i:33773 original size:21 final size:21
Alignment explanation
Indices: 33747--33788 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33737 TAAAAACATG
*
33747 AAGAACATGGTCTTTAACGGC
1 AAGAACATAGTCTTTAACGGC
33768 AAGAACATAGTCTTTAACGGC
1 AAGAACATAGTCTTTAACGGC
33789 GTTTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (21 bp):
AAGAACATAGTCTTTAACGGC
Found at i:37297 original size:41 final size:41
Alignment explanation
Indices: 37233--37330 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 41
37223 GCAGCGTTTC
* * *
37233 CCCATAAATGTCGCTATTGCTTAA-CTTTTAGCAACATTTTT
1 CCCATAAACGTCGCTACTACTTAACCTTTT-GCAACATTTTT
* * ** *
37274 TCCATAAACGTCGCTGCTACTTAACCTTTTGCGGCGTTTTT
1 CCCATAAACGTCGCTACTACTTAACCTTTTGCAACATTTTT
*
37315 CCCATAAACATCGCTA
1 CCCATAAACGTCGCTA
37331 ATGCTCTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 40 0.89
42 5 0.11
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (41 bp):
CCCATAAACGTCGCTACTACTTAACCTTTTGCAACATTTTT
Found at i:40057 original size:40 final size:41
Alignment explanation
Indices: 39898--40113 Score: 125
Period size: 41 Copynumber: 5.3 Consensus size: 41
39888 GTTTATGGGA
* * ** *
39898 AAACGCCGCTATTGCT-TAACCTTTAGCGGCGTTTTTCTCAT
1 AAACGCCGCTAATGCTCTCACCTTTAGCGGC-ACTTTCTTAT
* * * * * *
39939 AAATGCCGTTAATGCTCTGACATTTAGCAGCA-TTTTTTCAT
1 AAACGCCGCTAATGCTCTCACCTTTAGCGGCACTTTCTT-AT
** * * * * * *
39980 -AACTGTTGCTATTACTCTAACATTTAGTGGCGCTTTCTTAT
1 AAAC-GCCGCTAATGCTCTCACCTTTAGCGGCACTTTCTTAT
*
40021 AAACGCCGCTAAT-CTCTCACCTTTAGCGGCACTTTCTCAT
1 AAACGCCGCTAATGCTCTCACCTTTAGCGGCACTTTCTTAT
* * * * ** *
40061 AAATGTCGCTAATGCTCTGATCTTTAGCGGCGTTTTTCCTAT
1 AAACGCCGCTAATGCTCTCACCTTTAGCGGC-ACTTTCTTAT
40103 AAACGCCGCTA
1 AAACGCCGCTA
40114 TTGATTTACC
Statistics
Matches: 130, Mismatches: 38, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
40 39 0.30
41 57 0.44
42 34 0.26
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCTCACCTTTAGCGGCACTTTCTTAT
Found at i:40087 original size:81 final size:83
Alignment explanation
Indices: 39914--40113 Score: 208
Period size: 81 Copynumber: 2.4 Consensus size: 83
39904 CGCTATTGCT
* * * * * * * *
39914 TAACCTTTAGCGGCGTTTTTCTCATAAATGCCGTTAATGCTCTGACATTTAGCAGCATTTTTTCA
1 TAACATTTAGCGGCGTCTTTCTTATAAACGCCGCTAATGCTCTCACATTTAGCAGCACTTTCTCA
* * *
39979 TAACTGTTGCTATTACTC
66 TAAATGTCGCTAATACTC
* * *
39997 TAACATTTAGTGGCG-CTTTCTTATAAACGCCGCTAAT-CTCTCACCTTTAGCGGCACTTTCTCA
1 TAACATTTAGCGGCGTCTTTCTTATAAACGCCGCTAATGCTCTCACATTTAGCAGCACTTTCTCA
*
40060 TAAATGTCGCTAATGCTC
66 TAAATGTCGCTAATACTC
* * *
40078 TGATC-TTTAGCGGCGTTTTTCCTATAAACGCCGCTA
1 T-AACATTTAGCGGCGTCTTTCTTATAAACGCCGCTA
40114 TTGATTTACC
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
81 45 0.47
82 38 0.40
83 13 0.14
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (83 bp):
TAACATTTAGCGGCGTCTTTCTTATAAACGCCGCTAATGCTCTCACATTTAGCAGCACTTTCTCA
TAAATGTCGCTAATACTC
Found at i:40917 original size:27 final size:27
Alignment explanation
Indices: 40883--40941 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
40873 CTAATGATAT
40883 ATGAACAAAAGTTTATAAATATAGTTC
1 ATGAACAAAAGTTTATAAATATAGTTC
40910 ATGAACAAAAGTTTATAAATATAGTTC
1 ATGAACAAAAGTTTATAAATATAGTTC
40937 ATGAA
1 ATGAA
40942 TGAGCTATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (27 bp):
ATGAACAAAAGTTTATAAATATAGTTC
Found at i:41563 original size:8 final size:8
Alignment explanation
Indices: 41550--41620 Score: 65
Period size: 8 Copynumber: 8.8 Consensus size: 8
41540 TATTTGGTCA
41550 AATTATTT
1 AATTATTT
41558 AATTATTT
1 AATTATTT
**
41566 AATTAATAAA
1 AATT-AT-TT
**
41576 AAAAATTT
1 AATTATTT
41584 AA-TATTT
1 AATTATTT
41591 AATTATTGT
1 AATTATT-T
41600 -ATTATTT
1 AATTATTT
41607 AATTATTT
1 AATTATTT
41615 AATTAT
1 AATTAT
41621 AAAAAACAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
7 7 0.14
8 37 0.73
9 5 0.10
10 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (8 bp):
AATTATTT
Found at i:41651 original size:26 final size:26
Alignment explanation
Indices: 41611--41668 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
41601 TTATTTAATT
*
41611 ATTTAATTATAAAAAACAACTCAAAA
1 ATTTAATTATAAAAAACAACCCAAAA
*
41637 ATTTAATTACT-AAAAACAACCCAAAT
1 ATTTAATTA-TAAAAAACAACCCAAAA
41663 ATTTAA
1 ATTTAA
41669 ATATTTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (26 bp):
ATTTAATTATAAAAAACAACCCAAAA
Found at i:48047 original size:43 final size:43
Alignment explanation
Indices: 47761--48040 Score: 384
Period size: 43 Copynumber: 6.5 Consensus size: 43
47751 AGAAAAATGT
* * * *
47761 CGCTAAAGACCATGTTCTTTAGCGGTGTTTGTAGGTAAAGTGC
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* * *
47804 CGCTAAAGACCATGTTCTTTAACGGTGTTTGTGGG-GAAGCGC
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* *
47846 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGGAAAGGGC
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
**
47889 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCAT
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* ** *
47932 CGCTAAAGACCATGTTTTTTAGCGATGTTTGTGGGAAAAGCAC
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* *
47975 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGAAAAACGC
1 CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
48018 CGCTACAA-ACCATGTTCTTTAGC
1 CGCTA-AAGACCATGTTCTTTAGC
48041 CACGTTTTTC
Statistics
Matches: 213, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 38 0.18
43 173 0.81
44 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (43 bp):
CGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGC
Found at i:53148 original size:21 final size:21
Alignment explanation
Indices: 53124--53194 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
53114 ATTTGTTTCA
*
53124 GTAGAAGAGTCACTTGTATTG
1 GTAGAAGTGTCACTTGTATTG
**
53145 GTAGATTTGTCACTTGTATCT-
1 GTAGAAGTGTCACTTGTAT-TG
*
53166 GTAGAACTGTCACTTGTATTG
1 GTAGAAGTGTCACTTGTATTG
53187 GTAGAAGT
1 GTAGAAGT
53195 TTGCACTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (21 bp):
GTAGAAGTGTCACTTGTATTG
Found at i:59144 original size:20 final size:20
Alignment explanation
Indices: 59102--59137 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
59092 GTTCAAATTC
59102 AAAATCAAAATAATAATAAT
1 AAAATCAAAATAATAATAAT
59122 AAAAT-AAAATAA-AATA
1 AAAATCAAAATAATAATA
59138 CTATAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATCAAAATAATAATAAT
Found at i:59291 original size:17 final size:17
Alignment explanation
Indices: 59269--59305 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
59259 GTTTTAATAA
59269 ATCAACATAACAATTAT
1 ATCAACATAACAATTAT
59286 ATCAACATAACAATTAT
1 ATCAACATAACAATTAT
59303 ATC
1 ATC
59306 GCAAAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
ATCAACATAACAATTAT
Found at i:60224 original size:7 final size:7
Alignment explanation
Indices: 60208--60268 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
60198 TCGAAAAAAG
*
60208 TCAACTA
1 TCAACGA
60215 TCAACGA
1 TCAACGA
60222 TCAACGA
1 TCAACGA
60229 TCAACTG-
1 TCAAC-GA
* *
60236 TCAATGG
1 TCAACGA
*
60243 TCAAAG-
1 TCAACGA
*
60249 TCAACGG
1 TCAACGA
60256 TCAACGA
1 TCAACGA
60263 TCAACG
1 TCAACG
60269 GTCGGTTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
6 6 0.13
7 39 0.85
8 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (7 bp):
TCAACGA
Found at i:60269 original size:14 final size:13
Alignment explanation
Indices: 60215--60271 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
60205 AAGTCAACTA
*
60215 TCAACGATCAACGA
1 TCAACG-TCAACGG
*
60229 TCAACTGTCAATGG
1 TCAAC-GTCAACGG
*
60243 TCAAAGTCAACGG
1 TCAACGTCAACGG
60256 TCAACGATCAACGG
1 TCAACG-TCAACGG
60270 TC
1 TC
60272 GGTTAACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 12 0.33
14 23 0.64
15 1 0.03
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (13 bp):
TCAACGTCAACGG
Found at i:65920 original size:2 final size:2
Alignment explanation
Indices: 65913--65948 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
65903 AGAATAAATC
* *
65913 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65949 GTAACATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:67375 original size:7 final size:7
Alignment explanation
Indices: 67313--67365 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
67303 TTTCGAAAAA
67313 GGTCAAC
1 GGTCAAC
*
67320 GATCAAC
1 GGTCAAC
*
67327 GGTCAAT
1 GGTCAAC
*
67334 GGTAAAC
1 GGTCAAC
*
67341 TGTCAAC
1 GGTCAAC
67348 GGTCAAC
1 GGTCAAC
67355 GGTCAAC
1 GGTCAAC
67362 GGTC
1 GGTC
67366 GGTCAACGGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (7 bp):
GGTCAAC
Found at i:76140 original size:17 final size:18
Alignment explanation
Indices: 76101--76139 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
76091 ATTATTTCTC
*
76101 AAAAGCACTTTTGATATA
1 AAAAGCACTTTTGAAATA
*
76119 AAAAGTACTTTTGAAATA
1 AAAAGCACTTTTGAAATA
76137 AAA
1 AAA
76140 GCATTGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (18 bp):
AAAAGCACTTTTGAAATA
Found at i:78380 original size:26 final size:25
Alignment explanation
Indices: 78346--78456 Score: 114
Period size: 26 Copynumber: 4.3 Consensus size: 25
78336 GGCTTGATTT
*
78346 GAGCAAATCTCTATCTGGGCTCGTAA
1 GAGCTAAT-TCTATCTGGGCTCGTAA
* * *
78372 GAGCTAATCTCTGTTTGGGCTCATAA
1 GAGCTAAT-TCTATCTGGGCTCGTAA
*
78398 GAGCTCAATTCTGTCTGGGCTCGTAA
1 GAGCT-AATTCTATCTGGGCTCGTAA
* * *
78424 TAACTAAATTCTATCTGGGCTCGTAT
1 GAGCT-AATTCTATCTGGGCTCGTAA
78450 GAGCTAA
1 GAGCTAA
78457 ACTTCTGTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
25 2 0.03
26 66 0.93
27 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTAATTCTATCTGGGCTCGTAA
Found at i:78443 original size:52 final size:53
Alignment explanation
Indices: 78359--78464 Score: 126
Period size: 52 Copynumber: 2.0 Consensus size: 53
78349 CAAATCTCTA
* * * *
78359 TCTGGGCTCGTAAGAGCTAATCTCTGTTTGGGCTCATAAGAGCTCAA-TTCTG
1 TCTGGGCTCGTAAGAACTAATCTCTATCTGGGCTCATAAGAGCTAAACTTCTG
* * *
78411 TCTGGGCTCGTAATAACTAAAT-TCTATCTGGGCTCGTATGAGCTAAACTTCTG
1 TCTGGGCTCGTAAGAACT-AATCTCTATCTGGGCTCATAAGAGCTAAACTTCTG
78464 T
1 T
78465 AATGACTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
52 36 0.80
53 9 0.20
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (53 bp):
TCTGGGCTCGTAAGAACTAATCTCTATCTGGGCTCATAAGAGCTAAACTTCTG
Found at i:80639 original size:22 final size:22
Alignment explanation
Indices: 80588--80631 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
80578 AAATTGGATC
*
80588 TAGGGTTTGGGTGATTTGGTTT
1 TAGGGTTTGGGTGATTGGGTTT
80610 TAGGGTTTGGGT-ATTGGGTTT
1 TAGGGTTTGGGTGATTGGGTTT
80631 T
1 T
80632 CGTGGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (22 bp):
TAGGGTTTGGGTGATTGGGTTT
Found at i:84685 original size:3 final size:3
Alignment explanation
Indices: 84677--84708 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
84667 CCCATAAGTT
84677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
84709 TTCCACTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:87073 original size:20 final size:20
Alignment explanation
Indices: 87037--87074 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
87027 TTTTTCGAAA
**
87037 AAAAAGTCAACGGTCAACCC
1 AAAAAGTCAACAATCAACCC
87057 AAAAAGTCAACAATCAAC
1 AAAAAGTCAACAATCAAC
87075 TATCAATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAGTCAACAATCAACCC
Found at i:87087 original size:21 final size:21
Alignment explanation
Indices: 87062--87105 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
87052 AACCCAAAAA
87062 GTCAACAATCAACT-ATCAATG
1 GTCAACAATCAA-TGATCAATG
**
87083 GTCAACGGTCAATGATCAATG
1 GTCAACAATCAATGATCAATG
87104 GT
1 GT
87106 TGGGTTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (21 bp):
GTCAACAATCAATGATCAATG
Found at i:87168 original size:21 final size:20
Alignment explanation
Indices: 87144--87187 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
87134 TTGAATTAGA
* *
87144 TTTAGGGTTTGGGTGATTTGG
1 TTTAAGGTTTGGGT-ATTGGG
87165 TTTAAGGTTTGGGTATTGGG
1 TTTAAGGTTTGGGTATTGGG
87185 TTT
1 TTT
87188 TCATGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (20 bp):
TTTAAGGTTTGGGTATTGGG
Done.