Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009704.1 Kokia drynarioides strain JFW-HI SEQ_124423, 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: 190543
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:4742 original size:20 final size:21
Alignment explanation
Indices: 4702--4743 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4692 TGTTGACTTT
*
4702 ATAATTTATTTTATATAAATA
1 ATAATTTATTCTATATAAATA
*
4723 ATAATTTA-TCTATTTAAATA
1 ATAATTTATTCTATATAAATA
4743 A
1 A
4744 AATATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTTATTCTATATAAATA
Found at i:8530 original size:43 final size:43
Alignment explanation
Indices: 8478--8561 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
8468 TTTTCTATTT
* * *
8478 AATTCTTTTATAAATATTTTTGCTATATAATTTTTTGTCACTTC
1 AATTCTTTTATAAATATATTTACTATATAATCTTTT-TCACTTC
*
8522 AATT-TTTTATAAATATATTTATTATATAATCTTTTTCACT
1 AATTCTTTTATAAATATATTTACTATATAATCTTTTTCACT
8562 CACATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 5 0.14
43 27 0.75
44 4 0.11
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (43 bp):
AATTCTTTTATAAATATATTTACTATATAATCTTTTTCACTTC
Found at i:15069 original size:23 final size:22
Alignment explanation
Indices: 15039--15111 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
15029 GCTTTTTTTT
15039 TTTTTTTTCTGTTTTGGTTGATA
1 TTTTTTTTCTGTTTTGGTTG-TA
15062 TTTTTTTTCTGTTTTTGAGTTGT-
1 TTTTTTTTCTG-TTTTG-GTTGTA
*
15085 TTTTTTTAT-TGTTTTGATTGCTA
1 TTTTTTT-TCTGTTTTGGTTG-TA
15108 TTTT
1 TTTT
15112 CGTGTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
21 3 0.07
22 6 0.14
23 24 0.55
24 7 0.16
25 4 0.09
ACGTcount: A:0.08, C:0.04, G:0.15, T:0.73
Consensus pattern (22 bp):
TTTTTTTTCTGTTTTGGTTGTA
Found at i:15158 original size:12 final size:12
Alignment explanation
Indices: 15096--15162 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
15086 TTTTTTATTG
*
15096 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
*
15109 TTTCG-TGTTAT
1 TTTTGTTGTTAT
15120 TTTT-TCTGTTAT
1 TTTTGT-TGTTAT
* * *
15132 TTTTATTGCTGT
1 TTTTGTTGTTAT
15144 TTTTGTTGTTAT
1 TTTTGTTGTTAT
15156 TTTTGTT
1 TTTTGTT
15163 ATTTGTAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 8 0.19
12 30 0.70
13 5 0.12
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:15166 original size:56 final size:56
Alignment explanation
Indices: 15106--15236 Score: 149
Period size: 56 Copynumber: 2.3 Consensus size: 56
15096 TTTTGATTGC
* * * *
15106 TATTTTCGTGTTATTTTTTCTGTTATTTTTATTGCTGTTTTTGTTGTTATTTTTGT
1 TATTTTAGTGTTATTTTTACTGTTATTTTTACTGCTGTTTTGGTTGTTATTTTTGT
* * *
15162 TATTTGTAATGTT-GTTTTACTGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTTGT
1 TATTT-TAGTGTTATTTTTACTGTTATTTTTACTGCTGTTTTGGTTGTTATTTTTGT
* *
15218 T-GTTTGGATGTTATTTTTA
1 TATTTTAG-TGTTATTTTTA
15237 TGCGTTTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
54 1 0.02
55 6 0.10
56 49 0.80
57 5 0.08
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.67
Consensus pattern (56 bp):
TATTTTAGTGTTATTTTTACTGTTATTTTTACTGCTGTTTTGGTTGTTATTTTTGT
Found at i:15178 original size:33 final size:32
Alignment explanation
Indices: 15121--15192 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
15111 TCGTGTTATT
* * **
15121 TTTTCTGTTATTTTTATTGCTGTTTTTGTTGTTA
1 TTTT-TGTTATTTGTAATGCTG-TTTTACTGTTA
*
15155 TTTTTGTTATTTGTAATGTTGTTTTACTGTTA
1 TTTTTGTTATTTGTAATGCTGTTTTACTGTTA
15187 TTTTTG
1 TTTTTG
15193 CTGCTGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 15 0.45
33 14 0.42
34 4 0.12
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.69
Consensus pattern (32 bp):
TTTTTGTTATTTGTAATGCTGTTTTACTGTTA
Found at i:15243 original size:21 final size:21
Alignment explanation
Indices: 15182--15243 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
15172 GTTGTTTTAC
* *
15182 TGTTATTTTTGCTGCTGTTTTGGT
1 TGTTATTTTT-ATGC-G-TTTGGA
* *
15206 TGTTATTTTTGT-TGTTTGGA
1 TGTTATTTTTATGCGTTTGGA
15226 TGTTATTTTTATGCGTTT
1 TGTTATTTTTATGCGTTT
15244 TTACTATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.50
21 5 0.16
23 1 0.03
24 10 0.31
ACGTcount: A:0.08, C:0.05, G:0.23, T:0.65
Consensus pattern (21 bp):
TGTTATTTTTATGCGTTTGGA
Found at i:15437 original size:49 final size:47
Alignment explanation
Indices: 15344--15438 Score: 113
Period size: 50 Copynumber: 2.0 Consensus size: 47
15334 TATCTTAATA
* * *
15344 TAATTTTTTAATGTATTTTGAATTTATTTATTTTTTAATGTTTGTTT
1 TAATTTTTTAATGTATTTTGAATTTATATATTTTCTAATATTTGTTT
15391 TAATGTTTTTAA-GTATATTTGATATATTATATATTTTCTAA-ATTTGTT
1 TAAT-TTTTTAATGTAT-TTTGA-AT-TTATATATTTTCTAATATTTGTT
15439 GTATGTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 8 0.20
48 12 0.29
49 8 0.20
50 13 0.32
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.63
Consensus pattern (47 bp):
TAATTTTTTAATGTATTTTGAATTTATATATTTTCTAATATTTGTTT
Found at i:17716 original size:23 final size:23
Alignment explanation
Indices: 17644--17757 Score: 108
Period size: 25 Copynumber: 4.9 Consensus size: 23
17634 TTTACGGAAC
* *
17644 AAACAGAGAGTAC-CAAAGTA-G
1 AAACAGAGAGCACACAAAGTACT
* *
17665 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTACT
*
17687 AGGAAACAGAGAGCACACACAGTACT
1 ---AAACAGAGAGCACACAAAGTACT
17713 AAACAGAGAGAGCACACAAAGTACT
1 AAAC--AGAGAGCACACAAAGTACT
*
17738 AATCAGAGAGCACACAAAGT
1 AAACAGAGAGCACACAAAGT
17758 GCTGATTAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
21 16 0.21
23 20 0.26
25 35 0.46
26 5 0.07
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.10
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTACT
Found at i:23969 original size:42 final size:42
Alignment explanation
Indices: 23896--23979 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
23886 ACCTCAAGAA
* *
23896 ATCCAGCAAGCCAGCGATCAGCATTTTCCACCAACTCATTAC
1 ATCCAGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
* * * * *
23938 ATCCGGCAACCCAGCGGTCAGCGTTTCCCACCCACTCGTTAC
1 ATCCAGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
23980 GATGCATAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.20
Consensus pattern (42 bp):
ATCCAGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
Found at i:28858 original size:16 final size:17
Alignment explanation
Indices: 28836--28871 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
28826 CTATCAACTA
28836 ATTTTTTTG-ATAT-AT
1 ATTTTTTTGTATATAAT
28851 ATTTTTTTGTATATAAT
1 ATTTTTTTGTATATAAT
28868 ATTT
1 ATTT
28872 ATATGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTTTTTGTATATAAT
Found at i:46167 original size:11 final size:11
Alignment explanation
Indices: 46153--46203 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
46143 ATTATTAAAT
46153 ATAATTTAATA
1 ATAATTTAATA
*
46164 ATAATGATAATAA
1 ATAAT-TTAAT-A
*
46177 ATAATTTAATC
1 ATAATTTAATA
*
46188 ATATTTTAAT-
1 ATAATTTAATA
46198 ATAATT
1 ATAATT
46204 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 5 0.15
11 14 0.42
12 8 0.24
13 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:46205 original size:61 final size:65
Alignment explanation
Indices: 46140--46271 Score: 191
Period size: 61 Copynumber: 2.1 Consensus size: 65
46130 ATATAATAAG
* * * * *
46140 ATTATTATTAAATATAATTTAATAATAATGATAAT-AAATA-A-TTTAATCATATT-TTAATATA
1 ATTATTATAAAATATAATTTAATAAAAATAAAAATAAAATATATTTTAATCACATTATTAATATA
46201 ATTATTATAAAATATAATTTAATAAAAATAAAAATAAAATATATTTTAATCACATTATTAATATA
1 ATTATTATAAAATATAATTTAATAAAAATAAAAATAAAATATATTTTAATCACATTATTAATATA
46266 ATTATT
1 ATTATT
46272 TTTATATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 31 0.50
62 5 0.08
63 1 0.02
64 11 0.18
65 14 0.23
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (65 bp):
ATTATTATAAAATATAATTTAATAAAAATAAAAATAAAATATATTTTAATCACATTATTAATATA
Found at i:46214 original size:16 final size:15
Alignment explanation
Indices: 46195--46250 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
46185 ATCATATTTT
*
46195 AATATAATTATTATAA
1 AATATAATT-TAATAA
46211 AATATAATTTAATAA
1 AATATAATTTAATAA
*
46226 AA-ATAA--AAATAA
1 AATATAATTTAATAA
*
46238 AATATATTTTAAT
1 AATATAATTTAAT
46251 CACATTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 4 0.12
15 10 0.30
16 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAATTTAATAA
Found at i:46263 original size:27 final size:26
Alignment explanation
Indices: 46188--46303 Score: 85
Period size: 27 Copynumber: 4.3 Consensus size: 26
46178 TAATTTAATC
46188 ATATTTTAATATAATTATT-ATAAAAT
1 ATATTTTAATA-AATTATTAATAAAAT
* * **
46214 ATAATTTAATAAAAATAAAAATAAAAT
1 ATATTTTAAT-AAATTATTAATAAAAT
* *
46241 ATATTTTAATCACATTATTAATATAAT
1 ATATTTTAAT-AAATTATTAATAAAAT
*
46268 -TATTTTTATATTAAATTA-TATTAAAAT
1 ATA-TTTTA-A-TAAATTATTAATAAAAT
46295 ATTATTTTA
1 A-TATTTTA
46304 GTATTATATT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
26 15 0.22
27 40 0.58
28 11 0.16
29 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATTTTAATAAATTATTAATAAAAT
Found at i:46296 original size:18 final size:18
Alignment explanation
Indices: 46275--46331 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
46265 AATTATTTTT
46275 ATATTAAATTATATTAAA
1 ATATTAAATTATATTAAA
**
46293 ATATTATTTTAGTATT---
1 ATATTAAATTA-TATTAAA
*
46309 ATATTAAATTATAGTAAA
1 ATATTAAATTATATTAAA
46327 ATATT
1 ATATT
46332 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 3 0.10
16 9 0.30
18 14 0.47
19 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
ATATTAAATTATATTAAA
Found at i:46311 original size:34 final size:34
Alignment explanation
Indices: 46273--46348 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 34
46263 ATAATTATTT
* *
46273 TTATATTAAATTATATTAAAATA-TTATTTTAGTA
1 TTATATTAAATTATAGTAAAATATTTATTTTA-AA
46307 TTATATTAAATTATAGTAAAATATTTTATTTTAAA
1 TTATATTAAATTATAGTAAAATA-TTTATTTTAAA
46342 TTATATT
1 TTATATT
46349 TTGGAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 22 0.58
35 8 0.21
36 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (34 bp):
TTATATTAAATTATAGTAAAATATTTATTTTAAA
Found at i:46341 original size:15 final size:15
Alignment explanation
Indices: 46317--46379 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
46307 TTATATTAAA
*
46317 TTATAGTAAAATATT
1 TTATATTAAAATATT
*
46332 TTATTTTAAATTATATT
1 TTATATTAAA--ATATT
** *
46349 TTGGAATAAAATATT
1 TTATATTAAAATATT
46364 TTATATTAAAATATT
1 TTATATTAAAATATT
46379 T
1 T
46380 CAAATATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 26 0.70
17 11 0.30
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:47229 original size:5 final size:6
Alignment explanation
Indices: 47213--47238 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47203 TAGGAAATTT
47213 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
47239 GATAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:51177 original size:121 final size:120
Alignment explanation
Indices: 51001--51231 Score: 381
Period size: 121 Copynumber: 1.9 Consensus size: 120
50991 TGTTTCTCAA
* * *
51001 ACTTTTTTGATGAACTTCATTTTCTCTATCCATATTAAACTTTGAAAACACCTCATCAATTTCAG
1 ACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACACCTCATCAATTTCAG
* * *
51066 TCTACGAAGAATTTGACTTAAAATTTGAGCTTTTCATCTTTTAAATTCGTTCCAAG
66 CCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATC-TTTAAATTCGTTCCAAG
*
51122 ACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACACCTCATCAATTTGAG
1 ACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACACCTCATCAATTTCAG
*
51187 CCTTCAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTTAAAT
66 CCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTTAAAT
51232 ATTGTGTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
120 7 0.07
121 95 0.93
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (120 bp):
ACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACACCTCATCAATTTCAG
CCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTTAAATTCGTTCCAAG
Found at i:59976 original size:7 final size:7
Alignment explanation
Indices: 59964--59992 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
59954 CACAAACCGG
59964 TGCCAAC
1 TGCCAAC
59971 TGCCAAC
1 TGCCAAC
59978 TGCCAAC
1 TGCCAAC
59985 TGCCAAC
1 TGCCAAC
59992 T
1 T
59993 CCTCCAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.41, G:0.14, T:0.17
Consensus pattern (7 bp):
TGCCAAC
Found at i:61958 original size:21 final size:19
Alignment explanation
Indices: 61896--61969 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
61886 AAATATAACA
*
61896 TTTATAATTTTCTATATTT
1 TTTATAAATTTCTATATTT
* * *
61915 TTAAT-ATTTTCTATAATTA
1 TTTATAAATTTCTAT-ATTT
61934 TTTATAAATTTCTAATATTT
1 TTTATAAATTTCT-ATATTT
*
61954 CTTTATGAATTT-TATA
1 -TTTATAAATTTCTATA
61970 ATTTATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 14 0.31
20 10 0.22
21 12 0.27
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATAAATTTCTATATTT
Found at i:61968 original size:30 final size:28
Alignment explanation
Indices: 61896--61970 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 28
61886 AAATATAACA
* * *
61896 TTTATAATTTTCTATATTTTTAATATTT
1 TTTATAATTTTATAAATTTCTAATATTT
*
61924 TCTATAATTATTTATAAATTTCTAATATTT
1 TTTATAA-T-TTTATAAATTTCTAATATTT
61954 CTTTATGAATTTTATAA
1 -TTTAT-AATTTTATAA
61971 TTTATATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 6 0.16
29 1 0.03
30 24 0.63
31 5 0.13
32 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTATAATTTTATAAATTTCTAATATTT
Found at i:62475 original size:18 final size:18
Alignment explanation
Indices: 62449--62487 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
62439 GAGACTGTAA
* *
62449 ATATTATTAATGGATAAT
1 ATATCATTAATAGATAAT
62467 ATATCATTAATAGATAAT
1 ATATCATTAATAGATAAT
62485 ATA
1 ATA
62488 AAAGATAACA
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:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (18 bp):
ATATCATTAATAGATAAT
Found at i:65691 original size:60 final size:60
Alignment explanation
Indices: 65580--65692 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
65570 TTAATATAAT
* * **
65580 ATTTGGTACCTGAACTTGATACTTTTTCCTAATTTGGTATCTAAATTTTTTTTGGACCCA
1 ATTTGATACCTGAACTTGACACTTTTTCCTAATTTGGTATCTAAAGCTTTTTTGGACCCA
* * * *
65640 ATTTGATACTTGAACTTGACATTTTTTTCTTAATTTGGT-TCTTAAGCTTTTTT
1 ATTTGATACCTGAACTTGACA-CTTTTTCCTAATTTGGTATCTAAAGCTTTTTT
65693 TGAATATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 29 0.66
61 15 0.34
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.51
Consensus pattern (60 bp):
ATTTGATACCTGAACTTGACACTTTTTCCTAATTTGGTATCTAAAGCTTTTTTGGACCCA
Found at i:65919 original size:30 final size:32
Alignment explanation
Indices: 65883--65962 Score: 112
Period size: 30 Copynumber: 2.6 Consensus size: 32
65873 TTGATCCTAA
*
65883 AAAGTTTAAGTACCAACTTAAAAAAAT-TA-C
1 AAAGTTTAAGTACCAAATTAAAAAAATATATC
*
65913 AAAGTTTAAGTACCAAATTAAAAATATATATC
1 AAAGTTTAAGTACCAAATTAAAAAAATATATC
*
65945 AAA-TTTAAGTATCAAATT
1 AAAGTTTAAGTACCAAATT
65963 GGACCAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 25 0.56
31 16 0.36
32 4 0.09
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (32 bp):
AAAGTTTAAGTACCAAATTAAAAAAATATATC
Found at i:66465 original size:50 final size:50
Alignment explanation
Indices: 66389--66493 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
66379 AAAATATTAA
*
66389 TCATACAAAGAGATACGAAAGGGTGTAAAACTAATGTAAGTGGATCCCTC
1 TCATACAAAGAGATACGAAAGAGTGTAAAACTAATGTAAGTGGATCCCTC
*
66439 TCATACAAAGAGATATGAAAGAGTGTAAAACTAATGTAAGTGGATCCCTC
1 TCATACAAAGAGATACGAAAGAGTGTAAAACTAATGTAAGTGGATCCCTC
*
66489 CCATA
1 TCATA
66494 ATATAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (50 bp):
TCATACAAAGAGATACGAAAGAGTGTAAAACTAATGTAAGTGGATCCCTC
Found at i:66610 original size:2 final size:2
Alignment explanation
Indices: 66603--66631 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66593 TAATTAATGC
66603 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
66632 AAAGATATTT
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:72992 original size:1 final size:1
Alignment explanation
Indices: 72988--73013 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
72978 AAAAAAGTCC
72988 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
73014 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:88628 original size:12 final size:12
Alignment explanation
Indices: 88611--88637 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
88601 ACAAATTTCC
88611 AAAATCAGAGAT
1 AAAATCAGAGAT
88623 AAAATCAGAGAT
1 AAAATCAGAGAT
88635 AAA
1 AAA
88638 GAAACATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAATCAGAGAT
Found at i:88994 original size:28 final size:28
Alignment explanation
Indices: 88971--89029 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
88961 AAAATGTGAT
*
88971 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGACACTCGGGGGCAAAATGGTAA
*
88999 TTTTGGACACTCGGGGGTAAAATGG-AA
1 TTTTGGACACTCGGGGGCAAAATGGTAA
89026 TTTT
1 TTTT
89030 AGAAAGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGACACTCGGGGGCAAAATGGTAA
Found at i:89043 original size:28 final size:27
Alignment explanation
Indices: 88984--89141 Score: 131
Period size: 28 Copynumber: 5.7 Consensus size: 27
88974 TGGATACTCG
* * * **
88984 GGGGCAAAATGGTAATTTTGGACACTCG
1 GGGGTAAAATGG-AATTTTGGAAAGTTA
*
89012 GGGGTAAAATGGAATTTTAGAAAGTTCA
1 GGGGTAAAATGGAATTTTGGAAAGTT-A
*
89040 GGGGTAAAATGGTATTTTTGGTGAAA-TT-
1 GGGGTAAAATGG-AATTTT-G-GAAAGTTA
*
89068 GGGGTCAAAATGGAATTTTGGAAAGTTT
1 GGGGT-AAAATGGAATTTTGGAAAGTTA
** *
89096 GGGGGGAAATGTAATTTTGGAAAGTTCA
1 GGGGTAAAATGGAATTTTGGAAAGTT-A
*
89124 GGGGTAAAATGGTATTTT
1 GGGGTAAAATGGAATTTT
89142 TTAGTGAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.04
27 32 0.30
28 51 0.49
29 12 0.11
30 2 0.02
31 4 0.04
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (27 bp):
GGGGTAAAATGGAATTTTGGAAAGTTA
Found at i:89106 original size:84 final size:86
Alignment explanation
Indices: 88981--89171 Score: 246
Period size: 85 Copynumber: 2.3 Consensus size: 86
88971 TTTTGGATAC
* *
88981 TCGGGGGCAAAATGGTAATTTTGGACACTCGGGGGTAAAATGGAATTTTAGAAAGTTCAGGGGTA
1 TCGGGGTCAAAATGGTAATTTTGGAAACTCGGGGGTAAAATGGAATTTTAGAAAGTTCAGGGGTA
*
89046 AAATGGTA-TTTTTGGTGAAA
66 AAATGGTATTTTTTAGTGAAA
* * * * * *
89066 TTGGGGTCAAAATGG-AATTTTGGAAAGTTTGGGGG-GAAATGTAATTTTGGAAAGTTCAGGGGT
1 TCGGGGTCAAAATGGTAATTTTGGAAA-CTCGGGGGTAAAATGGAATTTTAGAAAGTTCAGGGGT
89129 AAAATGGTATTTTTTAGTGAAA
65 AAAATGGTATTTTTTAGTGAAA
* *
89151 TCGAGGTCAAAAT-ATAATTTT
1 TCGGGGTCAAAATGGTAATTTT
89172 CAGACAGTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 44 0.48
85 47 0.52
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (86 bp):
TCGGGGTCAAAATGGTAATTTTGGAAACTCGGGGGTAAAATGGAATTTTAGAAAGTTCAGGGGTA
AAATGGTATTTTTTAGTGAAA
Found at i:89127 original size:27 final size:27
Alignment explanation
Indices: 89018--89141 Score: 83
Period size: 27 Copynumber: 4.4 Consensus size: 27
89008 CTCGGGGGTA
* *
89018 AAATGGAATTTTAGAAAGTTCAGGGGTA
1 AAATGGAATTTTGGAAAGTTCAGGGG-G
* *
89046 AAATGGTATTTTTGGTGAAA-TT--GGGGTCA
1 AAATGG-AATTTT-G-GAAAGTTCAGGGG--G
**
89075 AAATGGAATTTTGGAAAGTTTGGGGGG
1 AAATGGAATTTTGGAAAGTTCAGGGGG
* *
89102 AAATGTAATTTTGGAAAGTTCAGGGGTA
1 AAATGGAATTTTGGAAAGTTCAGGGG-G
*
89130 AAATGGTATTTT
1 AAATGGAATTTT
89142 TTAGTGAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.05
27 26 0.34
28 25 0.32
29 16 0.21
30 2 0.03
31 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (27 bp):
AAATGGAATTTTGGAAAGTTCAGGGGG
Found at i:91025 original size:17 final size:17
Alignment explanation
Indices: 90992--91058 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
90982 TTATTTTAAT
* *
90992 TTTAAA-TACATTTAAA
1 TTTAAAGTAAATTCAAA
91008 TTTAAAGTAAATTCAAA
1 TTTAAAGTAAATTCAAA
* * **
91025 TTCAAAGTGAATTTGAA
1 TTTAAAGTAAATTCAAA
*
91042 TTTAAAATAAATTCAAA
1 TTTAAAGTAAATTCAAA
91059 CTTATTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
16 6 0.15
17 33 0.85
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (17 bp):
TTTAAAGTAAATTCAAA
Found at i:93049 original size:14 final size:15
Alignment explanation
Indices: 93030--93062 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
93020 TGAAGCTCTT
*
93030 TTTTATT-TTTATTA
1 TTTTATTATTTATAA
93044 TTTTATTATTTATAA
1 TTTTATTATTTATAA
93059 TTTT
1 TTTT
93063 TAATACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTATAA
Found at i:94908 original size:30 final size:30
Alignment explanation
Indices: 94874--94935 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
94864 TACATTAAAA
*
94874 TTGCAAATGGTGAAATTCAAACTCGAACCT
1 TTGCAAATGGTGAAACTCAAACTCGAACCT
*
94904 TTGCAAATGGTGAAACTCAAACTCGGACCT
1 TTGCAAATGGTGAAACTCAAACTCGAACCT
94934 TT
1 TT
94936 AAGGTTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (30 bp):
TTGCAAATGGTGAAACTCAAACTCGAACCT
Found at i:103971 original size:25 final size:25
Alignment explanation
Indices: 103943--103991 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
103933 TTTTTATATT
*
103943 AATATATTTGTTATAATTAAATTTA
1 AATATATTTCTTATAATTAAATTTA
* *
103968 AATATATTTCTTATTATTTAATTT
1 AATATATTTCTTATAATTAAATTT
103992 CAATTCGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATATATTTCTTATAATTAAATTTA
Found at i:115907 original size:30 final size:31
Alignment explanation
Indices: 115855--115917 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
115845 AGTTTATATG
*
115855 TTTATAATTTTTAAATGATT-AAATCAAATT
1 TTTATAATTTTTAAAGGATTAAAATCAAATT
* * * *
115885 TTTATTATTTTTAAGGGGTTAAAATGAAATT
1 TTTATAATTTTTAAAGGATTAAAATCAAATT
115916 TT
1 TT
115918 ATCGTTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGATTAAAATCAAATT
Found at i:116599 original size:15 final size:17
Alignment explanation
Indices: 116560--116597 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
116550 TGGCTTAATG
*
116560 TAAAAATATATACAAAT
1 TAAAAATATATAAAAAT
116577 TAAAAATATA-AAAAAT
1 TAAAAATATATAAAAAT
116593 TAAAA
1 TAAAA
116598 TAAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATATATAAAAAT
Found at i:119142 original size:5 final size:5
Alignment explanation
Indices: 119132--119159 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
119122 ATTAAACGGT
119132 GGAAA GGAAA GGAAA GGAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGA
119160 TTGATTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:124363 original size:16 final size:17
Alignment explanation
Indices: 124333--124368 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
124323 CTATTAGTAA
*
124333 TTAAAGTAAAGATAATT
1 TTAAAGTAAAAATAATT
124350 TTAAA-TAAAAATAATT
1 TTAAAGTAAAAATAATT
124366 TTA
1 TTA
124369 CTAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TTAAAGTAAAAATAATT
Found at i:139126 original size:22 final size:23
Alignment explanation
Indices: 139085--139127 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
139075 TTAATAACAT
*
139085 TATAAAAATAAATTGTCAAATCA
1 TATAAAAATAAATTGACAAATCA
*
139108 TATAAAATTAAATT-ACAAAT
1 TATAAAAATAAATTGACAAAT
139128 TTTAGCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TATAAAAATAAATTGACAAATCA
Found at i:160569 original size:4 final size:4
Alignment explanation
Indices: 160560--160584 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
160550 TGAAAAAATT
160560 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
160585 AACCTCGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:183849 original size:29 final size:29
Alignment explanation
Indices: 183794--183849 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
183784 GTTTAATATG
* * *
183794 TAATTATATGCATGAACTTTGGTTTTGTA
1 TAATTATATACATGAAATTTGGATTTGTA
* *
183823 TAATTTTATACATGAAATTTTGATTTG
1 TAATTATATACATGAAATTTGGATTTG
183850 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.50
Consensus pattern (29 bp):
TAATTATATACATGAAATTTGGATTTGTA
Done.