Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015073.1 Kokia drynarioides strain JFW-HI SEQ_130117, 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: 106010
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Warning! 385 characters in sequence are not A, C, G, or T
Found at i:4696 original size:31 final size:30
Alignment explanation
Indices: 4610--4697 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
4600 TGTATATATG
* *
4610 AACTTTAA-TTTGATGTAATTATACACGTGA
1 AACTTTAATTTTGATTTAA-TATATACGTGA
** * * *
4640 AACTTTAATCGTGGTTAAAATATATACTTGA
1 AACTTTAATTTTGATT-TAATATATACGTGA
4671 AACTTTAATTTTGATTTAATCATATAC
1 AACTTTAATTTTGATTTAAT-ATATAC
4698 ATTTAAAGAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
30 11 0.25
31 31 0.70
32 2 0.05
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTTGATTTAATATATACGTGA
Found at i:6343 original size:13 final size:13
Alignment explanation
Indices: 6327--6351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6317 GGTCTATTTG
6327 TTTTACAAACAAA
1 TTTTACAAACAAA
6340 TTTTACAAACAA
1 TTTTACAAACAA
6352 TATATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTTACAAACAAA
Found at i:8399 original size:29 final size:27
Alignment explanation
Indices: 8366--8427 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 27
8356 TAAATCTTAA
*
8366 AATTATACATTAATTATGATTTTATGTGT
1 AATTATACATAAATTATGA-TTT-TGTGT
*
8395 AATTATATACATAAATTTTGATTTTGTGT
1 AA-T-TATACATAAATTATGATTTTGTGT
8424 AATT
1 AATT
8428 TTATACGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 9 0.31
30 4 0.14
31 14 0.48
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (27 bp):
AATTATACATAAATTATGATTTTGTGT
Found at i:8432 original size:29 final size:31
Alignment explanation
Indices: 8368--8433 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
8358 AATCTTAAAA
*
8368 TTATACATTAATTATGATTTTATGTGTAATT
1 TTATACATAAATTATGATTTTATGTGTAATT
* *
8399 ATATACATAAATTTTGA-TTT-TGTGTAATT
1 TTATACATAAATTATGATTTTATGTGTAATT
8428 TTATAC
1 TTATAC
8434 GTGAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
30 3 0.10
31 14 0.45
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (31 bp):
TTATACATAAATTATGATTTTATGTGTAATT
Found at i:8440 original size:29 final size:28
Alignment explanation
Indices: 8369--8445 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
8359 ATCTTAAAAT
*
8369 TATACATTAATTATGATTTTATGTGTAATTA
1 TATACATAAATT-TGA-TTT-TGTGTAATTA
*
8400 TATACATAAATTTTGATTTTGTGTAATTT
1 TATACATAAA-TTTGATTTTGTGTAATTA
* *
8429 TATACGTGAATTTGATT
1 TATACATAAATTTGATT
8446 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.17
29 17 0.41
30 3 0.07
31 12 0.29
32 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (28 bp):
TATACATAAATTTGATTTTGTGTAATTA
Found at i:15255 original size:16 final size:18
Alignment explanation
Indices: 15216--15249 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15206 TAAGTTTATA
15216 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
15233 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
15250 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:15366 original size:23 final size:23
Alignment explanation
Indices: 15314--15367 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
15304 ATATAGACAT
*
15314 TAAAATAATATTAAGATGTATCA
1 TAAAAAAATATTAAGATGTATCA
*
15337 TACAAAAATATTAAGAT-TA-CTA
1 TAAAAAAATATTAAGATGTATC-A
15359 TAAAAAAAT
1 TAAAAAAAT
15368 TCAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 11 0.41
23 15 0.56
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
TAAAAAAATATTAAGATGTATCA
Found at i:21249 original size:2 final size:2
Alignment explanation
Indices: 21212--21240 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21202 NNNNNNNNNN
21212 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21241 TACAGAGAGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21978 original size:19 final size:19
Alignment explanation
Indices: 21942--21981 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21932 ATTCAAAAAT
**
21942 AAAAAAATTAAATTTATAA
1 AAAAAAATTAAAAATATAA
21961 AAAAAAATTAAAAATATAA
1 AAAAAAATTAAAAATATAA
21980 AA
1 AA
21982 GAAGTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAAATTAAAAATATAA
Found at i:24859 original size:21 final size:22
Alignment explanation
Indices: 24830--24876 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
24820 TTAGATATAA
24830 TAATAAAATATAAACA-TATATT
1 TAATAAAATA-AAACAGTATATT
*
24852 TAAT-AAATAAAATAGTATATT
1 TAATAAAATAAAACAGTATATT
24873 TAAT
1 TAAT
24877 CACTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATAAAATAAAACAGTATATT
Found at i:36336 original size:46 final size:46
Alignment explanation
Indices: 36269--36362 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
36259 ATTTCATGTG
36269 AAAGGACAATTCCTTTTAGTTCCAACATTATGCAATTCAACCAAAT
1 AAAGGACAATTCCTTTTAGTTCCAACATTATGCAATTCAACCAAAT
36315 AAAGGACAATTCCTTTTAGTTCCAACATTATGCAATTCAACCAAAT
1 AAAGGACAATTCCTTTTAGTTCCAACATTATGCAATTCAACCAAAT
36361 AA
1 AA
36363 GTGAATAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (46 bp):
AAAGGACAATTCCTTTTAGTTCCAACATTATGCAATTCAACCAAAT
Found at i:42968 original size:26 final size:27
Alignment explanation
Indices: 42929--42981 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
42919 ATATGTAATT
42929 AATAATATACTTTGATTCTATTAATAA
1 AATAATATACTTTGATTCTATTAATAA
* *
42956 AATAATATA-TTTGATTTTATTGATAA
1 AATAATATACTTTGATTCTATTAATAA
42982 GTGTCAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (27 bp):
AATAATATACTTTGATTCTATTAATAA
Found at i:46179 original size:24 final size:24
Alignment explanation
Indices: 46144--46198 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 24
46134 AAATACTTGG
46144 ATTATATTAAATGTTATTCTAAATT
1 ATTA-ATTAAATGTTATTCTAAATT
46169 ATTAATTAAATGTTATTCTAAATT
1 ATTAATTAAATGTTATTCTAAATT
46193 ATTAAT
1 ATTAAT
46199 ATCTTTCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
ATTAATTAAATGTTATTCTAAATT
Found at i:48430 original size:71 final size:71
Alignment explanation
Indices: 48314--48529 Score: 414
Period size: 71 Copynumber: 3.0 Consensus size: 71
48304 CCATTAGAGG
48314 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGGTAA
1 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGGTAA
48379 GGAATC
66 GGAATC
*
48385 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGATAA
1 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGGTAA
48450 GGAATC
66 GGAATC
*
48456 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGATTACTCGATGTTATTGGGTAA
1 TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGGTAA
48521 GGAATC
66 GGAATC
48527 TGT
1 TGT
48530 TTTCAAAATT
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 142 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (71 bp):
TGTAGCTTAAATCTTCAAGACTAAAATGCTGGATGGTTGTGTGGTTACTCGATGTTATTGGGTAA
GGAATC
Found at i:51393 original size:100 final size:100
Alignment explanation
Indices: 51220--51411 Score: 305
Period size: 100 Copynumber: 1.9 Consensus size: 100
51210 GGGCGAGCAG
* *
51220 AACATTAGTTATCCAAATTATACGTTGTGGAGCGCACACATGTTCTTGATAGAAAAGCTGAAAAA
1 AACATTAGTTATCCAAATTATACGTTGTGGAGAGCACACATGTCCTTGATAGAAAAGCTGAAAAA
* * * *
51285 TGGGCAATAGCGAACGGACGAACTGAACGATGCAA
66 TGGACAATAACAAACAGACGAACTGAACGATGCAA
*
51320 AACATTAGTTATCCAAATTATACGTTGTGGAGATCACACATGTCCTTGATAGAAAAG-TCGAAAA
1 AACATTAGTTATCCAAATTATACGTTGTGGAGAGCACACATGTCCTTGATAGAAAAGCT-GAAAA
51384 ATGGACAATAACAAACAGACGAACTGAA
65 ATGGACAATAACAAACAGACGAACTGAA
51412 AGATAATGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.01
100 83 0.99
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (100 bp):
AACATTAGTTATCCAAATTATACGTTGTGGAGAGCACACATGTCCTTGATAGAAAAGCTGAAAAA
TGGACAATAACAAACAGACGAACTGAACGATGCAA
Found at i:55422 original size:19 final size:20
Alignment explanation
Indices: 55398--55437 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
55388 CGATGTAGAA
*
55398 TAAT-AAAATAATAAATGTC
1 TAATAAAAATAATAAACGTC
55417 TAATAAAAATAATAAACGTC
1 TAATAAAAATAATAAACGTC
55437 T
1 T
55438 TTATTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (20 bp):
TAATAAAAATAATAAACGTC
Found at i:56519 original size:3 final size:3
Alignment explanation
Indices: 56436--56506 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
56426 TTAATGACAT
* * ** **
56436 TAA TAA TAT TAA TAA TAA TAA CTACT TCT TAA TAA TAA TAA TAA TGT
1 TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA TAA TAA TAA
* *
56483 TAG TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
56507 ACATCGTAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:56699 original size:75 final size:75
Alignment explanation
Indices: 56572--56726 Score: 285
Period size: 75 Copynumber: 2.1 Consensus size: 75
56562 TGGAAAGGTC
56572 GATC-GGTTACTGTCCTTTGATCAGAGTCCACCGATCCACTGTCCGCAGTCGTGGGAACGCCCCC
1 GATCTGGTTACTGTCCTTTGATCAGAGTCCACCGATCCACTGTCCGCAGTCGTGGGAACGCCCCC
56636 TTCACATGCA
66 TTCACATGCA
* *
56646 GATCTGGTTACTGTCCTTTGATCGGAGTCCACCGATCCGCTGTCCGCAGTCGTGGGAACGCCCCC
1 GATCTGGTTACTGTCCTTTGATCAGAGTCCACCGATCCACTGTCCGCAGTCGTGGGAACGCCCCC
56711 TTCACATGCA
66 TTCACATGCA
56721 GATCTG
1 GATCTG
56727 CAATGGAAAC
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
74 4 0.05
75 74 0.95
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (75 bp):
GATCTGGTTACTGTCCTTTGATCAGAGTCCACCGATCCACTGTCCGCAGTCGTGGGAACGCCCCC
TTCACATGCA
Found at i:62435 original size:17 final size:18
Alignment explanation
Indices: 62405--62439 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
62395 TTGTAAATAG
*
62405 TTTTTATAATTTTTTTAA
1 TTTTTATAAATTTTTTAA
62423 TTTTT-TAAATTTTTTAA
1 TTTTTATAAATTTTTTAA
62440 AAATTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATAAATTTTTTAA
Found at i:62444 original size:11 final size:9
Alignment explanation
Indices: 62405--62440 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
62395 TTGTAAATAG
62405 TTTTTATAAT
1 TTTTTA-AAT
*
62415 TTTTTTAAT
1 TTTTTAAAT
62424 TTTTTAAAT
1 TTTTTAAAT
62433 TTTTTAAA
1 TTTTTAAA
62441 AATTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:66787 original size:30 final size:30
Alignment explanation
Indices: 66747--66811 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
66737 AGTATTTAAG
*
66747 AATTTCTAAAAAGATTAAATTAAAATTTTAT
1 AATTTCT-AAAAGATTAAAATAAAATTTTAT
* *
66778 AATTT-TAAAAGGTTAAAATACAATTTTAT
1 AATTTCTAAAAGATTAAAATAAAATTTTAT
*
66807 TATTT
1 AATTT
66812 ATTAACTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.80
30 1 0.03
31 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (30 bp):
AATTTCTAAAAGATTAAAATAAAATTTTAT
Found at i:70135 original size:19 final size:20
Alignment explanation
Indices: 70103--70140 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
70093 GAAAATTCAA
70103 AAAATTAAATAAAATAGATG
1 AAAATTAAATAAAATAGATG
*
70123 AAAATTTAA-AAAATAGAT
1 AAAATTAAATAAAATAGAT
70141 AAAGTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAATTAAATAAAATAGATG
Found at i:70154 original size:29 final size:29
Alignment explanation
Indices: 70083--70154 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
70073 AGAAATTCTA
*
70083 AAAATACATAGAAAATTCAAAAAATTAAAT
1 AAAATAGA-AGAAAATTCAAAAAATTAAAT
* * *
70113 AAAATAGATGAAAATTTAAAAAA-TAGAT
1 AAAATAGAAGAAAATTCAAAAAATTAAAT
*
70141 AAAGTGAGAAGAAA
1 AAAAT-AGAAGAAA
70155 TGAGAGGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 8 0.23
29 20 0.57
30 7 0.20
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (29 bp):
AAAATAGAAGAAAATTCAAAAAATTAAAT
Found at i:75268 original size:3 final size:3
Alignment explanation
Indices: 75262--75288 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
75252 TGCAGCAGCC
75262 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
75289 GGTCATAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:87628 original size:28 final size:28
Alignment explanation
Indices: 87596--87653 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
87586 AAAATACAAA
* *
87596 AAAAAATAAAAAAGT-TTTACTTTTAATAT
1 AAAAAA-AAAAAACTGTTTA-TTGTAATAT
87625 AAAAAAAAAAAACTGTTTATTGTAATAT
1 AAAAAAAAAAAACTGTTTATTGTAATAT
87653 A
1 A
87654 TTTTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAAAAAAAAACTGTTTATTGTAATAT
Found at i:89953 original size:22 final size:22
Alignment explanation
Indices: 89928--89970 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
89918 TATTTTACCC
*
89928 TTTAAA-AATATAAAAAGTTAAT
1 TTTAAATAATA-AAAAAATTAAT
89950 TTTAAATAATAAAAAAATTAA
1 TTTAAATAATAAAAAAATTAA
89971 ATGTATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAATAATAAAAAAATTAAT
Found at i:91096 original size:2 final size:2
Alignment explanation
Indices: 91089--91113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91079 GTTAACTTTC
91089 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
91114 TTATGCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94933 original size:3 final size:3
Alignment explanation
Indices: 94922--94964 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
94912 TTACAAGTAA
*
94922 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
94965 CCATAGCCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:103199 original size:2 final size:2
Alignment explanation
Indices: 103192--103216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103182 CTGCTGCATT
103192 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
103217 CGCAAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103855 original size:15 final size:15
Alignment explanation
Indices: 103835--103881 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
103825 ATAAAAATAA
103835 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
103850 TTATATTTAAAATA-
1 TTATATTTTAATTAT
*
103864 TTACATTTTAATTAT
1 TTATATTTTAATTAT
103879 TTA
1 TTA
103882 CTTTATAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:103879 original size:14 final size:14
Alignment explanation
Indices: 103834--103879 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
103824 TATAAAAATA
103834 ATTATATTTTAATT
1 ATTATATTTTAATT
* *
103848 ATTTATATTTAAAAT
1 A-TTATATTTTAATT
*
103863 ATTACATTTTAATT
1 ATTATATTTTAATT
103877 ATT
1 ATT
103880 TACTTTATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATATTTTAATT
Found at i:104638 original size:2 final size:2
Alignment explanation
Indices: 104631--104660 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
104621 TCTCTTCAAT
*
104631 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104661 ACATTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.