Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold515
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: 459219
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 4 of 4
Found at i:413144 original size:26 final size:25
Alignment explanation
Indices: 413097--413149 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
413087 TTTTTAAGCT
* * *
413097 TTTTTAAATAATAACAATTAATTTA
1 TTTTTAAATAAAAACAAATAATATA
*
413122 TTTTTAAATAAAAATAACATAATATA
1 TTTTTAAATAAAAACAA-ATAATATA
413148 TT
1 TT
413150 AATTACAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTTAAATAAAAACAAATAATATA
Found at i:413703 original size:21 final size:21
Alignment explanation
Indices: 413662--413704 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
413652 ACGCTTGCCA
*
413662 ATTATATAATATATTTTTTAT
1 ATTATATAATATATTTATTAT
*
413683 ATTATCTAATA-ATTATATTAT
1 ATTATATAATATATT-TATTAT
413704 A
1 A
413705 AAAATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATATAATATATTTATTAT
Found at i:417236 original size:16 final size:16
Alignment explanation
Indices: 417210--417256 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
417200 TAGTTTAATT
417210 AATATATTATATATTAA
1 AATA-ATTATATATTAA
417227 AATAA-T-TATATT-A
1 AATAATTATATATTAA
417240 AATAATTA-ATA-TAA
1 AATAATTATATATTAA
417254 AAT
1 AAT
417257 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.26
14 14 0.52
15 1 0.04
16 1 0.04
17 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATTATATATTAA
Found at i:417244 original size:13 final size:14
Alignment explanation
Indices: 417219--417256 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
417209 TAATATATTA
417219 TATATTAAAATAAT
1 TATATTAAAATAAT
417233 TATATT-AAATAAT
1 TATATTAAAATAAT
417246 TA-ATATAAAAT
1 TATAT-TAAAAT
417257 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 10 0.45
14 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATTAAAATAAT
Found at i:423808 original size:27 final size:25
Alignment explanation
Indices: 423771--423848 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 25
423761 CTAACACGTA
423771 TATTTA-AATTATTTTTATATATTT
1 TATTTATAATTATTTTTATATATTT
423795 TGATATTATAATTATATTTT-TATTATTT
1 T-AT-TTATAATTAT-TTTTATA-TATTT
* *
423823 TATTTTTATATTAATTTTAATATATT
1 TATTTATA-ATT-ATTTTTATATATT
423849 AATAATTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
24 1 0.02
25 2 0.05
26 7 0.16
27 20 0.45
28 14 0.32
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTTATAATTATTTTTATATATTT
Found at i:423862 original size:43 final size:43
Alignment explanation
Indices: 423779--423863 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
423769 TATATTTAAA
* *
423779 TTATTTTTATATATTTTGATATTATAATTATATTTTTATTATT
1 TTATTTTTATATATTTTAATATTATAATTATATTTATATTATT
423822 TTATTTTTATATTAATTTTAATA-TATTAA-TA-ATTTATATTAT
1 TTATTTTTATA-T-ATTTTAATATTA-TAATTATATTTATATTAT
423864 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
43 21 0.57
44 5 0.14
45 11 0.30
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (43 bp):
TTATTTTTATATATTTTAATATTATAATTATATTTATATTATT
Found at i:423924 original size:21 final size:21
Alignment explanation
Indices: 423879--423936 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
423869 TTTTAAAAAT
*
423879 TTATTTAATTATATTATATTT
1 TTATTTAATTATATTATATTA
423900 TTATTT-ATATATATTAT-TTA
1 TTATTTAAT-TATATTATATTA
423920 --ATTATAATTAATATTAT
1 TTATT-TAATT-ATATTAT
423937 TATACCAGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 13 0.41
21 14 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAATTATATTATATTA
Found at i:423934 original size:17 final size:16
Alignment explanation
Indices: 423828--423934 Score: 75
Period size: 17 Copynumber: 6.8 Consensus size: 16
423818 TATTTTATTT
423828 TTATATTAAT-TTTAA
1 TTATATTAATATTTAA
423843 -TATATTAATAATTTATA
1 TTATATTAAT-ATTTA-A
*
423860 TTATATAAAT-TTTAA
1 TTATATTAATATTTAA
*
423875 --AAATT--TATTTAA
1 TTATATTAATATTTAA
* *
423887 TTATATTATATTTTTAT
1 TTATATTA-ATATTTAA
*
423904 TTATATATATTATTTAA
1 TTATAT-TAATATTTAA
423921 TTATAATTAATATT
1 TTAT-ATTAATATT
423935 ATTATACCAG
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
11 1 0.01
12 5 0.07
13 3 0.04
14 13 0.19
15 1 0.01
16 8 0.11
17 27 0.39
18 12 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTAATATTTAA
Found at i:424380 original size:22 final size:24
Alignment explanation
Indices: 424332--424382 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
424322 ATTATTTTTG
424332 ATAAAATTATGATAATAGTAAATTA
1 ATAAAATTATGATAATAG-AAATTA
424357 ATAAATATTAT-ATAATA-AAA-TA
1 ATAAA-ATTATGATAATAGAAATTA
424379 ATAA
1 ATAA
424383 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.24
23 3 0.12
25 11 0.44
26 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
ATAAAATTATGATAATAGAAATTA
Found at i:424407 original size:22 final size:23
Alignment explanation
Indices: 424365--424416 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
424355 TAATAAATAT
424365 TATATAATAAAATAATAATTTTAAA
1 TATA-AATAAAATAATAA-TTTAAA
*
424390 -ATAAATAAAATTAT-ATTTAAA
1 TATAAATAAAATAATAATTTAAA
424411 TATAAA
1 TATAAA
424417 AATTGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.24
22 6 0.24
23 10 0.40
24 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TATAAATAAAATAATAATTTAAA
Found at i:424649 original size:2 final size:2
Alignment explanation
Indices: 424644--424678 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
424634 AAAATAACTT
*
424644 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
424679 GAGTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:424967 original size:3 final size:3
Alignment explanation
Indices: 424959--424985 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
424949 TGACTGATGC
424959 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
424986 ATTTAAATCT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:425804 original size:148 final size:147
Alignment explanation
Indices: 425520--425805 Score: 421
Period size: 148 Copynumber: 1.9 Consensus size: 147
425510 AAACTGGTAG
*
425520 TGAAGGTTCGAATTCTAGAATGGGAGGAGTTAGATTGTGGAATGAAAGAGGACGACCTCCCATTG
1 TGAAGGTTCGAATCCTAGAATGGGAGGAGTTAGATTGTGGAATGAAAGAGGACGACCTCCCATTG
* * * * *
425585 TGTGAATTATGGGATGAGAGAGGACTGTTAGATAGTCAAATTTGTTTTTGATACGTGGCAGTGAA
66 TGTGAATTACGGGATGAGAGAAGACTATTAGATAGTCAAATTCGATTTTGATACGTGGCAGTGAA
425650 GTTTTTTAAATTCATCT
131 GTTTTTTAAATTCATCT
* * * * *
425667 TGAAGGTTCGAATCCTAGGATGGGATGAGTTTGGATTGTGGGATGAAAGAGGATGACCTCCCATT
1 TGAAGGTTCGAATCCTAGAATGGGAGGAG-TTAGATTGTGGAATGAAAGAGGACGACCTCCCATT
*
425732 GTGTGGATTACGGGATGAGAGAAGACTATTAGATAGTCAAATTCGATTTTGATGCAC-TGGCAGT
65 GTGTGAATTACGGGATGAGAGAAGACTATTAGATAGTCAAATTCGATTTTGAT--ACGTGGCAGT
*
425796 GGAGTTTTTT
128 GAAGTTTTTT
425806 TAACGCCGCA
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
147 26 0.21
148 79 0.64
149 16 0.13
150 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.32
Consensus pattern (147 bp):
TGAAGGTTCGAATCCTAGAATGGGAGGAGTTAGATTGTGGAATGAAAGAGGACGACCTCCCATTG
TGTGAATTACGGGATGAGAGAAGACTATTAGATAGTCAAATTCGATTTTGATACGTGGCAGTGAA
GTTTTTTAAATTCATCT
Found at i:430631 original size:29 final size:29
Alignment explanation
Indices: 430574--430635 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
430564 TTTTTATTAT
430574 ATTTTTATTATTATATAATAAATATAATA
1 ATTTTTATTATTATATAATAAATATAATA
*
430603 ATTTTTATTATT-T-TAAGTAAAAATAAATA
1 ATTTTTATTATTATATAA-TAAATAT-AATA
430632 ATTT
1 ATTT
430636 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 3 0.10
28 7 0.23
29 20 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTTTTATTATTATATAATAAATATAATA
Found at i:430652 original size:29 final size:30
Alignment explanation
Indices: 430579--430663 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
430569 ATTATATTTT
*
430579 TATTATTATATAATAAATATAATAATTTTTAT
1 TATT-TTATATAA-AAATATAATAATTTTTAA
430611 TATTTTA-AGTAAAAATA-AATAATTTATTAA
1 TATTTTATA-TAAAAATATAATAATTT-TTAA
* *
430641 T-TTTTATTTAAAATTATTAATAA
1 TATTTTATATAAAAATA-TAATAA
430664 ATTAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 20 0.44
30 10 0.22
31 11 0.24
32 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TATTTTATATAAAAATATAATAATTTTTAA
Found at i:434708 original size:22 final size:22
Alignment explanation
Indices: 434682--434728 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
434672 GAAACTCACT
434682 AAAACCTTAAAATTGGAATAAA
1 AAAACCTTAAAATTGGAATAAA
434704 AAAACCTTAAAATTGGAATAAA
1 AAAACCTTAAAATTGGAATAAA
434726 AAA
1 AAA
434729 TTGGCTCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAACCTTAAAATTGGAATAAA
Found at i:435140 original size:4 final size:4
Alignment explanation
Indices: 435131--435202 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
435121 TATGAATGTG
* *
435131 ATAT ATAT ATAT ATAC ATAT ATAT ATAT ATAT ACAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
435179 ACAT ACAT ACAT ACAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT
435203 TAATATTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (4 bp):
ATAT
Found at i:435154 original size:18 final size:18
Alignment explanation
Indices: 435131--435201 Score: 106
Period size: 18 Copynumber: 3.8 Consensus size: 18
435121 TATGAATGTG
435131 ATATATATATATATACAT
1 ATATATATATATATACAT
435149 ATATATATATATATACAT
1 ATATATATATATATACAT
435167 ATATATATATATACATACAT
1 ATATATATATAT--ATACAT
* *
435187 ACATACATATATATA
1 ATATATATATATATA
435202 TTAATATTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 33 0.67
20 16 0.33
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATATATATATACAT
Found at i:444967 original size:50 final size:48
Alignment explanation
Indices: 444908--445027 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 48
444898 TTTATATATC
444908 ATTTAATTTTTTTTAAATTTCACAAAA-GAATTATTAAATGATATAAAATT
1 ATTTAATTTTTTTTAAATTT-A-AAAATGAATTATTAAATGATATAAAA-T
444958 ATTTAATTTTTTTTAAAATTTAAAAATGAATTATTAAATGATATAAAAT
1 ATTTAATTTTTTTT-AAATTTAAAAATGAATTATTAAATGATATAAAAT
*
445007 AGTTTAATTTTTATATAAATT
1 A-TTTAATTTTT-TTTAAATT
445028 GATGATCTTA
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
49 6 0.09
50 51 0.78
51 8 0.12
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (48 bp):
ATTTAATTTTTTTTAAATTTAAAAATGAATTATTAAATGATATAAAAT
Found at i:446196 original size:30 final size:31
Alignment explanation
Indices: 446162--446247 Score: 72
Period size: 30 Copynumber: 2.8 Consensus size: 31
446152 TTATATTATT
*
446162 ATTTATTAATTAAAATAATATTTTATTTA-A
1 ATTTATTAATTAAAATAATATTTTATTAATA
*
446192 ATTTAATT-ATAAAAAT-ATAATTTT-TTAATA
1 ATTT-ATTAATTAAAATAAT-ATTTTATTAATA
* * *
446222 ATTTAATAATTTTAAATAATAATTTA
1 ATTTATTAA-TTAAAATAATATTTTA
446248 AATCATCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
29 7 0.16
30 22 0.51
31 12 0.28
32 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTTATTAATTAAAATAATATTTTATTAATA
Found at i:446200 original size:27 final size:27
Alignment explanation
Indices: 446135--446220 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
446125 TTGTAATCAG
* * *
446135 ATTTAATTTAATTTAATTTATATTATT
1 ATTTAATTTAATTAAAATAATATTATT
446162 ATTT-A-TTAATTAAAATAATATT-TT
1 ATTTAATTTAATTAAAATAATATTATT
*
446186 ATTTAAATTTAATTATAAA-AATATAATT
1 ATTT-AATTTAATTA-AAATAATATTATT
*
446214 TTTTAAT
1 ATTTAAT
446221 AATTTAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
24 6 0.12
25 14 0.29
26 2 0.04
27 19 0.39
28 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTAATTTAATTAAAATAATATTATT
Found at i:446422 original size:11 final size:12
Alignment explanation
Indices: 446394--446456 Score: 71
Period size: 11 Copynumber: 5.5 Consensus size: 12
446384 TGTATTTATT
446394 AATATAATATAA
1 AATATAATATAA
446406 AA-ATAAT-TAA
1 AATATAATATAA
446416 AATATAATATAA
1 AATATAATATAA
*
446428 AATA-AAGATAA
1 AATATAATATAA
*
446439 TATA-AATATATA
1 AATATAATATA-A
446451 AATATA
1 AATATA
446457 TTAAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 5 0.12
11 24 0.56
12 13 0.30
13 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:446423 original size:27 final size:29
Alignment explanation
Indices: 446393--446456 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
446383 TTGTATTTAT
*
446393 TAATATAATATAAAAATAAT-TAAA-ATA
1 TAATATAAAATAAAAATAATATAAATATA
*
446420 TAATATAAAATAAAGATAATATAAATATA
1 TAATATAAAATAAAAATAATATAAATATA
446449 TAAATATA
1 T-AATATA
446457 TTAAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 18 0.56
28 4 0.12
29 4 0.12
30 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TAATATAAAATAAAAATAATATAAATATA
Found at i:446533 original size:20 final size:20
Alignment explanation
Indices: 446508--446557 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
446498 ATATATTAAT
* * *
446508 TTATAATATTTTAAATATAA
1 TTATAATATATAAAAAATAA
446528 TTATAATATATAAAAAATAA
1 TTATAATATATAAAAAATAA
*
446548 ATATAATATA
1 TTATAATATA
446558 AATTCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATAATATATAAAAAATAA
Found at i:446847 original size:37 final size:33
Alignment explanation
Indices: 446796--446898 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 33
446786 GTATAATATT
* *
446796 TTAAATATATAATATATAATATTTTAAATATAA
1 TTAAATTTTTAATATATAATATTTTAAATATAA
*
446829 TTAAATTTTT-AT-TA-AATATTTTAAATATAT
1 TTAAATTTTTAATATATAATATTTTAAATATAA
446859 TTAAATTTTTATTAAATATATAATATTTTAAATATAA
1 TTAAA--TTT-TT-AATATATAATATTTTAAATATAA
446896 TTA
1 TTA
446899 TAATATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 20 0.34
31 2 0.03
32 5 0.08
33 10 0.17
35 2 0.03
36 2 0.03
37 18 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTAAATTTTTAATATATAATATTTTAAATATAA
Found at i:446922 original size:19 final size:19
Alignment explanation
Indices: 446876--446926 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
446866 TTTATTAAAT
*
446876 ATATAATATTTTAAATATAA
1 ATATAATA-TATAAATATAA
*
446896 TTATAATATATAAATATAA
1 ATATAATATATAAATATAA
446915 CATA-AATATATA
1 -ATATAATATATA
446927 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATATATAAATATAA
Found at i:446931 original size:11 final size:11
Alignment explanation
Indices: 446791--446931 Score: 76
Period size: 11 Copynumber: 13.9 Consensus size: 11
446781 TATAAGTATA
*
446791 ATATTTTAAAT
1 ATATATTAAAT
* *
446802 ATATAATATAT
1 ATATATTAAAT
*
446813 AATATTTTAAAT
1 -ATATATTAAAT
446825 ATA-ATTAAAT
1 ATATATTAAAT
* *
446835 TTTTATTAAAT
1 ATATATTAAAT
446846 AT-T-TTAAAT
1 ATATATTAAAT
446855 ATAT-TTAAAT
1 ATATATTAAAT
* *
446865 TTTTATT-AA-
1 ATATATTAAAT
446874 ATATA-T-AAT
1 ATATATTAAAT
446883 AT-T-TTAAAT
1 ATATATTAAAT
*
446892 ATA-ATTATA-
1 ATATATTAAAT
446901 ATATA-TAAAT
1 ATATATTAAAT
*
446911 ATA-ACATAAAT
1 ATATA-TTAAAT
446922 ATATATTAAA
1 ATATATTAAA
446932 AAATTTAAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
8 5 0.05
9 25 0.25
10 27 0.27
11 33 0.33
12 9 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATTAAAT
Found at i:446943 original size:67 final size:65
Alignment explanation
Indices: 446801--446943 Score: 148
Period size: 67 Copynumber: 2.1 Consensus size: 65
446791 ATATTTTAAA
* ** **
446801 TATATAATATATAATATTTTAAATATAATTAAATTTTTATTAAATATTTTAAATATATTTAAATT
1 TATA-AATATATAATATTTTAAATATAATTAAA-TTATATTAAATATCATAAATATATTTAAAAA
446866 TT
64 TT
446868 TATTAAATATATAATATTTTAAATATAATTATAA-TATA-TAAATATAACATAAATATATATTAA
1 TA-TAAATATATAATATTTTAAATATAATTA-AATTATATTAAATAT--CATAAATATAT-TT-A
446931 AAAATT
60 AAAATT
446937 TA-AAATA
1 TATAAATA
446944 ACTTACATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
65 7 0.11
66 3 0.05
67 42 0.65
68 6 0.09
69 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (65 bp):
TATAAATATATAATATTTTAAATATAATTAAATTATATTAAATATCATAAATATATTTAAAAATT
Found at i:447140 original size:10 final size:10
Alignment explanation
Indices: 447125--447169 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
447115 AATTTTATAT
447125 ATAATATAAA
1 ATAATATAAA
447135 ATAATATAAA
1 ATAATATAAA
*
447145 ATAATAAATAA
1 ATAATATA-AA
447156 ATAA-ATAAA
1 ATAATATAAA
447165 TATAA
1 -ATAA
447170 AAATATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 23 0.74
11 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATATAAA
Found at i:447162 original size:12 final size:11
Alignment explanation
Indices: 447127--447174 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
447117 TTTTATATAT
*
447127 AATATAAAATA
1 AATAAAAAATA
447138 ATATAAAATAATA
1 A-ATAAAA-AATA
447151 AATAAATAAATA
1 AATAAA-AAATA
447163 AATATAAAAATA
1 AATA-AAAAATA
447175 TCAAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 1 0.03
12 23 0.72
13 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:447221 original size:30 final size:29
Alignment explanation
Indices: 447156--447281 Score: 87
Period size: 30 Copynumber: 4.2 Consensus size: 29
447146 TAATAAATAA
* ** * *
447156 ATAAATAAATATAAAAATATCAAAATTTT
1 ATAAATAAATATTAATTTATAAAAATTAT
447185 ATTAAATAAATTATTAATTTATAAAAATTAT
1 A-TAAATAAA-TATTAATTTATAAAAATTAT
* * *
447216 ATAAATATATAATATTTTA-AATATAATTAT
1 ATAAATAAATATTAATTTATAA-A-AATTAT
* *
447246 ATATAAAAAATATATAATTAAT-AAAA-TAT
1 ATA-AATAAATAT-TAATTTATAAAAATTAT
447275 ATAAATA
1 ATAAATA
447282 TTAAATCTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
28 5 0.07
29 16 0.21
30 26 0.34
31 23 0.30
32 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAAATAAATATTAATTTATAAAAATTAT
Found at i:447286 original size:7 final size:8
Alignment explanation
Indices: 447120--447287 Score: 53
Period size: 8 Copynumber: 20.1 Consensus size: 8
447110 TAAATAATTT
447120 TATATATAA
1 TATATA-AA
447129 TATA-AAA
1 TATATAAA
447136 TAATATAAA
1 T-ATATAAA
447145 -ATAATAAA
1 TAT-ATAAA
*
447153 TAAATAAA
1 TATATAAA
447161 TAAATATAAA
1 T--ATATAAA
*
447171 AATATCAAA
1 TATAT-AAA
* * *
447180 -ATTTTAT
1 TATATAAA
*
447187 TAAATAAA
1 TATATAAA
*
447195 T-TATTAATT
1 TATA-TAA-A
*
447204 TATAAAAA
1 TATATAAA
447212 TTATATAAA
1 -TATATAAA
447221 TATAT-AA
1 TATATAAA
*
447228 TATTTTAAA
1 TA-TATAAA
*
447237 TATAATTATA
1 TAT-A-TAAA
*
447247 TATAAAAAA
1 TAT-ATAAA
*
447256 TATATAAT
1 TATATAAA
447264 TA-ATAAAA
1 TATAT-AAA
447272 TATATAAA
1 TATATAAA
447280 TAT-TAAA
1 TATATAAA
447287 T
1 T
447288 CTAAATAGCT
Statistics
Matches: 118, Mismatches: 23, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
7 18 0.15
8 52 0.44
9 32 0.27
10 16 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:447572 original size:20 final size:19
Alignment explanation
Indices: 447531--447577 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
447521 TATTAAAATT
* *
447531 TATATTAAATAAATTATTAA
1 TATA-TAAAAAAATTATAAA
447551 TATATAAAAAAATATATAAA
1 TATATAAAAAAAT-TATAAA
447571 TATATAA
1 TATATAA
447578 TATTTCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAAAAAAATTATAAA
Found at i:448391 original size:24 final size:23
Alignment explanation
Indices: 448334--448395 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
448324 TTTATTTTTT
448334 ATAATT-TTTAATTTATTAACAA
1 ATAATTATTTAATTTATTAACAA
448356 A-AATTAATTTTAATTTTATTAA-ATA
1 ATAATT-A-TTTAA-TTTATTAACA-A
448381 ATAATTATTT-ATTTA
1 ATAATTATTTAATTTA
448396 AATTTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 1 0.03
24 9 0.26
25 11 0.32
26 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATTATTTAATTTATTAACAA
Found at i:448720 original size:19 final size:19
Alignment explanation
Indices: 448685--448723 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
448675 CAATCATTTT
*
448685 AAATACAAAATTTAAAATA
1 AAATACAAAATTAAAAATA
448704 AAATA-AAAACTTAAAAATA
1 AAATACAAAA-TTAAAAATA
448723 A
1 A
448724 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AAATACAAAATTAAAAATA
Found at i:449147 original size:22 final size:24
Alignment explanation
Indices: 449086--449147 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
449076 ATTTATTTTT
449086 AATTAAAAAATAATATAATATATTA
1 AATT-AAAAATAATATAATATATTA
449111 ATATTAAAATTATAATAT-ATA-ATTA
1 A-ATTAAAA--ATAATATAATATATTA
449136 AATTAAAAATAA
1 AATTAAAAATAA
449148 ATTTAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.12
24 7 0.21
25 10 0.29
26 6 0.18
27 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTAAAAATAATATAATATATTA
Found at i:449158 original size:30 final size:30
Alignment explanation
Indices: 449092--449163 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
449082 TTTTAATTAA
* * *
449092 AAAATAATATAA-TATATTAATATTAAAATT
1 AAAAT-ATATAATTAAATTAAAAATAAAATT
* *
449122 ATAATATATAATTAAATTAAAAATAAATTT
1 AAAATATATAATTAAATTAAAAATAAAATT
*
449152 AAAATATTTAAT
1 AAAATATATAAT
449164 GTATATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATATATAATTAAATTAAAAATAAAATT
Found at i:449526 original size:20 final size:18
Alignment explanation
Indices: 449514--449563 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
449504 ATATGATAAT
449514 ATTAAATATAATATAAAAA
1 ATTAAA-ATAATATAAAAA
449533 ATTAAAAT-A-AT--AAA
1 ATTAAAATAATATAAAAA
449547 ATTAAAAATAATATAAA
1 ATT-AAAATAATATAAA
449564 TATATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
16 3 0.12
17 3 0.12
18 2 0.08
19 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTAAAATAATATAAAAA
Found at i:449552 original size:33 final size:34
Alignment explanation
Indices: 449500--449563 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
449490 TAAGATTATT
* * *
449500 TTAAATATGATAATATTAAATATAATATAAAAAA
1 TTAAATATAATAAAATTAAAAATAATATAAAAAA
449534 TTAAA-ATAATAAAATTAAAAATAATATAAA
1 TTAAATATAATAAAATTAAAAATAATATAAA
449564 TATATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (34 bp):
TTAAATATAATAAAATTAAAAATAATATAAAAAA
Found at i:449558 original size:15 final size:14
Alignment explanation
Indices: 449526--449564 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
449516 TAAATATAAT
449526 ATAA-AAAATTAAA
1 ATAATAAAATTAAA
449539 ATAATAAAATTAAAA
1 ATAATAAAATT-AAA
449554 ATAATATAAAT
1 ATAATA-AAAT
449565 ATATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 9 0.39
16 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAATAAAATTAAA
Found at i:450159 original size:20 final size:20
Alignment explanation
Indices: 450134--450182 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
450124 TATTTTGTTT
450134 TATTAAAAATAAATTATTTA
1 TATTAAAAATAAATTATTTA
** *
450154 TATTAATATTTAAATTTTTTA
1 TATTAA-AAATAAATTATTTA
450175 -ATTAAAAA
1 TATTAAAAA
450183 AAACACCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAAATAAATTATTTA
Found at i:451595 original size:24 final size:23
Alignment explanation
Indices: 451555--451600 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
451545 TTTCCATTGT
*
451555 ATATTTAGTAATTTTAAAGATTTG
1 ATATTTAGTAATATT-AAGATTTG
451579 ATATTCTAGT-ATATTAAGATTT
1 ATATT-TAGTAATATTAAGATTT
451601 ATTCACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (23 bp):
ATATTTAGTAATATTAAGATTTG
Found at i:451807 original size:17 final size:17
Alignment explanation
Indices: 451783--451820 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 17
451773 TAATAAATAC
451783 AAATATATATTTAATAAAT
1 AAATAT-TATTTAA-AAAT
451802 AAATATTATTTAAAAAT
1 AAATATTATTTAAAAAT
451819 AA
1 AA
451821 GTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTATTTAAAAAT
Found at i:451932 original size:6 final size:6
Alignment explanation
Indices: 451925--451998 Score: 96
Period size: 6 Copynumber: 12.3 Consensus size: 6
451915 TATAATTTTA
* * * *
451925 ATTATA ATTATA AATTATT ATTATT ATTATT TTTAAT A-TATT ATTATT
1 ATTATT ATTATT A-TTATT ATTATT ATTATT ATTATT ATTATT ATTATT
451973 ATTATT ATTATT ATTATT ATTATT AT
1 ATTATT ATTATT ATTATT ATTATT AT
451999 GTATAAAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
5 4 0.07
6 52 0.85
7 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATTATT
Found at i:451942 original size:7 final size:6
Alignment explanation
Indices: 451915--451998 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
451905 CAAAAGAAAA
* * * **
451915 TATAAT TTTAAT TATAAT TATAAAT TATTAT TATTAT TATTTT TAATATAT
1 TATAAT TATAAT TATAAT TAT-AAT TATAAT TATAAT TATAAT T-ATA-AT
* * * * *
451966 TATTAT TATTAT TATTAT TATTAT TATTAT TAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TAT
451999 GTATAAAAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
6 56 0.82
7 10 0.15
8 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATAAT
Found at i:451946 original size:3 final size:3
Alignment explanation
Indices: 451938--451998 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
451928 ATAATTATAA
* *
451938 ATT ATT ATT ATT ATT ATT TTT AAT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
451985 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
451999 GTATAAAAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:452296 original size:18 final size:19
Alignment explanation
Indices: 452260--452309 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
452250 AAAAATAAAT
452260 AAAATATAATATAACATAA
1 AAAATATAATATAACATAA
* *
452279 AAAATATTAT-TAATATAA
1 AAAATATAATATAACATAA
*
452297 ATAA-ATAATATAA
1 AAAATATAATATAA
452310 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 13 0.50
19 9 0.35
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATATAATATAACATAA
Found at i:452336 original size:12 final size:12
Alignment explanation
Indices: 452289--452336 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
452279 AAAATATTAT
452289 TAATATAAATAAA
1 TAATATAAA-AAA
452302 TAATATAATAAAA
1 TAATATAA-AAAA
*
452315 TTTATATAAAAAA
1 -TAATATAAAAAA
*
452328 TAATTTAAA
1 TAATATAAA
452337 TACTGATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 7 0.23
13 15 0.50
14 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATATAAAAAA
Found at i:453606 original size:8 final size:8
Alignment explanation
Indices: 453593--453631 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
453583 TGGACAAATG
453593 AATAAAAA
1 AATAAAAA
453601 AATAAAAA
1 AATAAAAA
453609 AATAAAAA
1 AATAAAAA
453617 AATAAAAA
1 AATAAAAA
453625 AATAAAA
1 AATAAAA
453632 TATCCAATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:457957 original size:25 final size:25
Alignment explanation
Indices: 457927--457977 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
457917 TGACATAACG
*
457927 TATTAAAATATTTTAAAATATTTAT
1 TATTAAAATATTATAAAATATTTAT
* *
457952 TATTAAATTATTATAAGATATTTAT
1 TATTAAAATATTATAAAATATTTAT
457977 T
1 T
457978 TTCATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTAAAATATTATAAAATATTTAT
Done.