Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold499
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: 498087
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 4 of 4
Found at i:422046 original size:17 final size:17
Alignment explanation
Indices: 421997--422047 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
421987 AAAATATGGC
*
421997 TAAAATATGAA-AAAAAA
1 TAAAATAT-AATAAAATA
*
422014 TAAAATATATTAAAATA
1 TAAAATATAATAAAATA
422031 TAAAA-ATAATATAAATA
1 TAAAATATAATA-AAATA
422048 CGATAGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAATATAATAAAATA
Found at i:424328 original size:10 final size:11
Alignment explanation
Indices: 424306--424334 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
424296 GAAGTTTTTA
424306 TGAAAAATGTT
1 TGAAAAATGTT
424317 TGAAAAAT-TT
1 TGAAAAATGTT
424327 TGAAAAAT
1 TGAAAAAT
424335 CATCTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (11 bp):
TGAAAAATGTT
Found at i:426582 original size:30 final size:31
Alignment explanation
Indices: 426548--426623 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 31
426538 CCAGTGATAT
426548 TGGG-TTTAGAAGGGTTGCCACCAACTTATG
1 TGGGCTTTAGAAGGGTTGCCACCAACTTATG
* ** * *
426578 TGGGTTTTAGAGAAAGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCAACTTATG
*
426610 TGGGCTTTAAAAGG
1 TGGGCTTTAGAAGG
426624 ATACCATTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.11
31 7 0.19
32 25 0.69
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCAACTTATG
Found at i:426651 original size:28 final size:28
Alignment explanation
Indices: 426608--427050 Score: 362
Period size: 28 Copynumber: 15.7 Consensus size: 28
426598 CACCGACTTG
** *
426608 TGTGGGCTTTAAAAGGATACCATTGACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
* *
426636 TATGGGTTTTGGAAGG-TGCC-TCTGACT
1 TGTGGGCTTTGGAAGGATGCCAT-TGACT
* *
426663 TGTGGGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
* * * * *
426691 TATGAGCTTTGAAAGGATGCTATTAACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
* *
426719 CGT-GGCTTTGGAAGGATGCCATTAACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
*
426746 TGTGGGCTTT-GAAGAGATGCCACTGACT
1 TGTGGGCTTTGGAAG-GATGCCATTGACT
* *
426774 TGTGGGCTTT-GAAGAGATACCACTGACT
1 TGTGGGCTTTGGAAG-GATGCCATTGACT
* * *
426802 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
* * *
426830 TGTGGGCTATGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-GAAGGATGCCATTGACT
* * * *
426858 TGTGAGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTG-GAAGGATGCCATTGACT
* * *
426887 TGTGGGCTTTGAAAAAGG-TGCTACTGACT
1 TGTGGGCTTTG--GAAGGATGCCATTGACT
* *
426916 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
* * *
426944 TGTGGGCTTTGAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTG--GAAGGATGCCATTGACT
* * *
426974 TGTGGGCTTTGAAAAAGGCTGCCACTGACT
1 TGTGGGCTTTG--GAAGGATGCCATTGACT
* *
427004 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGGAAGGATGCCATTGACT
427032 TGTGGGCTTT-GAAGAGATG
1 TGTGGGCTTTGGAAG-GATG
427051 AACGTTCTAG
Statistics
Matches: 365, Mismatches: 37, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.00
27 55 0.15
28 196 0.54
29 51 0.14
30 62 0.17
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGGAAGGATGCCATTGACT
Found at i:426965 original size:58 final size:56
Alignment explanation
Indices: 426608--427044 Score: 513
Period size: 56 Copynumber: 7.7 Consensus size: 56
426598 CACCGACTTG
* * * * * *
426608 TGTGGGCTTT-AAAAGGATACCATTGACTTATGGGTTTTGGAAGG-TGCCTCTGACT
1 TGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
426663 TGTGGGCTTTGAAAAGATGCCATTGACTTATGAGCTTTGAAAGGATGCTATTAACT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
426719 CGT-GGCTTTGGAAGGATGCCATTAACTTGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * *
426774 TGTGGGCTTTGAAGAGATACCACTGACTTGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
426830 TGTGGGCTATGAAAAGGTGCCACTGACTTGTGAGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
* *
426887 TGTGGGCTTTGAAAAAGGTGCTACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
426944 TGTGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAGGCTGCCACTGACT
1 TGTGGGCTTTG-AAAA-GATGCCACTGACTTGTGGGCTTTG--AAAGGATGCCACTGACT
*
427004 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
427045 GAGATGAACG
Statistics
Matches: 332, Mismatches: 40, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
54 3 0.01
55 77 0.23
56 89 0.27
57 61 0.18
58 72 0.22
59 3 0.01
60 27 0.08
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:428542 original size:30 final size:32
Alignment explanation
Indices: 428419--428521 Score: 174
Period size: 32 Copynumber: 3.3 Consensus size: 32
428409 CCAACGACAT
* *
428419 TGGG-TTTAGA-AAGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
428449 TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
428481 TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
428513 TGGGCTTTA
1 TGGGCTTTA
428522 AAAGGATGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
30 4 0.06
31 6 0.09
32 59 0.86
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.30
Consensus pattern (32 bp):
TGGGCTTTAGAGAAAGTTGCCACCGACTTGTG
Found at i:428564 original size:28 final size:28
Alignment explanation
Indices: 428447--428564 Score: 67
Period size: 32 Copynumber: 3.9 Consensus size: 28
428437 CACCAACTTG
* * *
428447 TGTGGGCTTTAGAGAAAGTTGCCACCGACTT
1 TGTGGGCTTTA-A-AAGGATGCCACTGAC-T
* * *
428478 GTGTGGGCTTTAGAGAAAGTTGCCACCGACTT
1 -TGTGGGCTTTA-A-AAGGATGCCACTGAC-T
*
428510 GTGTGGGCTTTAAAAGGATGTCACTGACT
1 -TGTGGGCTTTAAAAGGATGCCACTGACT
* *
428539 TGTGGGTTTTGAAAAGG-TGCCTCTGA
1 TGTGGGCTTT-AAAAGGATGCCACTGA
428565 TTAATTAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
28 16 0.21
29 7 0.09
30 11 0.14
31 1 0.01
32 43 0.55
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:429324 original size:21 final size:21
Alignment explanation
Indices: 429298--429338 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
429288 TATAGAAAAA
* *
429298 TAAAATATATTTTAATATATT
1 TAAAATATAATTCAATATATT
429319 TAAAATATAATTCAATATAT
1 TAAAATATAATTCAATATAT
429339 AACTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATATAATTCAATATATT
Found at i:429368 original size:16 final size:17
Alignment explanation
Indices: 429333--429366 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
429323 ATATAATTCA
*
429333 ATATATAACTATTATTTT
1 ATATATAAATATTA-TTT
429351 ATATATAAATATTATT
1 ATATATAAATATTATT
429367 ATTTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.13
18 13 0.87
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATAAATATTATTT
Found at i:429379 original size:20 final size:21
Alignment explanation
Indices: 429342--429382 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
429332 AATATATAAC
*
429342 TATTATTTTATATATAAATAT
1 TATTATTTAATATATAAATAT
429363 TATTATTTAATAT-TAAATAT
1 TATTATTTAATATATAAATAT
429383 GATGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTTAATATATAAATAT
Found at i:429440 original size:13 final size:12
Alignment explanation
Indices: 429391--429496 Score: 74
Period size: 13 Copynumber: 8.5 Consensus size: 12
429381 ATGATGTATA
* *
429391 AAATATAATTAT
1 AAATATATTTTT
429403 AAATATTATTTTGT
1 AAATA-TATTTT-T
429417 AAAT-TATTTTTT
1 AAATATA-TTTTT
429429 AAAGTATATTTTT
1 AAA-TATATTTTT
*
429442 -AATATAATTTT
1 AAATATATTTTT
429453 AAATATTATTTTT
1 AAATA-TATTTTT
* *
429466 AAGTTTAATTTGTT
1 AAATAT-ATTT-TT
429480 AAA-ATATTTTT
1 AAATATATTTTT
*
429491 AGATAT
1 AAATAT
429497 TTATTTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
11 12 0.16
12 24 0.32
13 28 0.37
14 11 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:429452 original size:11 final size:12
Alignment explanation
Indices: 429391--429464 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
429381 ATGATGTATA
*
429391 AAATATAATTAT
1 AAATATAATTTT
*
429403 AAATATTATTTTGT
1 AAATA-TAATTT-T
*
429417 AAAT-TATTTTTT
1 AAATATA-ATTTT
429429 AAAGTAT-ATTTT
1 AAA-TATAATTTT
*
429441 TAATATAATTTT
1 AAATATAATTTT
*
429453 AAATATTATTTT
1 AAATATAATTTT
429465 TAAGTTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 3 0.06
12 32 0.64
13 9 0.18
14 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (12 bp):
AAATATAATTTT
Found at i:429487 original size:25 final size:23
Alignment explanation
Indices: 429392--429496 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 23
429382 TGATGTATAA
*
429392 AATATAATTATAAATATTATTTTGT
1 AATATAATTTTAAATA-TATTTT-T
*
429417 AA-ATTATTTTTTAAAGTATATTTTT
1 AATA-TA-ATTTTAAA-TATATTTTT
429442 AATATAATTTTAAATATTATTTTT
1 AATATAATTTTAAATA-TATTTTT
*
429466 AAGTTTAATTTGTTAAA-ATATTTTT
1 AA-TATAA-TT-TTAAATATATTTTT
429491 AGATAT
1 A-ATAT
429497 TTATTTTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
23 2 0.03
24 17 0.26
25 23 0.35
26 17 0.26
27 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
AATATAATTTTAAATATATTTTT
Found at i:429497 original size:38 final size:36
Alignment explanation
Indices: 429419--429505 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 36
429409 TATTTTGTAA
*
429419 ATTATTTTTTAAAGTATATTTTTAATATAATTTTAAAT
1 ATTA-TTTTT-AAGTATATTTTTAAAATAATTTTAAAT
* * *
429457 ATTATTTTTAAGTTTAATTTGTTAAAATATTTTTAGAT
1 ATTATTTTTAAGTAT-ATTT-TTAAAATAATTTTAAAT
429495 ATTTATTTTTA
1 A-TTATTTTTA
429506 TTAATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.12
37 9 0.21
38 19 0.45
39 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (36 bp):
ATTATTTTTAAGTATATTTTTAAAATAATTTTAAAT
Found at i:429596 original size:16 final size:15
Alignment explanation
Indices: 429577--429608 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
429567 TAAATTTTTT
429577 ATAATATAAATTAAAA
1 ATAATATAAA-TAAAA
429593 ATAATATAAATAAAA
1 ATAATATAAATAAAA
429608 A
1 A
429609 CCAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATATAAATAAAA
Found at i:430185 original size:12 final size:12
Alignment explanation
Indices: 430154--430204 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
430144 TATTTTAAGG
*
430154 TAAATATCAAATA
1 TAAATAT-ATATA
* *
430167 CAAATATACATA
1 TAAATATATATA
430179 TAAATATATATA
1 TAAATATATATA
*
430191 TATATATATATA
1 TAAATATATATA
430203 TA
1 TA
430205 TGTTCAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
12 27 0.82
13 6 0.18
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAATATATATA
Found at i:430189 original size:2 final size:2
Alignment explanation
Indices: 430170--430205 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
430160 TCAAATACAA
* *
430170 AT AT AC AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
430206 GTTCAACAAG
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:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:434974 original size:24 final size:24
Alignment explanation
Indices: 434926--434980 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
434916 CATCAATTCC
*
434926 ATTTTATTATCTTAATTTAATTTG
1 ATTTTATTATATTAATTTAATTTG
*
434950 ATTTTATTATAATTTATTTAA-TTG
1 ATTTTATTAT-ATTAATTTAATTTG
*
434974 AGTTTAT
1 ATTTTAT
434981 ATTACTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (24 bp):
ATTTTATTATATTAATTTAATTTG
Found at i:435120 original size:28 final size:27
Alignment explanation
Indices: 435065--435120 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
435055 TTTATAATAT
* *
435065 TATTAAAATATTTTTTATTAATATAAA
1 TATTAAAATATTTTTTATTAAAAAAAA
435092 TATTAAAAATAATTTTTT-TTAAAAAAAA
1 TATT-AAAAT-ATTTTTTATTAAAAAAAA
435120 T
1 T
435121 TTATATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATTAAAATATTTTTTATTAAAAAAAA
Found at i:435650 original size:6 final size:5
Alignment explanation
Indices: 435624--435664 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
435614 TAAACTTGTA
435624 AATTT AATTT AATTT AATTT AAATTT AAATTT AATTT AATT
1 AATTT AATTT AATTT AATTT -AATTT -AATTT AATTT AATT
435665 CGACACGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:435654 original size:22 final size:21
Alignment explanation
Indices: 435622--435664 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
435612 GTTAAACTTG
435622 TAAATTTAATTTAATTTAATT
1 TAAATTTAATTTAATTTAATT
435643 TAAATTTAAATTTAATTTAATT
1 TAAATTT-AATTTAATTTAATT
435665 CGACACGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAATTTAATTTAATTTAATT
Found at i:435891 original size:20 final size:19
Alignment explanation
Indices: 435831--435891 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
435821 TAAAATCTTT
*
435831 TATTATTTAA-ATAATAAA
1 TATTATTTAATATAATGAA
* *
435849 TATTATTTAATATAATTAT
1 TATTATTTAATATAATGAA
435868 TATTATTTTAATATTAA-GAA
1 TATTA-TTTAATA-TAATGAA
435888 TATT
1 TATT
435892 TTTCATGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.28
19 11 0.31
20 12 0.33
21 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTATTTAATATAATGAA
Found at i:436158 original size:23 final size:23
Alignment explanation
Indices: 436132--436197 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 23
436122 TTTATTTATT
436132 ATATTATATTAAATAAAATTTAA
1 ATATTATATTAAATAAAATTTAA
436155 ATA-TATATTTAAAT--AATTTAA
1 ATATTATA-TTAAATAAAATTTAA
*
436176 A-ATT-TTTTAAA-AAAA-TTAA
1 ATATTATATTAAATAAAATTTAA
436195 ATA
1 ATA
436198 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
19 10 0.27
20 5 0.14
21 9 0.24
22 4 0.11
23 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTATATTAAATAAAATTTAA
Found at i:436732 original size:3 final size:3
Alignment explanation
Indices: 436724--436761 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
436714 CATCATTGTC
436724 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
436762 CTTACATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:439551 original size:18 final size:18
Alignment explanation
Indices: 439512--439551 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
439502 ATATTTACAT
*
439512 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
439530 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
439548 ATAA
1 ATAA
439552 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:450138 original size:22 final size:22
Alignment explanation
Indices: 450107--450159 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
450097 TTGGCGTGAC
450107 AATAATATATAGCTAAAATACAA
1 AATAATATATA-CTAAAATACAA
* *
450130 AA-AATATATATTAAAATATAA
1 AATAATATATACTAAAATACAA
450151 AATAATATA
1 AATAATATA
450160 AATACAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 14 0.52
23 2 0.07
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAATATATACTAAAATACAA
Found at i:452526 original size:21 final size:21
Alignment explanation
Indices: 452500--452540 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
452490 TATAGAGAAA
* *
452500 TAAAATATATTTTAATATATC
1 TAAAATATAATTCAATATATC
452521 TAAAATATAATTCAATATAT
1 TAAAATATAATTCAATATAT
452541 AAATACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAATATAATTCAATATATC
Found at i:457345 original size:21 final size:20
Alignment explanation
Indices: 457309--457361 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
457299 GTGGTAAAAT
* * *
457309 ATTAAATTTTAATTTTAATG
1 ATTAAAATTAAATTTTAATA
457329 ATTAAAAATTAAATTTTAATA
1 ATT-AAAATTAAATTTTAATA
*
457350 ATTATAATTAAA
1 ATTAAAATTAAA
457362 AAAATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTAAAATTAAATTTTAATA
Found at i:457359 original size:27 final size:27
Alignment explanation
Indices: 457303--457363 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
457293 GACGTGGTGG
* *
457303 TAAAATATTAAATTTTAATTTTAATGAT
1 TAAAA-ATTAAATTTTAATATTAATAAT
457331 TAAAAATTAAATTTTAATAATT-ATAAT
1 TAAAAATTAAATTTTAAT-ATTAATAAT
457358 TAAAAA
1 TAAAAA
457364 AATTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAAATTAAATTTTAATATTAATAAT
Found at i:457712 original size:108 final size:111
Alignment explanation
Indices: 457553--457772 Score: 326
Period size: 111 Copynumber: 2.0 Consensus size: 111
457543 TATTTTTTAA
*
457553 TAAAAATAATATTTAATTAAGTTTAAAAAATTTTACATTAAAATATTAAAATATTAATT-TTTTA
1 TAAAAATAATATTTAATTAAGTTTAAAAAA-TTTACATTAAAATATTAAAATATTAATTATTATA
457617 -AAATA-AAAAATAAAAAG-AGTTTATTATTATTATTTTTAATAAAAT
65 TAAATATAAAAATAAAAAGTA-TTTATTATTATTATTTTTAATAAAAT
457662 TAAAAATAATATTTAATTAAGTTTTAAAAAA-TTACATTAACAA-ATTAAAATATTAATTATTAT
1 TAAAAATAATATTTAATTAAG-TTTAAAAAATTTACATTAA-AATATTAAAATATTAATTATTAT
***
457725 ATTTTTATAAAAATAAAAAGTATTTATTATTATTATTTTTAATAAAAT
64 ATAAATATAAAAATAAAAAGTATTTATTATTATTATTTTTAATAAAAT
457773 AATTGATAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
108 24 0.24
109 27 0.27
110 11 0.11
111 38 0.38
112 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (111 bp):
TAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAAAATATTAAAATATTAATTATTATAT
AAATATAAAAATAAAAAGTATTTATTATTATTATTTTTAATAAAAT
Found at i:457756 original size:33 final size:34
Alignment explanation
Indices: 457703--457771 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
457693 TTACATTAAC
*
457703 AAATTAAAATATTAATTATTA-TATTTTT-ATAA
1 AAATAAAAATATTAATTATTATTATTTTTAATAA
*
457735 AAATAAAAAGTATTTATTATTATTATTTTTAATAA
1 AAATAAAAA-TATTAATTATTATTATTTTTAATAA
457770 AA
1 AA
457772 TAATTGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 8 0.25
33 11 0.34
34 7 0.22
35 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (34 bp):
AAATAAAAATATTAATTATTATTATTTTTAATAA
Found at i:461677 original size:88 final size:89
Alignment explanation
Indices: 461498--461767 Score: 237
Period size: 88 Copynumber: 3.0 Consensus size: 89
461488 CCATATCCTG
* * * * *
461498 TAACATATAAAATTAATCAACTTTTTTGCTTTTCTAT-AAAAAGAAATCTGATTCTCAAATATAA
1 TAACATTTACAATCAATCAACTTTTCT--TTTTCTATAAAAAAG-AATATGATTCTC-AATATAA
* * *
461562 TTTATGTATTAGTTTAAAT-TTTACAGTC
62 TTCATGCATTAGTTT-AATCATTACAGTC
* * *
461590 TGACATTTATAATCAATTAAC-TTT-TTTTTCTATAAAAAAGAATATGATTCTCTAATATAATTC
1 TAACATTTACAATCAATCAACTTTTCTTTTTCTATAAAAAAGAATATGATTCTC-AATATAATTC
*
461653 ATGCATTAGTTTAATCATTGCAGTC
65 ATGCATTAGTTTAATCATTACAGTC
* * * * *
461678 TAACATTTACACTTAATCAACTTTTCTTTTTTTATAAAAAA-AAAATTCGATT-TCAGATACAAT
1 TAACATTTACAATCAATCAACTTTTCTTTTTCTATAAAAAAGAATA-T-GATTCTCA-ATATAAT
* * *
461741 TCATGCATTAGTCTAATCCTTATAGTC
63 TCATGCATTAGTTTAATCATTACAGTC
461768 ATTCTTTTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
87 3 0.02
88 62 0.42
89 13 0.09
90 47 0.32
91 7 0.05
92 16 0.11
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (89 bp):
TAACATTTACAATCAATCAACTTTTCTTTTTCTATAAAAAAGAATATGATTCTCAATATAATTCA
TGCATTAGTTTAATCATTACAGTC
Found at i:461778 original size:68 final size:68
Alignment explanation
Indices: 461701--461835 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
461691 TAATCAACTT
461701 TTCTTTTTTTATAAAAAAAAAATTCGATT-TCAGATACAATTCATGCATTAGTCTAATCCTTATA
1 TTCTTTTTTTAT-AAAAAAAAATTCGATTCTCAGATACAATTCATGCATTAGTCTAATCCTTATA
461765 GTCA
65 GTCA
* * * *
461769 TTCTTTTTTTCTATAAAAAAATTTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTATAG
1 TTCTTTTTTTATAAAAAAAAATTCGATTCTCAGATACAATTCATGCATTAGTCTAATCCTTATAG
461834 TC
66 TC
461836 TGAAATTTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 14 0.23
68 48 0.77
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (68 bp):
TTCTTTTTTTATAAAAAAAAATTCGATTCTCAGATACAATTCATGCATTAGTCTAATCCTTATAG
TCA
Found at i:461996 original size:86 final size:84
Alignment explanation
Indices: 461771--462212 Score: 368
Period size: 85 Copynumber: 5.2 Consensus size: 84
461761 TATAGTCATT
* * ** *
461771 CTTTTTTTCTATAAAAAAATTTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTATAGTC
1 CTTTTTTTATA-AAAAAAAATCAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
* *
461836 TGAAATTTACAATTAATCAA
65 TGACATTTACAATCAATCAA
* * * * *
461856 -TTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTCATGCATTAGTCTAATCTTTACAGT
1 CTTTTTT-TATAAAAAA-AAATCAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
* *
461920 CTGATATTTATAATCAATCAA
64 CTGACATTTACAATCAATCAA
* *
461941 CTTTTTTGTATAAAAAAAAATACAATTCTCGGATATAATTCATGCATTAGTCTAATCCTTGCAGT
1 CTTTTTT-TATAAAAAAAAAT-CAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
* * ***
462006 -T-AC---T-CGATGAACTTTT
64 CTGACATTTACAATCAA-TCAA
** * * * * *
462022 CTTTTTTTAT--AAAAAAATCTAATTCTTTGATATAATTAATACATTAGTTTAAGT-TTTATAGT
1 CTTTTTTTATAAAAAAAAATC-AATTCTCAGATATAATTCATGCATTAGTCTAA-TCCTTACAGT
* *
462084 CTAACATTTACACTCAATCAA
64 CTGACATTTACAATCAATCAA
* * * *
462105 -TTTTTTTATAAAAAAAAAAAATCGATT-TCAAATACAATTTATGCATTAGTCTAATCCTTACAG
1 CTTTTTTTAT---AAAAAAAAATCAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAG
462168 TCTGACATTTACAATCAATCAA
63 TCTGACATTTACAATCAATCAA
*
462190 CTTTTTTTCTATAAAAAAGAATC
1 C-TTTTTT-TATAAAAAAAAATC
462213 TGATTTGCAG
Statistics
Matches: 283, Mismatches: 52, Indels: 44
0.75 0.14 0.12
Matches are distributed among these distances:
77 1 0.00
78 40 0.14
79 2 0.01
80 9 0.03
81 9 0.03
82 9 0.03
83 2 0.01
84 17 0.06
85 121 0.43
86 55 0.19
87 15 0.05
88 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (84 bp):
CTTTTTTTATAAAAAAAAATCAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTCT
GACATTTACAATCAATCAA
Found at i:462105 original size:249 final size:237
Alignment explanation
Indices: 461527--462207 Score: 670
Period size: 249 Copynumber: 2.8 Consensus size: 237
461517 ACTTTTTTGC
* * * ** * *
461527 TTTTCTATAAAAAGAAATCTGATTCTCAAATATAATTTATGTATTAGTTTAAATTTTACAGTCTG
1 TTTTCTAT-AAAA-AAATCTAATTCTCAGATATAATTAATACATTAGTTT-AATTTTATAGTCTA
* *
461592 ACATTTATAATCAATTAACTTTTTTTTCTATAAAAAAGAATATGATTCTCT-AATATAATTCATG
63 ACATTTACAATCAATCAA---TTTTTTCTATAAAAAAGAAT-TGATTCT-TAAATATAATTCATG
* * * * * *
461656 CATTAGTTTAATCATTGCAGTCTAACATTTACACTTAATCAACTTTTCTTTTTTTATAAAAAAAA
123 CATTAGTCTAATCATTACAGTCTGACATTTACAATCAATCAAC--TT-TTTTTCTAT-AAAAAAA
* * *
461721 AATTCGATTTCAGATACAATTCATGCATTAGTCTAATCCTTATAGTCATTCTTT
184 AATACAATTTCAGATACAATTCATGCATTAGTCTAATCCTTATACTCATTCTTT
* * * * * *
461775 TTTTCTATAAAAAAATTTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTATAGTCTGAA
1 TTTTCTATAAAAAAATCTAATTCTCAGATATAATTAATACATTAGTTTAAT-TTTATAGTCT-AA
* *
461840 -ATTTACAATTAATCAATTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTCATGCATTA
64 CATTTACAATCAATCAATTTTTTCTATAAAAAAGAA-TTGATTCTTAAATATAATTCATGCATTA
* * * *
461904 GTCTAATCTTTACAGTCTGATATTTATAATCAATCAAC-TTTTTTGTATAAAAAAAAATACAATT
128 GTCTAATCATTACAGTCTGACATTTACAATCAATCAACTTTTTTTCTATAAAAAAAAATACAATT
* * *
461968 CTCGGATATAATTCATGCATTAGTCTAATCCTTGCAGTTACTCGATGAACTTTTCT
193 -TCAGATACAATTCATGCATTAGTCTAATCCTT--A--TACTC-AT----TCTT-T
* **
462024 TTTTTTATAAAAAAATCTAATTCTTTGATATAATTAATACATTAGTTTAAGTTTTATAGTCTAAC
1 TTTTCTATAAAAAAATCTAATTCTCAGATATAATTAATACATTAGTTTAA-TTTTATAGTCTAAC
* * * * * *
462089 ATTTACACTCAATCAATTTTTT-TATAAAAAAAAAAAATCGATT-TCAAATACAATTTATGCATT
65 ATTTACAATCAATCAATTTTTTCTAT---AAAAAAGAATTGATTCTTAAATATAATTCATGCATT
*
462152 AGTCTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTTTTCTATAAAAAA
127 AGTCTAATCATTACAGTCTGACATTTACAATCAATCAACTTTTTTTCTATAAAAAA
462208 GAATCTGATT
Statistics
Matches: 364, Mismatches: 48, Indels: 40
0.81 0.11 0.09
Matches are distributed among these distances:
238 14 0.04
239 38 0.10
240 1 0.00
241 1 0.00
242 1 0.00
243 77 0.21
244 3 0.01
245 3 0.01
246 52 0.14
247 5 0.01
248 16 0.04
249 125 0.34
250 20 0.05
251 8 0.02
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (237 bp):
TTTTCTATAAAAAAATCTAATTCTCAGATATAATTAATACATTAGTTTAATTTTATAGTCTAACA
TTTACAATCAATCAATTTTTTCTATAAAAAAGAATTGATTCTTAAATATAATTCATGCATTAGTC
TAATCATTACAGTCTGACATTTACAATCAATCAACTTTTTTTCTATAAAAAAAAATACAATTTCA
GATACAATTCATGCATTAGTCTAATCCTTATACTCATTCTTT
Found at i:462122 original size:164 final size:166
Alignment explanation
Indices: 461856--462168 Score: 384
Period size: 164 Copynumber: 1.9 Consensus size: 166
461846 AATTAATCAA
* *
461856 TTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTCATGCATTAGTCTAATCTTTACAGTC
1 TTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTAATACATTAGTCTAATCTTTACAGTC
* * * * * ** *
461921 TGATATTTATAATCAATCAACTTTTTTGT-ATAAAAAAAAATACAATTCTCGGATATAATTCATG
66 TAACATTTACAATCAATCAACTTTTTTATAAAAAAAAAAAAT-CAATT-TCAAATACAATTCATG
*
461985 CATTAGTCTAATCCTTGCAGTTACTCGATGAACTTTTC
129 CATTAGTCTAATCCTTACAGTTACTCGATGAACTTTTC
* ** * *
462023 TTTTTT-TATAAAAAA-ATC-TAATTCTTTGATATAATTAATACATTAGTTTAAGT-TTTATAGT
1 TTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTAATACATTAGTCTAA-TCTTTACAGT
* * * *
462084 CTAACATTTACACTCAATCAATTTTTTTATAAAAAAAAAAAATCGATTTCAAATACAATTTATGC
65 CTAACATTTACAATCAATCAACTTTTTTATAAAAAAAAAAAATCAATTTCAAATACAATTCATGC
462149 ATTAGTCTAATCCTTACAGT
130 ATTAGTCTAATCCTTACAGT
462169 CTGACATTTA
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
163 32 0.26
164 63 0.51
165 14 0.11
166 9 0.07
167 6 0.05
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (166 bp):
TTTTTTCTATAAAAAAGAACTTAATTCTTAAATATAATTAATACATTAGTCTAATCTTTACAGTC
TAACATTTACAATCAATCAACTTTTTTATAAAAAAAAAAAATCAATTTCAAATACAATTCATGCA
TTAGTCTAATCCTTACAGTTACTCGATGAACTTTTC
Found at i:462364 original size:85 final size:87
Alignment explanation
Indices: 462249--462414 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 87
462239 AATCAACTTT
* * * *
462249 TTTTTTTAAATAAAAAAAGAATCTTATTCTCTGATATAATTCATGTA-TTATCTAATCGTTGT-A
1 TTTTTTT-AATAAAAAAAGAATCTAATTCTCAGATATAATTCATGTACTAATCTAATAGTTGTAA
*
462312 TCCTGACATTTACAATCAATTAAC
65 T-CTGACACTTACAATCAATTAAC
* *
462336 TTTTTTT-ATAAAAAAAGAAT-TAAATTCTCAGATATAATTTATGTACTAATCTAATATTTGTAA
1 TTTTTTTAATAAAAAAAGAATCT-AATTCTCAGATATAATTCATGTACTAATCTAATAGTTGTAA
462399 TCTGACACTTACAATC
65 TCTGACACTTACAATC
462415 TATGCATTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
84 1 0.01
85 33 0.48
86 26 0.38
87 9 0.13
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.42
Consensus pattern (87 bp):
TTTTTTTAATAAAAAAAGAATCTAATTCTCAGATATAATTCATGTACTAATCTAATAGTTGTAAT
CTGACACTTACAATCAATTAAC
Found at i:463170 original size:46 final size:46
Alignment explanation
Indices: 463120--463307 Score: 108
Period size: 46 Copynumber: 4.2 Consensus size: 46
463110 AAATTTTTTA
463120 TTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAATTT
1 TTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAATTT
* * * * *
463166 TTTT---AAACTTAATTAAATATTATTTTTTATTTTATTAA-A-AATTA
1 TTTTAAAAAACATAA-T-AAT-TAATATTTTAATTTATTAATATAATTT
** * ** * * **
463210 TAATAAAAAAC-T--T-GTTTTTATTTT-ATTATTTTAAAATTTTTTAT
1 TTTTAAAAAACATAATAATTAATATTTTAATT-TATTAATA-TAATT-T
*
463254 TTTTATAAAAATATAATAATTAATATTTTAATTTATTAATATAATTT
1 TTTTA-AAAAACATAATAATTAATATTTTAATTTATTAATATAATTT
463301 TTTTAAA
1 TTTTAAA
463308 CTTAATTAAA
Statistics
Matches: 100, Mismatches: 25, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
39 2 0.02
40 12 0.12
41 2 0.02
43 10 0.10
44 10 0.10
45 9 0.09
46 24 0.24
47 10 0.10
48 4 0.04
49 14 0.14
50 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.55
Consensus pattern (46 bp):
TTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAATTT
Found at i:463276 original size:135 final size:133
Alignment explanation
Indices: 463098--463457 Score: 510
Period size: 135 Copynumber: 2.7 Consensus size: 133
463088 ATAAAAAACT
463098 TTTTTTCA-TTTAAAATTTTTTATTTTA-AAAAACATAATAATTAATATTTTAATTTATTAATAT
1 TTTTTT-ATTTTAAAATTTTTTATTTTATAAAAA-ATAATAATTAATATTTTAATTTATTAATAT
* *
463161 AATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATT-AAA-AATTATAATAAAAAACTTG
64 AATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAATAATAATAATAAAAAACCT-
463224 TTTTTA
128 TTTTTA
463230 TTTTATTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAATATTTTAATTTATTAATA
1 TTTT-TTATTTTAAAATTTTTTA-TTTTATAAAAA-ATAATAATTAATATTTTAATTTATTAATA
* * *
463295 TAATTTTTTTAAACTTAATTAAATACTATTTTTAATTTTATTAAAATAATAATAATAATAAACCT
63 TAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAATAATAATAATAAAAAACCT
463360 TTTTTA
128 TTTTTA
*
463366 TTTTTTATTTT--AA-TTTTTA-TTT-T--AAAA-AATAATTAATATTTTAATTTGTTAATATAA
1 TTTTTTATTTTAAAATTTTTTATTTTATAAAAAATAATAATTAATATTTTAATTTATTAATAT-A
*
463423 ATTTTTTTAAATTTAATTAAATATTATTTTTTATT
65 ATTTTTTTAAACTTAATTAAATATTATTTTTTATT
463458 AAAAATAATA
Statistics
Matches: 211, Mismatches: 10, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
125 27 0.13
126 34 0.16
127 3 0.01
129 1 0.00
130 3 0.01
132 11 0.05
133 18 0.09
134 5 0.02
135 81 0.38
136 13 0.06
137 15 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (133 bp):
TTTTTTATTTTAAAATTTTTTATTTTATAAAAAATAATAATTAATATTTTAATTTATTAATATAA
TTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAATAATAATAATAAAAAACCTTTT
TTA
Found at i:463341 original size:23 final size:22
Alignment explanation
Indices: 463274--463345 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
463264 ATATAATAAT
*
463274 TAATA-TTTTAATTTATTAATA
1 TAATATTTTTAATTTATTAAAA
* *
463295 TAATTTTTTTAAACTTAATT-AAA
1 TAATATTTTT-AA-TTTATTAAAA
*
463318 TACTATTTTTAATTTTATTAAAA
1 TAATATTTTTAA-TTTATTAAAA
463341 TAATA
1 TAATA
463346 ATAATAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 4 0.10
22 11 0.28
23 19 0.49
24 5 0.13
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTTTTAATTTATTAAAA
Found at i:463382 original size:12 final size:12
Alignment explanation
Indices: 463361--463390 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
463351 AATAAACCTT
*
463361 TTTTATTTTTTA
1 TTTTAATTTTTA
463373 TTTTAATTTTTA
1 TTTTAATTTTTA
463385 TTTTAA
1 TTTTAA
463391 AAAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:463496 original size:125 final size:123
Alignment explanation
Indices: 463133--463497 Score: 376
Period size: 135 Copynumber: 2.8 Consensus size: 123
463123 TAAAAAACAT
* *
463133 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATATTATTTTTTATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATACTA-TTTTTATAT
* * * * * *
463198 TATTAAA-AATTATAATAAAAAACTTGTTTTTATTTTATTATTTTAAAATTTTTTATTTTTATAA
65 TATAAAATAATAATAATAATAAACAT-TTTTAAATTT-TTATTTT--AA-TTTTTA--TTT-T--
463262 AAATA
120 AAA-A
*
463267 TAATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATACTATTTTTAATT
1 -AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATACTATTTTT-ATA
* * *
463332 TTATTAAAATAATAATAATAATAAACCTTTTTTATTTTTTATTTTAATTTTTATTTTAAAA
64 TTA-TAAAATAATAATAATAATAAACATTTTTAAATTTTTATTTTAATTTTTATTTTAAAA
* * *
463393 AATAATTAATATTTTAATTTGTTAATATAAATTTTTTTAAATTTAATTAAATATTATTTTT-TAT
1 AATAATTAATATTTTAATTTATTAATAT-AATTTTTTTAAACTTAATTAAATACTATTTTTATAT
* **
463457 TA-AAAATAATAATTAATACATTATTATTTATTAAATTTTTA
65 TATAAAATAATAA-TAATA-ATAAACATTT-TTAAATTTTTA
463498 AACTTAATTA
Statistics
Matches: 208, Mismatches: 15, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
122 10 0.05
123 5 0.02
124 10 0.05
125 36 0.17
126 31 0.15
127 3 0.01
129 1 0.00
130 3 0.01
132 6 0.03
133 2 0.01
134 5 0.02
135 67 0.32
136 14 0.07
137 15 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (123 bp):
AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATACTATTTTTATATT
ATAAAATAATAATAATAATAAACATTTTTAAATTTTTATTTTAATTTTTATTTTAAAA
Found at i:463568 original size:14 final size:14
Alignment explanation
Indices: 463551--463599 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
463541 AATTATTAAA
463551 AAAAATATATTTTT
1 AAAAATATATTTTT
463565 AAAAATAT-TTTTAT
1 AAAAATATATTTT-T
* *
463579 AAAAATTTATTTAT
1 AAAAATATATTTTT
463593 AAAAATA
1 AAAAATA
463600 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 23 0.77
15 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAAATATATTTTT
Found at i:464231 original size:37 final size:39
Alignment explanation
Indices: 464173--464273 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
464163 TAAAAACATT
* *
464173 ATATATAAA-AATATGATATAAATATTATA-ATTTTAATA-A
1 ATATA-AAATAATAT-A-ATAAATATAATATATTTAAATATA
464212 ATATAAAATAATATAATAAATATAATATATTTAAATATA
1 ATATAAAATAATATAATAAATATAATATATTTAAATATA
* *
464251 AT-TAATAATTATTTAATAAATAT
1 ATATAA-AATAATATAATAAATAT
464274 CGTGTTCATA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 11 0.20
38 15 0.28
39 28 0.52
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATAAAATAATATAATAAATATAATATATTTAAATATA
Found at i:464237 original size:28 final size:28
Alignment explanation
Indices: 464175--464273 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
464165 AAAACATTAT
* * *
464175 ATATAA-AAATATGATATAAATATTATAA
1 ATATAATAAATATAAAAT-AATATAATAA
* *
464203 TTTTAATAAATATAAAATAATATAATAA
1 ATATAATAAATATAAAATAATATAATAA
* *
464231 ATATAATATATTTAAATATAAT-TAATAA
1 ATATAATAAATATAAA-ATAATATAATAA
*
464259 TTATTTAATAAATAT
1 --ATATAATAAATAT
464274 CGTGTTCATA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
28 31 0.56
29 14 0.25
30 10 0.18
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATAATAAATATAAAATAATATAATAA
Found at i:464406 original size:23 final size:23
Alignment explanation
Indices: 464362--464406 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
464352 ATATATATAC
* *
464362 ATAAATTATTAAATTTACATTTA
1 ATAAATTATAAAATTTAAATTTA
464385 ATAAATT-TAAAATTCTAAATTT
1 ATAAATTATAAAATT-TAAATTT
464407 TTACAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAATTATAAAATTTAAATTTA
Found at i:464435 original size:3 final size:3
Alignment explanation
Indices: 464427--464463 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
464417 AAAATTTTTG
464427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
464464 TCAACGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:464744 original size:33 final size:33
Alignment explanation
Indices: 464707--464783 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
464697 ATAATTATTT
*
464707 TTAATATA-TTATATTTATATAAATTTTAACATA
1 TTAATATATTTATA-TCATATAAATTTTAACATA
*
464740 TTAATA-ATTTATATCATATAAATTTTAATATA
1 TTAATATATTTATATCATATAAATTTTAACATA
* *
464772 ATCATATATTTA
1 TTAATATATTTA
464784 AATTATTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 22 0.58
33 16 0.42
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (33 bp):
TTAATATATTTATATCATATAAATTTTAACATA
Found at i:465017 original size:2 final size:2
Alignment explanation
Indices: 465010--465039 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
465000 AAGCAGAAGC
465010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
465040 GTATTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:465383 original size:15 final size:16
Alignment explanation
Indices: 465361--465395 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
465351 TTATTTTTTC
* *
465361 TAAAAAAAATAATATT
1 TAAAAAAATTAAAATT
465377 TAAAAAAATTAAAATT
1 TAAAAAAATTAAAATT
465393 TAA
1 TAA
465396 TCTCTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAAAATTAAAATT
Found at i:467287 original size:18 final size:16
Alignment explanation
Indices: 467260--467311 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
467250 ATAATATAAT
467260 TTTTAAATTATTTTTTA
1 TTTT-AATTATTTTTTA
* *
467277 TATTTATATTATATTATA
1 T-TTTA-ATTATTTTTTA
*
467295 TTTTAATTATTTGTTA
1 TTTTAATTATTTTTTA
467311 T
1 T
467312 GTATTATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTAATTATTTTTTA
Found at i:467525 original size:20 final size:19
Alignment explanation
Indices: 467490--467536 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
467480 AAAATAATTG
467490 ATATAAAATAATATAAAGA
1 ATATAAAATAATATAAAGA
* *
467509 ATATAAATATTATATAAA-T
1 ATATAAA-ATAATATAAAGA
467528 ATATAAAAT
1 ATATAAAAT
467537 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATATAAAATAATATAAAGA
Found at i:467541 original size:20 final size:20
Alignment explanation
Indices: 467490--467526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
467480 AAAATAATTG
*
467490 ATATAAA-ATAATATAAAGA
1 ATATAAATATTATATAAAGA
467509 ATATAAATATTATATAAA
1 ATATAAATATTATATAAA
467527 TATATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATAAATATTATATAAAGA
Found at i:467568 original size:18 final size:18
Alignment explanation
Indices: 467532--467574 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
467522 ATAAATATAT
*
467532 AAAATT-TTATTTTAATA
1 AAAATTATTAATTTAATA
*
467549 AAAATTATTAATTTATTA
1 AAAATTATTAATTTAATA
*
467567 AAATTTAT
1 AAAATTAT
467575 GTTATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTATTAATTTAATA
Found at i:467833 original size:2 final size:2
Alignment explanation
Indices: 467826--467857 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
467816 GATCAAGGCA
467826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
467858 TAAATCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:471431 original size:28 final size:29
Alignment explanation
Indices: 471396--471461 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
471386 AATCATGATA
**
471396 ACACAAATTTAATAAAA-AAAAGAATAAC
1 ACACAAATACAATAAAAGAAAAGAATAAC
*
471424 ACACAAATACAATAAAATGAAAAGAATCAC
1 ACACAAATACAATAAAA-GAAAAGAATAAC
*
471454 ACAGAAAT
1 ACACAAAT
471462 CCACGGAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 15 0.47
30 17 0.53
ACGTcount: A:0.65, C:0.14, G:0.06, T:0.15
Consensus pattern (29 bp):
ACACAAATACAATAAAAGAAAAGAATAAC
Found at i:475349 original size:25 final size:25
Alignment explanation
Indices: 475321--475383 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 25
475311 TTTATTATAT
*
475321 ATAAATTTATATATTATTAAATTAA
1 ATAAATTTATATATTATTAAATAAA
*
475346 ATAAATTT-T-TATTA-AAAATAAA
1 ATAAATTTATATATTATTAAATAAA
475368 AT-AATTTATAT-TTATT
1 ATAAATTTATATATTATT
475384 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 5 0.16
22 12 0.38
23 6 0.19
24 1 0.03
25 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAAATTTATATATTATTAAATAAA
Found at i:475373 original size:21 final size:22
Alignment explanation
Indices: 475321--475379 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
475311 TTTATTATAT
* *
475321 ATAAATTTATATATTATTAAATTAA
1 ATAAA-TT-TATATTA-AAAATAAA
*
475346 ATAAATTTTTATTAAAAATAAA
1 ATAAATTTATATTAAAAATAAA
475368 AT-AATTTATATT
1 ATAAATTTATATT
475380 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 6 0.20
24 2 0.07
25 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATTTATATTAAAAATAAA
Found at i:475509 original size:2 final size:2
Alignment explanation
Indices: 475502--475539 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
475492 GTTCGCAGTG
* *
475502 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
475540 CCGTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:475868 original size:26 final size:26
Alignment explanation
Indices: 475839--475896 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
475829 ATAAATTTGA
*
475839 TATAAATT-ATATTTAATATAATTTTT
1 TATAAATTAATATTTAA-ATAATTATT
* *
475865 TATAATTTAATATTTAAATTATTATT
1 TATAAATTAATATTTAAATAATTATT
475891 TATAAA
1 TATAAA
475897 ATAAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATAAATTAATATTTAAATAATTATT
Found at i:475886 original size:19 final size:19
Alignment explanation
Indices: 475864--475926 Score: 51
Period size: 20 Copynumber: 3.4 Consensus size: 19
475854 ATATAATTTT
475864 TTATAATTTAATATTTAAA
1 TTATAATTTAATATTTAAA
* * * *
475883 TTATTATTTATAAAATAAAA
1 TTATAATTTA-ATATTTAAA
*
475903 TAATAATTT--TATTTAAA
1 TTATAATTTAATATTTAAA
475920 TT-TAATT
1 TTATAATT
475927 AAAAATATAT
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
19 9 0.27
20 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATAATTTAATATTTAAA
Found at i:475954 original size:22 final size:20
Alignment explanation
Indices: 475916--475955 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
475906 TAATTTTATT
475916 TAAATTTAATTAAAAATATA
1 TAAATTTAATTAAAAATATA
475936 TAAATATTAATATAAAAATA
1 TAAAT-TTAAT-TAAAAATA
475956 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:476003 original size:22 final size:23
Alignment explanation
Indices: 475963--476008 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
475953 ATAATTTTTT
475963 TAATAATTTAATATATTTT-AAA
1 TAATAATTTAATATATTTTCAAA
*
475985 TAATAATTTAA-ATTTTTTTCAAA
1 TAATAATTTAATA-TATTTTCAAA
476008 T
1 T
476009 GCAATTAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 16 0.76
23 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATAATTTAATATATTTTCAAA
Found at i:479625 original size:2 final size:2
Alignment explanation
Indices: 479618--479650 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
479608 ATTTTCCTTT
479618 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
479651 AAATTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:484351 original size:4 final size:4
Alignment explanation
Indices: 484338--484367 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
484328 ATGCTGTAAT
484338 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
484368 TTTTTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:485090 original size:22 final size:25
Alignment explanation
Indices: 485043--485104 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
485033 ATTTAATTAG
*
485043 TAAATTTATTATTAAATCATTTAAA-
1 TAAATTTATTA-TAAATCATTAAAAT
485068 TAAATTTATTATAAA-CA-TAAAAT
1 TAAATTTATTATAAATCATTAAAAT
*
485091 TAAAATTATATATA
1 TAAATTTAT-TATA
485105 TCTTTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 4 0.12
23 10 0.30
24 8 0.24
25 11 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAATTTATTATAAATCATTAAAAT
Found at i:487354 original size:132 final size:132
Alignment explanation
Indices: 487117--487384 Score: 491
Period size: 132 Copynumber: 2.0 Consensus size: 132
487107 CCTTTACACA
* * *
487117 ATACCTTCACTGCTGTTCTGCATCTTTCTAACAGGCTGCACCACATATTCCACACAACACCCTCA
1 ATACCTTCACCGCTGTTCGGCATCTTTCTAACAGGCTGCACCACATATACCACACAACACCCTCA
487182 TGCTGTTCTCCTTTGTGCTCTGTTTTCTTCTTCCATTAACCTTCCATAAGTTTCCTTTCTTTCTT
66 TGCTGTTCTCCTTTGTGCTCTGTTTTCTTCTTCCATTAACCTTCCATAAGTTTCCTTTCTTTCTT
*
487247 TC
131 GC
487249 ATACCTTCACCGCTGTTCGGCATCTTTCTAACAGGCTGCACCACATATACCACACAACACCCTCA
1 ATACCTTCACCGCTGTTCGGCATCTTTCTAACAGGCTGCACCACATATACCACACAACACCCTCA
*
487314 TGCTGTTCTCCTTTGTGCTCTGTTTTCTTCTTCCATTAACCTTCTATAAGTTTCCTTTCTTTCTT
66 TGCTGTTCTCCTTTGTGCTCTGTTTTCTTCTTCCATTAACCTTCCATAAGTTTCCTTTCTTTCTT
487379 GC
131 GC
487381 ATAC
1 ATAC
487385 TTCTTCTCCT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.18, C:0.32, G:0.10, T:0.40
Consensus pattern (132 bp):
ATACCTTCACCGCTGTTCGGCATCTTTCTAACAGGCTGCACCACATATACCACACAACACCCTCA
TGCTGTTCTCCTTTGTGCTCTGTTTTCTTCTTCCATTAACCTTCCATAAGTTTCCTTTCTTTCTT
GC
Found at i:487521 original size:11 final size:12
Alignment explanation
Indices: 487501--487525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
487491 TTCCTCTTTC
487501 TTTTCTTTTTTT
1 TTTTCTTTTTTT
487513 TTTTCTTTTTTT
1 TTTTCTTTTTTT
487525 T
1 T
487526 GCCTTCCGTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:488298 original size:8 final size:8
Alignment explanation
Indices: 488285--488315 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
488275 AATATTATGG
488285 TCTTTTTT
1 TCTTTTTT
488293 TCTTTTTT
1 TCTTTTTT
488301 T-TTTTTT
1 TCTTTTTT
488308 TCTTTTTT
1 TCTTTTTT
488316 CAGATTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TCTTTTTT
Found at i:488307 original size:15 final size:15
Alignment explanation
Indices: 488287--488315 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
488277 TATTATGGTC
488287 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
488302 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
488316 CAGATTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (15 bp):
TTTTTTTCTTTTTTT
Found at i:490463 original size:18 final size:17
Alignment explanation
Indices: 490440--490474 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
490430 CATATTTAAT
490440 AATATAACAAATTTAAAA
1 AATATAA-AAATTTAAAA
*
490458 AATATAATAATTTAAAA
1 AATATAAAAATTTAAAA
490475 TTTCATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAAAAATTTAAAA
Found at i:490604 original size:3 final size:3
Alignment explanation
Indices: 490596--490620 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
490586 AAATTACATA
490596 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
490621 GTAACAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:490768 original size:20 final size:20
Alignment explanation
Indices: 490726--490768 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
490716 CAATAGTTAA
* * **
490726 TTATTTAAATTTTATTATTT
1 TTATTTAAATTATATAAAAT
490746 TTATTTAAATTATATAAAAT
1 TTATTTAAATTATATAAAAT
490766 TTA
1 TTA
490769 CTTTTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTAAATTATATAAAAT
Found at i:491700 original size:28 final size:29
Alignment explanation
Indices: 491646--491723 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
491636 ACCAAGTCAA
* * * **
491646 CAAAAATATAAGAATAATTTTTTAAA-TT
1 CAAAAAAAAAAGAAAAATTTTAAAAATTT
491674 CAAAAAAAAAAGAAAAATTTTAAAAATTT
1 CAAAAAAAAAAGAAAAATTTTAAAAATTT
* *
491703 TAAAAAATAAAATAAAAATTT
1 CAAAAAA-AAAAGAAAAATTT
491724 AGAAAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 21 0.51
29 8 0.20
30 12 0.29
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (29 bp):
CAAAAAAAAAAGAAAAATTTTAAAAATTT
Found at i:491718 original size:21 final size:20
Alignment explanation
Indices: 491694--491739 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
491684 AGAAAAATTT
491694 TAAAAATTTTA-AAAAATAAAA
1 TAAAAA-TTTAGAAAAA-AAAA
*
491715 TAAAAATTTAGAAAAAAATA
1 TAAAAATTTAGAAAAAAAAA
491735 TAAAA
1 TAAAA
491740 TATCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAATTTAGAAAAAAAAA
Found at i:491719 original size:20 final size:19
Alignment explanation
Indices: 491696--491765 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 19
491686 AAAAATTTTA
491696 AAAATTTTAAAAAATAAAAT
1 AAAA-TTTAAAAAATAAAAT
*
491716 AAAAATTTAGAAAAA-AATAT
1 -AAAATTTA-AAAAATAAAAT
* * *
491736 AAAATATCAAAAAT-TAAT
1 AAAATTTAAAAAATAAAAT
491754 AAAATTTAAAAA
1 AAAATTTAAAAA
491766 TTTAAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 17 0.43
19 6 0.15
20 8 0.20
21 9 0.22
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (19 bp):
AAAATTTAAAAAATAAAAT
Found at i:491747 original size:16 final size:17
Alignment explanation
Indices: 491726--491813 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
491716 AAAAATTTAG
*
491726 AAAAAAATATAAAATAT
1 AAAAAATTATAAAATAT
*
491743 CAAAAATTAATAAAAT-T
1 AAAAAATT-ATAAAATAT
*
491760 TAAAAATT-TAAAA-AT
1 AAAAAATTATAAAATAT
*
491775 AAAAAATTATAAAATTGT
1 AAAAAATTATAAAA-TAT
491793 AAAAAATCTATAAAATA-
1 AAAAAAT-TATAAAATAT
491810 AAAA
1 AAAA
491814 GAACATCGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
15 13 0.22
16 5 0.08
17 18 0.31
18 16 0.27
19 7 0.12
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (17 bp):
AAAAAATTATAAAATAT
Found at i:491797 original size:18 final size:18
Alignment explanation
Indices: 491726--491808 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 18
491716 AAAAATTTAG
*
491726 AAAAAAATATAAAA-TAT
1 AAAAAATTATAAAATTAT
*
491743 CAAAAATTAATAAAATT-T
1 AAAAAATT-ATAAAATTAT
491761 -AAAAATT-TAAAA--AT
1 AAAAAATTATAAAATTAT
*
491775 AAAAAATTATAAAATTGT
1 AAAAAATTATAAAATTAT
491793 AAAAAATCTATAAAAT
1 AAAAAAT-TATAAAAT
491809 AAAAAGAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
14 1 0.02
15 12 0.22
16 5 0.09
17 13 0.24
18 15 0.27
19 9 0.16
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (18 bp):
AAAAAATTATAAAATTAT
Found at i:492155 original size:13 final size:13
Alignment explanation
Indices: 492134--492168 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
492124 GGTAAATCAA
*
492134 AAAAGAAAAGGGAG
1 AAAA-AAAAGAGAG
492148 AAAAAAAAGAGAG
1 AAAAAAAAGAGAG
492161 AAAAAAAA
1 AAAAAAAA
492169 AGGAAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAG
Found at i:492535 original size:19 final size:19
Alignment explanation
Indices: 492500--492538 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
492490 CTTTCTTTTT
*
492500 TTTTAATTTATTTTTTAAA
1 TTTTAATTTATTATTTAAA
492519 TTTTAA-TTATATATTTAAA
1 TTTTAATTTAT-TATTTAAA
492538 T
1 T
492539 AATAATTTTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAATTTATTATTTAAA
Found at i:492633 original size:10 final size:10
Alignment explanation
Indices: 492620--492653 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
492610 TGTTTTTAAG
492620 TTTTTTATAT
1 TTTTTTATAT
492630 TTTTTTATAT
1 TTTTTTATAT
492640 TTTTAATTATAT
1 TTTT--TTATAT
492652 TT
1 TT
492654 GAATTTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
12 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:493509 original size:13 final size:13
Alignment explanation
Indices: 493491--493517 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
493481 CGTACCAAAG
493491 ACATTAAAAAATA
1 ACATTAAAAAATA
493504 ACATTAAAAAATA
1 ACATTAAAAAATA
493517 A
1 A
493518 AAATGTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
ACATTAAAAAATA
Found at i:493944 original size:17 final size:16
Alignment explanation
Indices: 493914--493948 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
493904 CAAGTTAATT
493914 ATTCAAATCATTTAAA
1 ATTCAAATCATTTAAA
* *
493930 ATTCAAATTATTTTAA
1 ATTCAAATCATTTAAA
493946 ATT
1 ATT
493949 TGAATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTCAAATCATTTAAA
Found at i:494010 original size:16 final size:16
Alignment explanation
Indices: 493978--494024 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
493968 TTTATTTTTT
*
493978 ATTAAATT-AAATTAA
1 ATTAAATTGAATTTAA
493993 ATTAAATTGAATTTAA
1 ATTAAATTGAATTTAA
494009 ATTTAAA-TGAATTTAA
1 A-TTAAATTGAATTTAA
494025 TTTGGATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 8 0.28
16 16 0.55
17 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTAAATTGAATTTAA
Found at i:494013 original size:6 final size:5
Alignment explanation
Indices: 493978--494016 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
493968 TTTATTTTTT
*
493978 ATTAA ATTAA ATTAA ATTAA ATTGAA TTTAA ATTTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATT-AA ATTAA A-TTAA AT
494017 GAATTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (5 bp):
ATTAA
Found at i:495496 original size:19 final size:19
Alignment explanation
Indices: 495456--495509 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
495446 TATTATATTT
495456 AATATTTATTTAAT-ATTAA
1 AATATTT-TTTAATGATTAA
* *
495475 AATATTTTTTAATGTTTGA
1 AATATTTTTTAATGATTAA
*
495494 AATTTTGTTTTAATGA
1 AATATT-TTTTAATGA
495510 ATGGAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.21
19 15 0.52
20 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
AATATTTTTTAATGATTAA
Found at i:496230 original size:2 final size:2
Alignment explanation
Indices: 496213--496256 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
496203 TCATTTCAAC
* *
496213 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
496255 AT
1 AT
496257 TGCAGGGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:497858 original size:23 final size:21
Alignment explanation
Indices: 497826--497868 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
497816 AAAAACTTAT
497826 TTAATATTTTATTATTATTATTA
1 TTAATATTTTATT-TT-TTATTA
*
497849 TTAATTTTTTATTTTTTATT
1 TTAATATTTTATTTTTTATT
497869 TTTCAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTAATATTTTATTTTTTATTA
Done.