Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002276.1 Hibiscus syriacus cultivar Beakdansim tig00004630_pilon, 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: 831455
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:577266 original size:2 final size:2
Alignment explanation
Indices: 577261--577320 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
577251 ATTTTACTAT
*
577261 TA TA TA TA TT TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
577302 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
577321 TCTACAAGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:577266 original size:17 final size:19
Alignment explanation
Indices: 577244--577318 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 19
577234 ATTGTTGTTA
*
577244 TATATACATTT-TA-CTAT
1 TATATACATTTATATATAT
*
577261 TATATATATTTATATATAT
1 TATATACATTTATATATAT
* *
577280 TATATATATATATATATAT
1 TATATACATTTATATATAT
* *
577299 ATATATATATATATATATAT
1 -TATATACATTTATATATAT
577319 ATTCTACAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.19
18 2 0.04
19 21 0.40
20 19 0.37
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATACATTTATATATAT
Found at i:578104 original size:38 final size:38
Alignment explanation
Indices: 578053--578147 Score: 122
Period size: 37 Copynumber: 2.5 Consensus size: 38
578043 AATGATCGTC
* *
578053 CTAGGATTCAAACTCCTAAAAAATAGGATAGAA-TTTTG
1 CTAGGATTCAAACTCCTAAAAAATAGGATA-AAGTTCTA
*
578091 CTAGGATTCAAACT-CTTAAAAATAGGATAAAGTTCTA
1 CTAGGATTCAAACTCCTAAAAAATAGGATAAAGTTCTA
* *
578128 CTATGATTTAAACTCCTAAA
1 CTAGGATTCAAACTCCTAAA
578148 GATAAGATCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 2 0.04
37 29 0.59
38 18 0.37
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (38 bp):
CTAGGATTCAAACTCCTAAAAAATAGGATAAAGTTCTA
Found at i:578740 original size:24 final size:24
Alignment explanation
Indices: 578713--578814 Score: 88
Period size: 24 Copynumber: 4.3 Consensus size: 24
578703 CTTTGCATTT
578713 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTATTA
* **
578737 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTATTA
*
578760 TT-TTATT-CTACT-TATTTATTA
1 TTATTATTACTATTATATTTATTA
* *
578781 TATATGTA-TATTTTTATATTTTATTA
1 T-TAT-TATTACTATTATA-TTTATTA
578807 TTATTATT
1 TTATTATT
578815 TTTTTACTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
20 5 0.08
21 6 0.10
22 5 0.08
23 5 0.08
24 25 0.42
25 6 0.10
26 8 0.13
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (24 bp):
TTATTATTACTATTATATTTATTA
Found at i:578837 original size:73 final size:76
Alignment explanation
Indices: 578731--578873 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 76
578721 ACTATTATAT
* *
578731 TTATTATTATTTTTACTATTATATTTTCCTTTTATTCTACTTAT-TTATTATATATGTA-TATTT
1 TTATTATTATTTTTACTATTATACTTTCCTTTTATTATACTTATATTATTA-AT-TGTATTATTT
578794 TTATATTTTATTA
64 TTATATTTTATTA
* * * * *
578807 TTATTATT-TTTTTACT-TTCT-CTTTCTTTTTATTATTCTTGTATTATTACTTGTATTATTTTT
1 TTATTATTATTTTTACTATTATACTTTCCTTTTATTATACTTATATTATTAATTGTATTATTTTT
578869 ATATT
66 ATATT
578874 ATTTATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
72 4 0.07
73 29 0.50
74 9 0.16
75 8 0.14
76 8 0.14
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (76 bp):
TTATTATTATTTTTACTATTATACTTTCCTTTTATTATACTTATATTATTAATTGTATTATTTTT
ATATTTTATTA
Found at i:578858 original size:12 final size:11
Alignment explanation
Indices: 578836--578876 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
578826 TCTTTCTTTT
578836 TATTATTCTTG
1 TATTATTCTTG
578847 TATTATTACTTG
1 TATTATT-CTTG
* *
578859 TATTATTTTTA
1 TATTATTCTTG
578870 TATTATT
1 TATTATT
578877 TATTTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:578892 original size:2 final size:2
Alignment explanation
Indices: 578885--578909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578875 TTTATTTTTC
578885 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
578910 GCGTATGTTC
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:579908 original size:37 final size:37
Alignment explanation
Indices: 579855--579951 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
579845 AATGATCGTC
579855 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * * *
579892 TTGCTAGGATTCAAACTCTTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
579929 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
579952 GATAAGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:580544 original size:30 final size:29
Alignment explanation
Indices: 580508--580617 Score: 89
Period size: 30 Copynumber: 3.6 Consensus size: 29
580498 TTTTCTTTGC
580508 ATTTTTATTATTACTATTATATTTATTATT
1 ATTTTTATTATTA-TATTATATTTATTATT
* * *
580538 ATTTTTACTATTATATTTTCCTTTATTCTACTT
1 ATTTTTATTATTATATTAT-ATTTA-T-TA-TT
* *
580571 ATTTATATTA-TATATGTATATTTTTTA-T
1 ATTTTTATTATTATAT-TATATTTATTATT
580599 ATTTTATTATTATTATATT
1 A-TTT-TTATTATTATATT
580618 TTTTTACTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
28 2 0.03
29 8 0.13
30 24 0.38
31 7 0.11
32 10 0.16
33 12 0.19
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (29 bp):
ATTTTTATTATTATATTATATTTATTATT
Found at i:580563 original size:24 final size:23
Alignment explanation
Indices: 580510--580623 Score: 75
Period size: 24 Copynumber: 5.2 Consensus size: 23
580500 TTCTTTGCAT
580510 TTTTATTATTACTATTATATTTA
1 TTTTATTATTACTATTATATTTA
*
580533 TTATTATTTTTACTATTATATTT-
1 TT-TTATTATTACTATTATATTTA
** *
580556 TCCT-TTATT-CTACT-TATTTA
1 TTTTATTATTACTATTATATTTA
*
580576 TATTATATATGTA-TATT-T-TTTA
1 TTTTAT-TAT-TACTATTATATTTA
* *
580598 TATT-TTATTATTATTATATTT-
1 TTTTATTATTACTATTATATTTA
580619 TTTTA
1 TTTTA
580624 CTTTCTCTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
19 7 0.10
20 13 0.18
21 10 0.14
22 15 0.21
23 8 0.11
24 19 0.26
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (23 bp):
TTTTATTATTACTATTATATTTA
Found at i:580622 original size:27 final size:28
Alignment explanation
Indices: 580570--580621 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
580560 TTATTCTACT
580570 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
580598 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
580622 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:580655 original size:11 final size:11
Alignment explanation
Indices: 580639--580678 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
580629 TCTTTCTTTT
580639 TATTATTCTTG
1 TATTATTCTTG
*
580650 TATTATACTTG
1 TATTATTCTTG
* *
580661 TATTATTTTTA
1 TATTATTCTTG
580672 TATTATT
1 TATTATT
580679 TATTTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:580804 original size:11 final size:11
Alignment explanation
Indices: 580790--580826 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
580780 TTTATAATAT
580790 TATTATTTTTC
1 TATTATTTTTC
*
580801 TATTAATTTTC
1 TATTATTTTTC
580812 TA-TATTTTT-
1 TATTATTTTTC
580821 TATTAT
1 TATTAT
580827 CATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 2 0.09
10 9 0.39
11 12 0.52
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTTC
Found at i:580991 original size:2 final size:2
Alignment explanation
Indices: 580886--580972 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
580876 ATTTTACTAT
*
580886 TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580970 TA T
1 TA T
580973 TCTACACAAG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:581251 original size:22 final size:22
Alignment explanation
Indices: 581201--581295 Score: 57
Period size: 25 Copynumber: 4.0 Consensus size: 22
581191 TCGTCATTTA
*
581201 ATTTATTAATTTATATATATTTACTT
1 ATTTATTTATTT-TATATA-TTA--T
581227 ATTTATTTATTTTATATATTAT
1 ATTTATTTATTTTATATATTAT
* *
581249 ATTCGTACTTTGTTATTAT-TATTTT
1 ATT--TA-TTTATT-TTATATATTAT
* * *
581274 GTTTATTTGTTTTATTTATTAT
1 ATTTATTTATTTTATATATTAT
581296 TTTCTTTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.07
22 15 0.25
23 2 0.03
24 5 0.08
25 18 0.31
26 15 0.25
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.66
Consensus pattern (22 bp):
ATTTATTTATTTTATATATTAT
Found at i:581763 original size:37 final size:37
Alignment explanation
Indices: 581710--581806 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
581700 AATGATCGTC
581710 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-AAGTT
* * *
581747 TTGCTAGGATTCAAACTCTTAAAAATAGGATAAAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
* *
581784 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
581807 GATAAGATCC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 2 0.04
37 49 0.96
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:582394 original size:19 final size:18
Alignment explanation
Indices: 582370--582428 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
582360 TTTAAATTTT
582370 TATTATTACTATTA-TATTA
1 TATTATT-CT-TTACTATTA
582389 TATTATT-TTTACTATTA
1 TATTATTCTTTACTATTA
*
582406 TATT-TTCCTTTTATTATTA
1 TATTATT-C-TTTACTATTA
582425 TATT
1 TATT
582429 TATATGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 5 0.14
17 10 0.29
19 20 0.57
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTATTCTTTACTATTA
Found at i:582424 original size:31 final size:31
Alignment explanation
Indices: 582389--582458 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
582379 TATTATATTA
582389 TATTATTTTTACTAT-TATATTTTCCT-TTTAT
1 TATTATTTTTA-TATGTATATTTT-CTATTTAT
* *
582420 TATTATATTTATATGTATATTTTTTATTTAT
1 TATTATTTTTATATGTATATTTTCTATTTAT
582451 TATTATTT
1 TATTATTT
582459 ATTTTTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (31 bp):
TATTATTTTTATATGTATATTTTCTATTTAT
Found at i:582452 original size:47 final size:48
Alignment explanation
Indices: 582367--582458 Score: 120
Period size: 47 Copynumber: 1.9 Consensus size: 48
582357 TTCTTTAAAT
582367 TTTTATTATTACTATTATATTATATTATTTTTACTATTA-TATTTTCC
1 TTTTATTATTACTATTATATTATATTATTTTTACTATTATTATTTTCC
*
582414 TTTTATTATTA-TATTTATATGTATA-T-TTTTTATTTATTATTATTT
1 TTTTATTATTACTA-TTATAT-TATATTATTTTTA-CTATTATTATTT
582459 ATTTTTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
46 8 0.20
47 23 0.57
48 9 0.22
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (48 bp):
TTTTATTATTACTATTATATTATATTATTTTTACTATTATTATTTTCC
Found at i:582463 original size:19 final size:20
Alignment explanation
Indices: 582417--582467 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
582407 ATTTTCCTTT
*
582417 TATTATTATATTTATATGTA
1 TATTATTTTATTTATATGTA
582437 TATT-TTTTATTTATTAT-TA
1 TATTATTTTATTTA-TATGTA
582456 T-TTATTTT-TTTA
1 TATTATTTTATTTA
582468 CTTTCTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 7 0.25
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTATTTTATTTATATGTA
Found at i:583121 original size:30 final size:30
Alignment explanation
Indices: 583048--583121 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
583038 TACTTTGGTA
*
583048 TTATTATTT-TGTTTATTTGTTTTATTTATT
1 TTATTATTTAT-TTTATTTGTTTTATATATT
* *
583078 TTCTT-TTTCATTTTCTTT-TTTATATATATT
1 TTATTATTT-ATTTTATTTGTTT-TATATATT
583108 TTATTATTTATTTT
1 TTATTATTTATTTT
583122 TTTACTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
29 6 0.17
30 26 0.72
31 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (30 bp):
TTATTATTTATTTTATTTGTTTTATATATT
Found at i:583545 original size:37 final size:37
Alignment explanation
Indices: 583492--583588 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
583482 AATGATCGTC
583492 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
583529 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
583566 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
583589 GATAAGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:588806 original size:21 final size:20
Alignment explanation
Indices: 588781--588823 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
588771 ATTATTTCTA
588781 TTAAT-TTAGATATTTTATATT
1 TTAATCTTAGA-ATTTTA-ATT
*
588802 TTAATCTTATAATTTTAATT
1 TTAATCTTAGAATTTTAATT
588822 TT
1 TT
588824 CTTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATCTTAGAATTTTAATT
Found at i:588866 original size:26 final size:27
Alignment explanation
Indices: 588808--588866 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
588798 TATTTTAATC
* * *
588808 TTATAATTTTAATTTTCTTTATTTTGG
1 TTATTATTTTAATTTTATTTATTTTGA
* *
588835 TCATTATTTT-ATTTTATTTATTTTTA
1 TTATTATTTTAATTTTATTTATTTTGA
588861 TTATTA
1 TTATTA
588867 CCCCTTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (27 bp):
TTATTATTTTAATTTTATTTATTTTGA
Found at i:589391 original size:3 final size:3
Alignment explanation
Indices: 589383--589451 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
589373 TCTTTTTTAT
* *
589383 TTA TTA TTA TTT TTA TTA -TA TTA GTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
589429 TTA TTA ATA -GA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
589452 ATTTTGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 5 0.09
3 51 0.91
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:589404 original size:17 final size:17
Alignment explanation
Indices: 589379--589451 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
589369 TTTGTCTTTT
*
589379 TTATT-TATTATTATTT
1 TTATTATATTATTATTA
589395 TTATTATATTAGTATTATTA
1 TTATTATA-T--TATTATTA
589415 TTATTATATTATTATTA
1 TTATTATATTATTATTA
* *
589432 TTAATAGATTATTATTA
1 TTATTATATTATTATTA
589449 TTA
1 TTA
589452 ATTTTGTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
16 5 0.10
17 28 0.56
18 1 0.02
19 1 0.02
20 15 0.30
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:589412 original size:14 final size:14
Alignment explanation
Indices: 589379--589451 Score: 82
Period size: 14 Copynumber: 5.2 Consensus size: 14
589369 TTTGTCTTTT
589379 TTAT-TTATTATTA
1 TTATATTATTATTA
589392 TT-T-TTATTA-TA
1 TTATATTATTATTA
589403 TTAGTATTATTATTA
1 TTA-TATTATTATTA
589418 TTATATTATTATTA
1 TTATATTATTATTA
589432 TTAATAGATTATTATTA
1 TT-AT--ATTATTATTA
589449 TTA
1 TTA
589452 ATTTTGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.08
12 7 0.13
13 3 0.06
14 19 0.36
15 7 0.13
16 1 0.02
17 12 0.23
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:589434 original size:20 final size:20
Alignment explanation
Indices: 589379--589451 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
589369 TTTGTCTTTT
*
589379 TTAT-TTATTATTATTTTTA
1 TTATATTATTATTATTATTA
*
589398 TTATATTAGTATTATTATTA
1 TTATATTATTATTATTATTA
589418 TTATATTATTATTATTA--A
1 TTATATTATTATTATTATTA
*
589436 -TAGATTATTATTATTA
1 TTATATTATTATTATTA
589452 ATTTTGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.31
18 1 0.02
19 4 0.08
20 29 0.59
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTATATTATTATTATTATTA
Found at i:589661 original size:2 final size:2
Alignment explanation
Indices: 589654--589693 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
589644 ATTATTTTTA
* * *
589654 AT AT AT AT AT AT AT AT AT GT AT GT AT AT GT 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
589694 TTACTTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:594982 original size:72 final size:72
Alignment explanation
Indices: 594897--595032 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
594887 ATAAAATAAA
594897 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGAATAATATTCAGCTAAT
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGAATAATATTCAGCTAAT
594962 CTGTTAT
66 CTGTTAT
* * * * *
594969 GCTTGAGTTATCCCCCTAAAGTAATTGGTTAATTGCCCTGGCTTTATGGATAATATTCAGCTAA
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGAATAATATTCAGCTAA
595033 CTTATTATAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGAATAATATTCAGCTAAT
CTGTTAT
Found at i:598134 original size:75 final size:73
Alignment explanation
Indices: 597997--598246 Score: 199
Period size: 75 Copynumber: 3.4 Consensus size: 73
597987 ATCAACAAGA
* ** * * * * *
597997 AGCAAATGATGGGATATGCTTAAAGCCCATTTCAATCA-TAATCAGGAATATCGACGCGTTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGGAATAT--AGGCATTTTGA
*
598061 ATGTTCACGTC
63 ATGTTCATGTC
*
598072 AACAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTAGTGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATA-TAG-GCATTTTGAA
*
598137 CG-TC-TGT-
64 TGTTCATGTC
** * *
598144 ATTGGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAATTAGAATA-A--CATTTTA
1 A---GCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAG-AAATTGGAATATAGGCATTTTG
*
598206 AATGTTCATATC
62 AATGTTCATGTC
* * *
598218 AGTAATTGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
598247 CATCATTATG
Statistics
Matches: 142, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
71 32 0.23
72 3 0.02
73 4 0.03
74 5 0.04
75 84 0.59
76 14 0.10
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (73 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATAGGCATTTTGAATG
TTCATGTC
Found at i:599550 original size:22 final size:22
Alignment explanation
Indices: 599522--599600 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
599512 ACATCTACAT
599522 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
599544 TCTTCAAATATGGTAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
599566 TCTTTAAAGATGATTGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
599588 TTTTCAAATATGA
1 TCTTCAAAGATGA
599601 AAGCCTTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:599961 original size:3 final size:3
Alignment explanation
Indices: 599953--600021 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
599943 AATTATTTAA
* **
599953 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
600002 ATAT ATT ATT AAT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
600022 AATTAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 50 0.88
4 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:599971 original size:15 final size:15
Alignment explanation
Indices: 599944--600021 Score: 75
Period size: 15 Copynumber: 5.1 Consensus size: 15
599934 TTTTACTTAA
*
599944 ATTATTTAAATTATT
1 ATTATTAAAATTATT
*
599959 ATTTTTAAAATTATT
1 ATTATTAAAATTATT
**
599974 ATTATTATTATTATT
1 ATTATTAAAATTATT
**
599989 ATTATTATTATATATAT
1 ATTATTAAAAT-TAT-T
*
600006 ATTATTAATATTATT
1 ATTATTAAAATTATT
600021 A
1 A
600022 AATTAAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
15 38 0.69
16 6 0.11
17 11 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTAAAATTATT
Found at i:600469 original size:15 final size:15
Alignment explanation
Indices: 600449--600483 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
600439 CAAGAACAGA
*
600449 GAGAACAAACATGGC
1 GAGAACAAACACGGC
600464 GAGAACAAACACGGC
1 GAGAACAAACACGGC
600479 GAGAA
1 GAGAA
600484 AGACGAGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.29, T:0.03
Consensus pattern (15 bp):
GAGAACAAACACGGC
Found at i:601304 original size:28 final size:29
Alignment explanation
Indices: 601272--601331 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
601262 AGATTTCTTC
601272 AATATTTTAAATT-AGT-ATATTTAATTTT
1 AATATTTTAAATTCAGTAAT-TTTAATTTT
* *
601300 AATATTTTATATTCTGTAATTTTAATTTT
1 AATATTTTAAATTCAGTAATTTTAATTTT
601329 AAT
1 AAT
601332 TTTGATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.43
29 14 0.50
30 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
AATATTTTAAATTCAGTAATTTTAATTTT
Found at i:610368 original size:75 final size:75
Alignment explanation
Indices: 610201--610340 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 75
610191 ATTAACAAGA
* * * * *
610201 AGCAAATACTGGGGCATACTGAAAACCCCTCTTAATCAGAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAACCCCTCTTAATCAGAATCAAGAATGTTGACGCATTTTGAA
610266 CATTTATATC
66 CATTTATATC
* * *
610276 AGCAAATGCTGGGGCATGCTGAAAGCCCCT-TTCAATCAGAATGAAGAATGTTTACGCATTTTGA
1 AGCAAATGCTGGGGCATGCTGAAAACCCCTCTT-AATCAGAATCAAGAATGTTGACGCATTTTGA
610340 A
65 A
610341 TTCTTGTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 2 0.04
75 54 0.96
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAACCCCTCTTAATCAGAATCAAGAATGTTGACGCATTTTGAA
CATTTATATC
Found at i:611651 original size:22 final size:22
Alignment explanation
Indices: 611622--611676 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
611612 ATCTACACTC
611622 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
611644 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
611666 TTCAAAAATGA
1 TTCAAAGATGA
611677 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:612407 original size:45 final size:45
Alignment explanation
Indices: 612343--612947 Score: 967
Period size: 45 Copynumber: 13.4 Consensus size: 45
612333 CTATTTCCAA
612343 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
612388 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
612433 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
612478 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
612524 CATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
612569 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
612614 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCATCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
612659 CATCTGTAAGTCCTTCAGTACTTGATGTTCTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * **
612704 CATCTGTATGCCCTTCAGTGCTTGATGTTTTCCAAACCTTCATGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
612749 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACATTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
612794 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
612840 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
612886 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
612932 CATCTGTAAGTCCTTC
1 CATCTGTAAGCCCTTC
612948 TGTCGAAACG
Statistics
Matches: 524, Mismatches: 34, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
45 364 0.69
46 160 0.31
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:612833 original size:226 final size:226
Alignment explanation
Indices: 612343--612947 Score: 980
Period size: 226 Copynumber: 2.7 Consensus size: 226
612333 CTATTTCCAA
612343 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * *
612408 CATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTT
*
612473 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCT
131 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCT
* *
612538 TCAATGCTTGATGTTTTCAAAACCTTCAGGT
196 TCAATGCATGATGTTTTCAAAACATTCAGGT
* *
612569 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* * * * *
612634 CTTGATGTTTTCAAAACCATCGGGTCATCTGTAAGTCCTTCAGTACTTGATGTTCTCAAAACCTT
66 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTT
* * * * *
612699 CGAGTCATCTGTATGCCCTTCAGTGCTTGATGTTTTC-CAAACCTTCATGTCATCTGTAAGCCCT
131 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCT
*
612763 TCAGTGCATGATGTTTTCAAAACATTC-GAGT
196 TCAATGCATGATGTTTTCAAAACATTCAG-GT
612794 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
612859 GCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAAC
65 GCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAAC
*
612924 CTTCGGGTCATCTGTAAGTCCTTC
128 CTTCGGGTCATCTGTAAGCCCTTC
612948 TGTCGAAACG
Statistics
Matches: 346, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
224 1 0.00
225 80 0.23
226 198 0.57
227 41 0.12
228 26 0.08
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (226 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTT
CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCT
TCAATGCATGATGTTTTCAAAACATTCAGGT
Found at i:614718 original size:33 final size:33
Alignment explanation
Indices: 614676--614763 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
614666 TTTTGCTTCC
* *
614676 CCCTGCTGTTCATGAACCTCCTTCCTCGAATGT
1 CCCTGCTGTTCGTGAGCCTCCTTCCTCGAATGT
614709 CCCTGCTGTTCGTGAGCCTCCTTCCTCGAATGT
1 CCCTGCTGTTCGTGAGCCTCCTTCCTCGAATGT
614742 CCCTGCTGTTCGTGAGCCTCCT
1 CCCTGCTGTTCGTGAGCCTCCT
614764 CTCCAATGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.10, C:0.38, G:0.19, T:0.33
Consensus pattern (33 bp):
CCCTGCTGTTCGTGAGCCTCCTTCCTCGAATGT
Found at i:615015 original size:20 final size:20
Alignment explanation
Indices: 614961--615005 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
614951 ACAAAACATG
614961 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAGCAAATATTAGT
614981 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAGCAAATATTAGT
615001 GGTGG
1 GGTGG
615006 TAGTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (20 bp):
GGTGGCCAGCAAATATTAGT
Found at i:615692 original size:3 final size:3
Alignment explanation
Indices: 615686--615720 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
615676 ACATTATTAT
615686 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
615721 GATAGTATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:616047 original size:52 final size:52
Alignment explanation
Indices: 615978--616530 Score: 944
Period size: 52 Copynumber: 10.6 Consensus size: 52
615968 TCGCTCTCTA
* *
615978 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
616030 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
616082 TTTCGTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
616134 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
616186 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCAAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
616238 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
616290 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
616342 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
616394 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
616446 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
616498 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
616531 CCAACGATCG
Statistics
Matches: 473, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 473 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
Found at i:616585 original size:55 final size:55
Alignment explanation
Indices: 616526--616803 Score: 429
Period size: 55 Copynumber: 5.1 Consensus size: 55
616516 CTCGAACAAT
* *
616526 AATCTCCAACGATCGCATCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
616581 AATCTTCAACAATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
616636 AATCTTCAATGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
616689 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
616744 AATCTTCAACGATCACGTCTGCCCCCTATTTCTTC--AGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
616797 AATCTTC
1 AATCTTC
616804 TTTTGCTTCA
Statistics
Matches: 202, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
53 71 0.35
54 4 0.02
55 127 0.63
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:616731 original size:108 final size:110
Alignment explanation
Indices: 616526--616803 Score: 447
Period size: 108 Copynumber: 2.6 Consensus size: 110
616516 CTCGAACAAT
* *
616526 AATCTCCAACGATCGCATCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
616591 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* * *
616636 AATCTTCAATGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
616699 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
*
616744 AATCTTCAACGATCACGTCTGCCCCCTATTTCTTC--AGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
616804 TTTTGCTTCA
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
106 11 0.07
107 2 0.01
108 95 0.61
109 2 0.01
110 45 0.29
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTATGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:618080 original size:1 final size:1
Alignment explanation
Indices: 618071--618179 Score: 56
Period size: 1 Copynumber: 109.0 Consensus size: 1
618061 AACCCCCCCC
* * * * * * * * * *
618071 TTTTATTTTTTTGTTTTTTTTTTCTTCTTCTTTTTTTCTTCTTTTTTTTATTTTTTTTTTTCTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *** ** *
618136 TTTTATATTTTTTCCATTTTTTTTTTTTTCATTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
618180 ATCTTTAAGC
Statistics
Matches: 76, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.07, C:0.08, G:0.01, T:0.83
Consensus pattern (1 bp):
T
Found at i:618092 original size:11 final size:11
Alignment explanation
Indices: 618071--618179 Score: 73
Period size: 11 Copynumber: 10.0 Consensus size: 11
618061 AACCCCCCCC
618071 TTTTATTTTTT
1 TTTTATTTTTT
618082 TGTTT-TTTTTT
1 T-TTTATTTTTT
* * *
618093 TCTTCTTCTTT
1 TTTTATTTTTT
*
618104 TTTTCTTCTTTT
1 TTTTATT-TTTT
618116 TTTTA-TTTTT
1 TTTTATTTTTT
* *
618126 TTTT-TTCTAT
1 TTTTATTTTTT
*
618136 TTTTATATTTT
1 TTTTATTTTTT
**
618147 TTCCATTTTTT
1 TTTTATTTTTT
*
618158 TTTT-TTTCATT
1 TTTTATTT-TTT
618169 TTTTATTTTTT
1 TTTTATTTTTT
618180 ATCTTTAAGC
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
10 20 0.27
11 41 0.55
12 13 0.18
ACGTcount: A:0.07, C:0.08, G:0.01, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:618093 original size:14 final size:14
Alignment explanation
Indices: 618070--618179 Score: 68
Period size: 14 Copynumber: 7.8 Consensus size: 14
618060 GAACCCCCCC
*
618070 CTTTTATTTTT-TT
1 CTTTTTTTTTTCTT
*
618083 GTTTTTTTTTTCTT
1 CTTTTTTTTTTCTT
*
618097 CTTCTTTTTTTCTT
1 CTTTTTTTTTTCTT
*
618111 CTTTTTTTTAT-TT
1 CTTTTTTTTTTCTT
* *
618124 -TTTTTTTTCTATT
1 CTTTTTTTTTTCTT
618137 -TTTATATTTTTTCCATT
1 CTTT-T-TTTTTT-C-TT
*
618154 TTTTTTTTTTTCATT
1 CTTTTTTTTTTC-TT
618169 -TTTTATTTTTT
1 CTTTT-TTTTTT
618180 ATCTTTAAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
12 9 0.11
13 16 0.20
14 28 0.35
15 15 0.19
16 6 0.08
17 3 0.04
18 3 0.04
ACGTcount: A:0.07, C:0.09, G:0.01, T:0.83
Consensus pattern (14 bp):
CTTTTTTTTTTCTT
Found at i:618139 original size:32 final size:32
Alignment explanation
Indices: 618071--618179 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 32
618061 AACCCCCCCC
*
618071 TTTTAT-TTTTTTGTTT-TTTTTTTCTTCTTCTTT
1 TTTTATATTTTTT-TTTATTTTTTT-TT-TTCTAT
*
618104 TTTTCT-TCTTTTTTTTATTTTTTTTTTTCTAT
1 TTTTATAT-TTTTTTTTATTTTTTTTTTTCTAT
*
618136 TTTTATATTTTTTCCATT-TTTTTTTTTTTC-AT
1 TTTTATATTTTTT--TTTATTTTTTTTTTTCTAT
618168 TTTT-TATTTTTT
1 TTTTATATTTTTT
618180 ATCTTTAAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.12
32 21 0.31
33 24 0.36
34 14 0.21
ACGTcount: A:0.07, C:0.08, G:0.01, T:0.83
Consensus pattern (32 bp):
TTTTATATTTTTTTTTATTTTTTTTTTTCTAT
Found at i:618148 original size:17 final size:15
Alignment explanation
Indices: 618121--618179 Score: 75
Period size: 15 Copynumber: 3.8 Consensus size: 15
618111 CTTTTTTTTA
618121 TTTTT-TTTTTTCTAT
1 TTTTTATTTTTTC-AT
618136 TTTTATATTTTTTCCAT
1 TTTT-TATTTTTT-CAT
*
618153 TTTTTTTTTTTTCAT
1 TTTTTATTTTTTCAT
618168 TTTTTATTTTTT
1 TTTTTATTTTTT
618180 ATCTTTAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 18 0.46
16 8 0.21
17 12 0.31
18 1 0.03
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTTCAT
Found at i:618179 original size:8 final size:8
Alignment explanation
Indices: 618071--618179 Score: 73
Period size: 8 Copynumber: 13.4 Consensus size: 8
618061 AACCCCCCCC
618071 TTTTATTT
1 TTTTATTT
*
618079 TTTTGTTT
1 TTTTATTT
618087 TTTT-TTT
1 TTTTATTT
*
618094 CTTCTTCTTT
1 -TT-TTATTT
*
618104 TTTTCTTCT
1 TTTTATT-T
618113 TTTT-TTT
1 TTTTATTT
*
618120 ATTTTTTTT
1 -TTTTATTT
618129 TTTCTATTT
1 TTT-TATTT
*
618138 TTATATTT
1 TTTTATTT
*
618146 TTTCCATTT
1 TTT-TATTT
618155 TTTT-TTT
1 TTTTATTT
*
618162 TTTCA-TT
1 TTTTATTT
618169 TTTTATTT
1 TTTTATTT
618177 TTT
1 TTT
618180 ATCTTTAAGC
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
7 16 0.19
8 39 0.47
9 25 0.30
10 3 0.04
ACGTcount: A:0.07, C:0.08, G:0.01, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:619568 original size:14 final size:14
Alignment explanation
Indices: 619549--619575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
619539 TAGATTACGA
619549 AGCTGAATCGCCAG
1 AGCTGAATCGCCAG
619563 AGCTGAATCGCCA
1 AGCTGAATCGCCA
619576 TATACCTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (14 bp):
AGCTGAATCGCCAG
Found at i:625658 original size:32 final size:33
Alignment explanation
Indices: 625616--625701 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 33
625606 TTTTGCTTCC
* * *
625616 CCCTGCTGTTCATGAACCTCCTTCCTCGAATGT
1 CCCTGCTGTTCGTGAGCCTCCTTCCTCAAATGT
625649 -CCTGCTGTTCGTGAGCCTCCTTCCTCAAATGT
1 CCCTGCTGTTCGTGAGCCTCCTTCCTCAAATGT
625681 CCCTG-TGTTCGTGAGCCTCCT
1 CCCTGCTGTTCGTGAGCCTCCT
625702 CCCAATGTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 45 0.92
33 4 0.08
ACGTcount: A:0.12, C:0.36, G:0.19, T:0.34
Consensus pattern (33 bp):
CCCTGCTGTTCGTGAGCCTCCTTCCTCAAATGT
Found at i:625932 original size:19 final size:20
Alignment explanation
Indices: 625897--625941 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
625887 ACAAAACATG
625897 GGTGGCCAGCAAATATTAGT
1 GGTGGCCAGCAAATATTAGT
625917 GGTGGCCAGC-AATATTAGT
1 GGTGGCCAGCAAATATTAGT
625936 GGTGGC
1 GGTGGC
625942 GGTATAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (20 bp):
GGTGGCCAGCAAATATTAGT
Found at i:626620 original size:3 final size:3
Alignment explanation
Indices: 626614--626652 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
626604 ATATTATTAT
626614 TAA TAA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
626653 GTATCCCGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:626742 original size:45 final size:45
Alignment explanation
Indices: 626680--626879 Score: 283
Period size: 45 Copynumber: 4.4 Consensus size: 45
626670 GGTGTCTACA
* *
626680 CCTTCATTGCTTGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
1 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
* * * *
626725 CTTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGC
1 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
* *
626770 CCTTCAATGCATGATGTTTTCAAAACCTTTGGGTAATATGTAAGT
1 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
* * * *
626815 CCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGA
1 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
*
626860 CCTTCAGTGCATTATGTTTT
1 CCTTCAGTGCATGATGTTTT
626880 TAAACATTTC
Statistics
Matches: 136, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (45 bp):
CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGT
Found at i:626793 original size:90 final size:90
Alignment explanation
Indices: 626679--626879 Score: 330
Period size: 90 Copynumber: 2.2 Consensus size: 90
626669 GGGTGTCTAC
* * *
626679 ACCTTCATTGCTTGATGTTTTCAAAACCTTCGGGTAATATGTAAGTCTTTCAGTGCATGATGTTT
1 ACCTTCAATGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGTCCTTCAGTGCATGATGTTT
626744 TCAAAACCTTCGGGTCATCTGTAAG
66 TCAAAACCTTCGGGTCATCTGTAAG
* *
626769 CCCTTCAATGCATGATGTTTTCAAAACCTTTGGGTAATATGTAAGTCCTTCAGTGCATGATGTTT
1 ACCTTCAATGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGTCCTTCAGTGCATGATGTTT
*
626834 TCAAAGCCTTCGGGTCATCTGTAAG
66 TCAAAACCTTCGGGTCATCTGTAAG
* *
626859 ACCTTCAGTGCATTATGTTTT
1 ACCTTCAATGCATGATGTTTT
626880 TAAACATTTC
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 102 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (90 bp):
ACCTTCAATGCATGATGTTTTCAAAACCTTCGGGTAATATGTAAGTCCTTCAGTGCATGATGTTT
TCAAAACCTTCGGGTCATCTGTAAG
Found at i:627017 original size:3 final size:3
Alignment explanation
Indices: 627009--627063 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
626999 AATTATTTAA
* **
627009 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
*
627054 AAT ATT ATT A
1 ATT ATT ATT A
627064 AATTAAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:627035 original size:21 final size:24
Alignment explanation
Indices: 627009--627063 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
626999 AATTATTTAA
627009 ATTATTATT-TT-TA-AAATTATT
1 ATTATTATTATTATATAAATTATT
*
627030 ATTATTATTATTATATATATTATT
1 ATTATTATTATTATATAAATTATT
*
627054 AATATTATTA
1 ATTATTATTA
627064 AATTAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 2 0.07
24 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATTATTATTATATAAATTATT
Found at i:629557 original size:45 final size:46
Alignment explanation
Indices: 629490--630176 Score: 895
Period size: 45 Copynumber: 14.8 Consensus size: 46
629480 CTATTTCTCA
* * *
629490 CATCTGTAAGCCCTTCAGTGCATGATTTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
* * *
629535 CATCTGTAAGCCCTTCATTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
* * *
629580 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
*
629625 CATCTGTAAG-CCATTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGACC-TTCAGTGCAGGATGTTTTC--AAAAACCTTCGGGT
* **
629673 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAAGCCTTTAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAAA-CCTTCGGGT
* *
629721 CATCCGTAAGACCTTCAGTGAAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAA-CCTTCGGGT
* * *
629768 CATCTGTAAG-CCTTTTAGTGCATGATGTTTTCAAAAAAACCTTTGGGT
1 CATCTGTAAGACC-TTCAGTGCAGGATGTTTTC--AAAAACCTTCGGGT
* * * *
629816 TATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC--AAAAACCTTCGGGT
* *
629864 CATCTGTAAGACCTTCAGTTCAGGATGTTTTCAAAAAAGCCTTCGAGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAAA-CCTTCGGGT
*
629912 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAAGCCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAAA-CCTTCGGGT
* *
629960 CATCTGCAAGACCTTCAATGCAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAA-CCTTCGGGT
*
630007 CATCTGTAAGACCTTCAGTGCAGAATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
630052 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
630097 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
** *
630142 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAA
630177 TGATATTTTA
Statistics
Matches: 591, Mismatches: 39, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
44 2 0.00
45 242 0.41
46 8 0.01
47 93 0.16
48 237 0.40
49 9 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (46 bp):
CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAACCTTCGGGT
Found at i:629683 original size:48 final size:47
Alignment explanation
Indices: 629490--630176 Score: 907
Period size: 48 Copynumber: 14.7 Consensus size: 47
629480 CTATTTCTCA
* * *
629490 CATCTGTAAGCCCTTCAGTGCATGATTTTTTC--AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
* * *
629535 CATCTGTAAGCCCTTCATTGCATGATGTTTTC--AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
* * *
629580 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAACCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
*
629625 CATCTGTAAG-CCATTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGACC-TTCAGTGCAGGATGTTTTC-AAAAAACCTTCGGGT
* **
629673 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAAGCCTTTAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAA-CCTTCGGGT
* * *
629721 CATCCGTAAGACCTTCAGTGAAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
* * *
629768 CATCTGTAAG-CCTTTTAGTGCATGATGTTTTCAAAAAAACCTTTGGGT
1 CATCTGTAAGACC-TTCAGTGCAGGATGTTTTC-AAAAAACCTTCGGGT
* * * *
629816 TATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAAAACCTTCGGGT
* *
629864 CATCTGTAAGACCTTCAGTTCAGGATGTTTTCAAAAAAGCCTTCGAGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAA-CCTTCGGGT
*
629912 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAAGCCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAA-CCTTCGGGT
* * *
629960 CATCTGCAAGACCTTCAATGCAGGATGTTTTCAAAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
*
630007 CATCTGTAAGACCTTCAGTGCAGAATGTTTTC--AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
630052 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC--AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
630097 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC--AAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
** *
630142 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAA
630177 TGATATTTTA
Statistics
Matches: 587, Mismatches: 43, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
44 2 0.00
45 245 0.42
46 2 0.00
47 82 0.14
48 252 0.43
49 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (47 bp):
CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAACCTTCGGGT
Found at i:629806 original size:143 final size:139
Alignment explanation
Indices: 629490--630176 Score: 926
Period size: 143 Copynumber: 4.9 Consensus size: 139
629480 CTATTTCTCA
*
629490 CATCTGTAAGCCCTTCAGTGCATGATTTTTTC---AAAACCTTCGGGTCATCTGTAAGCCCTTCA
1 CATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
* * * *
629552 TTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAA
65 GTGCAGGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAA
*
629615 ACCTTCAGGT
130 ACCTTCGGGT
629625 CATCTGTAAGCCATTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
1 CATCTGTAAGCC-TTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
** * *
629690 GTGCAGGATGTTTTCAAAAAAGCCTTTAGGTCATCCGTAAGACCTTCAGTGAAGGATGTTTTCAA
65 GTGCAGGATGTTTTC-AAAAA-CCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAA
629755 AAAGCCTTCGGGT
128 AAA-CCTTCGGGT
* * *
629768 CATCTGTAAGCCTTTTAGTGCATGATGTTTTCAAAAAAACCTTTGGGTTATCTGTAAGCCCTTCA
1 CATCTGTAAGCC-TTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
* * *
629833 GTTCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTTCAGGATGTTTTCAA
65 GTGCAGGATGTTTTC--AAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTC-A
*
629898 AAAAGCCTTCGAGT
127 AAAA-CCTTCGGGT
* * * * *
629912 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAAGCCTTCAGGTCATCTGCAAGACCTTCA
1 CATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
* *
629977 ATGCAGGATGTTTTCAAAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAGAATGTTTTC-AA
65 GTGCAGGATGTTTTCAAAAA-CCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAA
630041 AACCTTCGGGT
129 AACCTTCGGGT
* *
630052 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC---AAAACCTTCGGGTCATCTGTAAGACCTTCA
1 CATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCA
** *
630114 GTGCAGGATGTTTTC-AAAACCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATGTTTTCAAA
65 GTGCAGGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAA
630177 TGATATTTTA
Statistics
Matches: 494, Mismatches: 44, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
134 2 0.00
135 65 0.13
136 6 0.01
137 41 0.08
138 43 0.09
140 44 0.09
141 39 0.08
142 9 0.02
143 157 0.32
144 86 0.17
145 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (139 bp):
CATCTGTAAGCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
TGCAGGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAA
CCTTCGGGT
Found at i:630434 original size:6 final size:6
Alignment explanation
Indices: 630381--630434 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
630371 TTTTTAAAAT
* * * * *
630381 TATTAT TATTAT TATAAA TATTAT TATTAA TATTAA TTTTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
630429 TATTAA
1 TATTAA
630435 ATAATAACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TATTAA
Found at i:631674 original size:14 final size:15
Alignment explanation
Indices: 631640--631679 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
631630 ATATTATATA
631640 TATTTAAATTATTTC
1 TATTTAAATTATTTC
631655 TA-TTAAATTATTT-
1 TATTTAAATTATTTC
*
631668 TATTTAACTTAT
1 TATTTAAATTAT
631680 AATTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAAATTATTTC
Found at i:632236 original size:17 final size:17
Alignment explanation
Indices: 632216--632266 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
632206 CTTTTTTATT
632216 TATTATTATTTTATTTA
1 TATTATTATTTTATTTA
632233 TATTATTATTTT-TATTA
1 TATTATTATTTTAT-TTA
632250 TATTATTACTTTTATTT
1 TATTATTA-TTTTATTT
632267 TTCTTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.03
17 23 0.74
18 6 0.19
19 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTATTTTATTTA
Found at i:632238 original size:14 final size:14
Alignment explanation
Indices: 632209--632256 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 14
632199 GTTTTGTCTT
632209 TTTTATTTATTATTA
1 TTTTATTTA-TATTA
632224 TTTTATTTATATTA
1 TTTTATTTATATTA
*
632238 --TTATTTTTATTA
1 TTTTATTTATATTA
*
632250 TATTATT
1 TTTTATT
632257 ACTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.37
14 10 0.33
15 9 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:632979 original size:12 final size:12
Alignment explanation
Indices: 632962--632986 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
632952 TCCCTTTTTA
632962 GAAACATTTCGT
1 GAAACATTTCGT
632974 GAAACATTTCGT
1 GAAACATTTCGT
632986 G
1 G
632987 CCCGGGCAAA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GAAACATTTCGT
Found at i:642352 original size:33 final size:33
Alignment explanation
Indices: 642310--642376 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
642300 CCTAGTACAG
642310 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
642343 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
642376 A
1 A
642377 GCACTACGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:642473 original size:20 final size:20
Alignment explanation
Indices: 642436--642474 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
642426 TATATTGGGC
* *
642436 TATTTTCTATTGTTTATGGA
1 TATTTTCTATGGTATATGGA
642456 TATTTTCTATGGTATATGG
1 TATTTTCTATGGTATATGG
642475 TTATGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (20 bp):
TATTTTCTATGGTATATGGA
Found at i:649997 original size:182 final size:182
Alignment explanation
Indices: 649704--650084 Score: 532
Period size: 182 Copynumber: 2.1 Consensus size: 182
649694 CGATCCAAAT
* *
649704 TAAAAATGTATCGATCCATATTAATATAACAGGTAAAAATATGATAAAACCGGTCACAAAAAGAT
1 TAAAAATGTATCGATCCACAATAATATAACAGGTAAAAATATGATAAAACCGGTCACAAAAAGAT
* * *
649769 AATACCGGTAAAGCCCTACCAGATATATTGAACGTGTTGATACTTTAATATAAGGATCGAAACTT
66 AAAACCGGTAAAGCCCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGAAACTT
*
649834 TGTGAATTTAAAAGAGAAACAGTTTTAGCACCTATAAAGTGTCGATACTTTA
131 TGTAAATTTAAAAGAGAAACAGTTTTAGCACCTATAAAGTGTCGATACTTTA
* * * * * *
649886 TAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGACT-GAATCGGT-ATCGAAATG
1 TAAAAATGTATCGATCCACAATAATATAACAGGTAAAAATATGA-TAAAACCGGTCA-CAAAAAG
* * ** * * *
649949 ATAAAATCGGTAAAGCGCTACTGGATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACAC
64 ATAAAACCGGTAAAGCCCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGAAAC
* *
650014 TTTGTAAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
129 TTTGTAAATTTAAAAGAGAAACAGTTTTAGCACCTATAAAGTGTCGATACTTTA
*
650068 TAAAAATTTATCGATCC
1 TAAAAATGTATCGATCC
650085 TTATGATAAC
Statistics
Matches: 175, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
181 1 0.01
182 173 0.99
183 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAATAATATAACAGGTAAAAATATGATAAAACCGGTCACAAAAAGAT
AAAACCGGTAAAGCCCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGAAACTT
TGTAAATTTAAAAGAGAAACAGTTTTAGCACCTATAAAGTGTCGATACTTTA
Found at i:652998 original size:249 final size:247
Alignment explanation
Indices: 652557--653024 Score: 661
Period size: 247 Copynumber: 1.9 Consensus size: 247
652547 AAGTGTCGAC
* * * * * *
652557 CATTTATAAAAAGTAACGACCCCAAAAACATCGAAATCGATAATTATAATGTAATGGGTAATTTT
1 CATTTATAAAAAGTAACGACCCCAAAAACATCAAAACCCATAATTAAAATGTAATAGATAATTTT
* * * *
652622 TCAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATAGGTCTACAACATGTATCGACACTT
66 TCAATATAACCAGTATAAATATACCAGTTTTATGAAAAATAAGTCTACAACATGTATCGACACTT
*
652687 ATTAATATTGTGTTGATATTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCG
131 ATTAATATTGTGTCGATATTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCG
*
652752 ATAC-TTCAAAGAGTGTCGATCTAAAAGGGTTGCACGCTTAAAGTTTCGATA
196 ATACTTTCAAAAAGTGTCGATCTAAAAGGGTTGCACGCTTAAAGTTTCGATA
* ** *
652803 CATTTATTAAAAGTGTCGATCCCAAAAACATCAAAACCCCATAATTAAAATGTAATAGATAATTT
1 CATTTATAAAAAGTAACGACCCCAAAAACATCAAAA-CCCATAATTAAAATGTAATAGATAATTT
* * *
652868 TGT-AATATAACCAGTATACATATACCAGTTTTATGAGAGAATAAGTCTATAACATGTATCGACA
65 T-TCAATATAACCAGTATAAATATACCAGTTTTATGA-AAAATAAGTCTACAACATGTATCGACA
* * * *
652932 CTTCTTAATATTGTGTCGATAATTTTTGTCCAGAATTGATGTCAAAAAGGGTGAACGCATAAAGT
128 CTTATTAATATTGTGTCGAT-ATTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGT
652997 GTCGATACATTTTCAAAAAGTGTCGATC
192 GTCGATAC--TTTCAAAAAGTGTCGATC
653025 CCGAAAACAT
Statistics
Matches: 192, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
246 31 0.16
247 53 0.28
248 43 0.22
249 49 0.26
252 16 0.08
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (247 bp):
CATTTATAAAAAGTAACGACCCCAAAAACATCAAAACCCATAATTAAAATGTAATAGATAATTTT
TCAATATAACCAGTATAAATATACCAGTTTTATGAAAAATAAGTCTACAACATGTATCGACACTT
ATTAATATTGTGTCGATATTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCACAAAGTGTCG
ATACTTTCAAAAAGTGTCGATCTAAAAGGGTTGCACGCTTAAAGTTTCGATA
Found at i:653142 original size:200 final size:200
Alignment explanation
Indices: 652774--653356 Score: 866
Period size: 200 Copynumber: 2.9 Consensus size: 200
652764 GTGTCGATCT
* * * *
652774 AAAAGGGTTGCACGCTTAAAGTTTCGATACATTTAT-TAAAAGTGTCGATCCCAAAAACATCAAA
1 AAAAGGG-TGAACGCATAAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCAAA
* * * *
652838 ACCCCATAATTAAAATGTAATAGATAATTTTGTAATATAACCAGTATACATATACC-AGTTTTAT
64 A-CCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGA-TTTTAT
* * * *
652902 GAGAGAATAAGTCTATAACATGTATCGACACTTCTTAATATTGTGTCGATAATTTTTGTCCAGAA
127 GAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAA
* *
652967 TTGATGTCA
192 TGGATGCCA
*
652976 AAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCGAAAACATCAAAAC
1 AAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAAC
*
653041 CCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGATA
66 CCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGA
*
653106 GAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATACTTTATGTCCAGAATGGA
131 GAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGA
653171 TGCCA
196 TGCCA
* * * *
653176 AAAAGGGTGAATGCACAAAGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAAC
1 AAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAAC
* *
653241 CCATAATTATAATGTAATAGGTAATTTTTTAATATAA-CGGTATAAATATACCGATTTTATAAGA
66 CCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGA
* * * *
653305 GACTAGGTCTACAACATGTAGCGACACTTTTTTATTTTGTGTCGATACTTTT
131 GAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATACTTTT
653357 AAATAATGTG
Statistics
Matches: 349, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
199 72 0.21
200 219 0.63
201 51 0.15
202 7 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (200 bp):
AAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAAC
CCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGA
GAATAGGTCTACAACATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGA
TGCCA
Found at i:656568 original size:21 final size:20
Alignment explanation
Indices: 656538--656583 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
656528 GGTGCACGCA
656538 TAAAATGTCGATACATTTAT
1 TAAAATGTCGATACATTTAT
*
656558 TAAAAGTGTCGATATATTTAT
1 TAAAA-TGTCGATACATTTAT
656579 TAAAA
1 TAAAA
656584 CTATCGATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (20 bp):
TAAAATGTCGATACATTTAT
Found at i:656590 original size:21 final size:21
Alignment explanation
Indices: 656545--656591 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
656535 GCATAAAATG
* *
656545 TCGATACATTTATTAAAAGTG
1 TCGATACATTTATTAAAACTA
*
656566 TCGATATATTTATTAAAACTA
1 TCGATACATTTATTAAAACTA
656587 TCGAT
1 TCGAT
656592 CCCAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (21 bp):
TCGATACATTTATTAAAACTA
Found at i:657231 original size:87 final size:87
Alignment explanation
Indices: 657084--657246 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
657074 AAATAGGTCA
*
657084 ATATAAACGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
657149 CCGGTTAAATGTCTATTTTATT
66 CCGGTTAAATGTCTATTTTATT
* * * *
657171 ATATAAGCGCTACTTATTACATTAAATAAGCGCTACCTAATATGTTATTGTACTTTATAATATTT
1 ATATAAACGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
657236 CCGGTTAAATG
66 CCGGTTAAATG
657247 ATATAACATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGTCTATTTTATT
Found at i:663621 original size:23 final size:23
Alignment explanation
Indices: 663587--663672 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
663577 ACATATTATA
*
663587 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
663610 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
663633 CAGTC-CTTCGG-GACAAATTCTACG
1 -TGGCACTTCGGTG-C-AATTCTACG
663657 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
663673 ATTTATACGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.63
24 16 0.33
25 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:667533 original size:34 final size:30
Alignment explanation
Indices: 667478--667548 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 30
667468 ATTAATTTCA
*
667478 TTTTAATTTAAAATAATTTAATGAATTTAATAT
1 TTTTTATTTAAAATAATTTAAT---TTTAATAT
*
667511 TTTTTATTTAAAA-AATTATTAATTTTGATAT
1 TTTTTATTTAAAATAA-T-TTAATTTTAATAT
667542 TTTTTAT
1 TTTTTAT
667549 GATATTGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 14 0.41
32 2 0.06
33 13 0.38
34 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTTATTTAAAATAATTTAATTTTAATAT
Found at i:668570 original size:78 final size:78
Alignment explanation
Indices: 668441--668595 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
668431 GTGGTTAGTA
*
668441 GACTGTTAGAGAATTAGTTAGAAGCAGTTACTTTTCAGCTCTTGTATTGTAGCTTGTACATTGTA
1 GACTGTTAGAGAATTAGTTAGAAGCAATTACTTTTCAGCTCTTGTATTGTAGCTTGTACATTGTA
668506 TTATATATTGCAT
66 TTATATATTGCAT
*
668519 GACTGTTAGAGAATTAGTTAGAAGCAATTACTTTTCAGCTCTTGTATTGTAGTTTGTACATTGTA
1 GACTGTTAGAGAATTAGTTAGAAGCAATTACTTTTCAGCTCTTGTATTGTAGCTTGTACATTGTA
668584 TTATATATTGCA
66 TTATATATTGCA
668596 GGTCAGCTAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (78 bp):
GACTGTTAGAGAATTAGTTAGAAGCAATTACTTTTCAGCTCTTGTATTGTAGCTTGTACATTGTA
TTATATATTGCAT
Found at i:675651 original size:219 final size:218
Alignment explanation
Indices: 675272--675715 Score: 798
Period size: 219 Copynumber: 2.0 Consensus size: 218
675262 ATCAAAATGT
* *
675272 GCGCCATCCACATTTTTTCTTGTAACAGGAAGTTAAATCCAGTCGGCAATTTGAAAGAGGGTCTA
1 GCGCCATCCACATTTTTTCTTGTAACAGGAAGTCAAATCCAGTCAGCAATTTGAAAGAGGGTCTA
* * *
675337 GAGAACCTCAATACATAAATGCAGCCATTCATAAACCAAATCAAAGAATGGTGATTTCTATTTTG
66 CAGAACATCAAAACATAAATGCAGCCATTCATAAACCAAATCAAAGAATGGTGATTTCTATTTTG
675402 CTGATGAGCTAATAGACGGATTACCTGTCTAAGCTGCATTTCTGTCATGTTAAAAGTGCAAATTC
131 CTGATGAGCTAATAGACGGATTACCTGTCTAAGCTGCATTTCTGTCATGTT-AAAGTGCAAATTC
* *
675467 CTTACATATAATTTTCTATCAACA
195 CCTACATATAATTTTCCATCAACA
675491 GCGCCATCCACATTTTTTCTTGTAACAGGAAGTCAAATCCAGTCAGCAATTTGAAAGAGGGTCTA
1 GCGCCATCCACATTTTTTCTTGTAACAGGAAGTCAAATCCAGTCAGCAATTTGAAAGAGGGTCTA
675556 CAGAACATCAAAACATAAATGCAGCCATTCATAAACCAAATCAAAGAATGGTGATTTCTATTTTG
66 CAGAACATCAAAACATAAATGCAGCCATTCATAAACCAAATCAAAGAATGGTGATTTCTATTTTG
*
675621 CTGATGAGCTAATAGACGGATTACCTGTCTAAGGTGCATTTCTGTCATGTTAAAGTGCAAATTCC
131 CTGATGAGCTAATAGACGGATTACCTGTCTAAGCTGCATTTCTGTCATGTTAAAGTGCAAATTCC
675686 CTACATATAATTTTCCATCAACA
196 CTACATATAATTTTCCATCAACA
*
675709 GCACCAT
1 GCGCCAT
675716 ATGGTCCAGC
Statistics
Matches: 216, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
218 41 0.19
219 175 0.81
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (218 bp):
GCGCCATCCACATTTTTTCTTGTAACAGGAAGTCAAATCCAGTCAGCAATTTGAAAGAGGGTCTA
CAGAACATCAAAACATAAATGCAGCCATTCATAAACCAAATCAAAGAATGGTGATTTCTATTTTG
CTGATGAGCTAATAGACGGATTACCTGTCTAAGCTGCATTTCTGTCATGTTAAAGTGCAAATTCC
CTACATATAATTTTCCATCAACA
Found at i:677586 original size:298 final size:304
Alignment explanation
Indices: 677018--677621 Score: 1141
Period size: 298 Copynumber: 2.0 Consensus size: 304
677008 ACGAATAAAG
677018 AATTAGCATTATAAAAATTTAGTAATGAGGCAAATGTGAGTTCAACTTATTTAATTAATTATTTT
1 AATTAGCATTATAAAAATTTAGTAATGAGGCAAATGTGAGTTCAACTTATTTAATTAATTATTTT
677083 GATCGATGACGACTTACGATAAGTCAATCTCACATTATTTATTTCAAAGATATGAATTATGTTTT
66 GATCGATGACGACTTACGATAAGTCAATCTCACATTATTTATTTCAAAGATATGAATTATGTTTT
677148 AATTATGGAATTATATCTGTAATATTTTAATAAGTTTTATGAATGGTTTTTTGGTATGAACTGCC
131 AATTATGGAATTATATCTGTAATATTTTAATAAGTTTTATGAATGGTTTTTTGGTATGAACTGCC
*
677213 AATGTCATGTTTTATGAATATGATTTGAATATAATTATGATTCTGATATGATTTTTATCAAATGA
196 AATGTCATGTTTTATGAATATGATTTGAACATAATTATGATTCTGATATGATTTTTATCAAATGA
677278 TTATGAATTGAGCTAAAAGTCCATTGTATGTTGT-TTGAGAGTA
261 TTATGAATTGAGCTAAAAGTCCATTGTATGTTGTATTGAGAGTA
677321 AATTAGCATTATAAAAATTTAGTAATGAGGCAAATGTGAGTTC-AC-TATTT-ATTAATTATTTT
1 AATTAGCATTATAAAAATTTAGTAATGAGGCAAATGTGAGTTCAACTTATTTAATTAATTATTTT
677383 GATCGATGACGACTTACGATAAGTCAATCTCACATTATTTATTTC-AAGATATGAATTATGTTTT
66 GATCGATGACGACTTACGATAAGTCAATCTCACATTATTTATTTCAAAGATATGAATTATG-TTT
677447 TAATTATGGAATTATATCTGTAATATTTTAAT-AGTTTTATGAAT-GTTTTTTGGTATGAACTGC
130 TAATTATGGAATTATATCTGTAATATTTTAATAAGTTTTATGAATGGTTTTTTGGTATGAACTGC
677510 CAATGTCATGTTTTATGAATATGATTTGAACATAATTATGATTCTGATATGATTTTTATCAAATG
195 CAATGTCATGTTTTATGAATATGATTTGAACATAATTATGATTCTGATATGATTTTTATCAAATG
677575 ATTATGAATTGAGCTAAAAGTCCATTGTATGTTGTATTGAGAGTA
260 ATTATGAATTGAGCTAAAAGTCCATTGTATGTTGTATTGAGAGTA
677620 AA
1 AA
677622 AGGTATAATT
Statistics
Matches: 298, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
298 118 0.40
299 38 0.13
300 92 0.31
301 5 0.02
302 2 0.01
303 43 0.14
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (304 bp):
AATTAGCATTATAAAAATTTAGTAATGAGGCAAATGTGAGTTCAACTTATTTAATTAATTATTTT
GATCGATGACGACTTACGATAAGTCAATCTCACATTATTTATTTCAAAGATATGAATTATGTTTT
AATTATGGAATTATATCTGTAATATTTTAATAAGTTTTATGAATGGTTTTTTGGTATGAACTGCC
AATGTCATGTTTTATGAATATGATTTGAACATAATTATGATTCTGATATGATTTTTATCAAATGA
TTATGAATTGAGCTAAAAGTCCATTGTATGTTGTATTGAGAGTA
Found at i:679468 original size:27 final size:27
Alignment explanation
Indices: 679428--679482 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
679418 GATGAACCTC
* *
679428 ATTGTATAAAATGATGTAATGCTCGAT
1 ATTGTATAAAATGATATAATACTCGAT
679455 ATTGTA-AAAGATGATATAATACTCGAT
1 ATTGTATAAA-ATGATATAATACTCGAT
679482 A
1 A
679483 CAATTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (27 bp):
ATTGTATAAAATGATATAATACTCGAT
Found at i:680872 original size:29 final size:29
Alignment explanation
Indices: 680817--680892 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
680807 ATTCTTGTCT
*
680817 TAACCTAAAAATATATTTTAATATTATCA
1 TAACTTAAAAATATATTTTAATATTATCA
* ** * *
680846 TAACTTAAAAATATGTTTTGTTTTTATCT
1 TAACTTAAAAATATATTTTAATATTATCA
680875 TAACTTTTAAAAATATAT
1 TAAC--TTAAAAATATAT
680893 CTGTAACACC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (29 bp):
TAACTTAAAAATATATTTTAATATTATCA
Found at i:688086 original size:18 final size:18
Alignment explanation
Indices: 688050--688087 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
688040 TTCAGTGTTC
* *
688050 ATCCCGAAGGACTATTAT
1 ATCCCGAAGGACCACTAT
688068 ATCCCGAAGGACCACTAT
1 ATCCCGAAGGACCACTAT
688086 AT
1 AT
688088 ACATCCTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (18 bp):
ATCCCGAAGGACCACTAT
Found at i:690090 original size:23 final size:23
Alignment explanation
Indices: 690064--690128 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
690054 CAGCTCATAT
690064 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* **
690087 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
*
690110 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
690129 ATAATAATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:690306 original size:103 final size:103
Alignment explanation
Indices: 690143--690360 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
690133 TAATGTCCAT
* *
690143 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
690208 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
690246 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
690311 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
690349 AAGGACCACATA
1 AAGGACCACATA
690361 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:695699 original size:23 final size:23
Alignment explanation
Indices: 695673--695755 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 23
695663 TATCATTCAT
695673 ATCTCTTATCTCATGCTCCTATG
1 ATCTCTTATCTCATGCTCCTATG
* *
695696 ATCTCTTATGT-ATGTCATTATCATTCAT-
1 ATCTCTTATCTCATG-C----TC-CT-ATG
695724 ATCTCTTATCTCATGCTCCTATG
1 ATCTCTTATCTCATGCTCCTATG
695747 ATCTCTTAT
1 ATCTCTTAT
695756 GTCCATATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
22 5 0.11
23 21 0.45
24 2 0.04
27 2 0.04
28 12 0.26
29 5 0.11
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.47
Consensus pattern (23 bp):
ATCTCTTATCTCATGCTCCTATG
Found at i:695710 original size:51 final size:51
Alignment explanation
Indices: 695655--695757 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
695645 TGCATACATA
695655 TATGTCATTATCATTCATATCTCTTATCTCATGCTCCTATGATCTCTTATG
1 TATGTCATTATCATTCATATCTCTTATCTCATGCTCCTATGATCTCTTATG
695706 TATGTCATTATCATTCATATCTCTTATCTCATGCTCCTATGATCTCTTATG
1 TATGTCATTATCATTCATATCTCTTATCTCATGCTCCTATGATCTCTTATG
695757 T
1 T
695758 CCATATCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.48
Consensus pattern (51 bp):
TATGTCATTATCATTCATATCTCTTATCTCATGCTCCTATGATCTCTTATG
Found at i:696123 original size:23 final size:23
Alignment explanation
Indices: 696097--696183 Score: 129
Period size: 23 Copynumber: 3.8 Consensus size: 23
696087 CAGCTCATAT
*
696097 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
* *
696120 AATTGCACCGGAGTGCCGCGAAG
1 AATTGCACCGGAGTGCCACGTAG
*
696143 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
696166 AATTGCACCGTAGTGCCA
1 AATTGCACCGGAGTGCCA
696184 TATAATAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.17
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:696370 original size:103 final size:103
Alignment explanation
Indices: 696199--696416 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
696189 TAATGTCCAT
* *
696199 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
696264 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
696302 AAGGGCCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
696367 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
696405 AATGACCACATA
1 AAGGACCACATA
696417 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:698483 original size:30 final size:29
Alignment explanation
Indices: 698411--698496 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
698401 TACAATATCT
* * * *
698411 TATTTTTATTTTAACTTATTACATATATA
1 TATTCTTATCTTAAATTATTAAATATATA
* * *
698440 TATTCTCAACTTAAATTATTAAATATATTC
1 TATTCTTATCTTAAATTATTAAATATA-TA
698470 TATTCTTATCTTAAATTATTAAATATA
1 TATTCTTATCTTAAATTATTAAATATA
698497 ATTGATCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.52
Consensus pattern (29 bp):
TATTCTTATCTTAAATTATTAAATATATA
Found at i:698584 original size:28 final size:27
Alignment explanation
Indices: 698546--698606 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
698536 ACATATAATG
* *
698546 AATATTTTATTTTTGTTTTAATTTAAA
1 AATATTTTATTTTTATCTTAATTTAAA
*
698573 AATATATTTATTTTTATCTTAATTTTAA
1 AATAT-TTTATTTTTATCTTAATTTAAA
698601 AATATT
1 AATATT
698607 ATAAGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
AATATTTTATTTTTATCTTAATTTAAA
Found at i:698627 original size:28 final size:29
Alignment explanation
Indices: 698596--698655 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
698586 TTATCTTAAT
*
698596 TTTAAAATATTATAAGAATAAA-TATATA
1 TTTAAAATAATATAAGAATAAACTATATA
*
698624 TTTAAATTAATATAAGAATAAACTATATA
1 TTTAAAATAATATAAGAATAAACTATATA
698653 TTT
1 TTT
698656 TTAGTGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTAAAATAATATAAGAATAAACTATATA
Found at i:702466 original size:30 final size:29
Alignment explanation
Indices: 702413--702488 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
702403 TATTTTTATT
* *
702413 TTAACTTATTACATATATATATTCTCAAC
1 TTAAATTATTAAATATATATATTCTCAAC
* *
702442 TTAAATTATTAAATATATTATATTCTTATC
1 TTAAATTATTAAATATA-TATATTCTCAAC
702472 TTAAATTATTAAATATA
1 TTAAATTATTAAATATA
702489 ATTGATCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 15 0.36
30 27 0.64
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAAATTATTAAATATATATATTCTCAAC
Found at i:702615 original size:28 final size:29
Alignment explanation
Indices: 702574--702633 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
702564 TTATCTTAAT
*
702574 TTTAAAATATTATAAGAATAAA-TATATA
1 TTTAAAATAATATAAGAATAAACTATATA
*
702602 TTTAAATTAATATAAGAATAAACTATATA
1 TTTAAAATAATATAAGAATAAACTATATA
702631 TTT
1 TTT
702634 TTAGTGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
TTTAAAATAATATAAGAATAAACTATATA
Found at i:713443 original size:23 final size:24
Alignment explanation
Indices: 713423--713470 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
713413 AGAAAATATT
713423 TTTTA-TTTTTACTTTTGAATAAA
1 TTTTATTTTTTACTTTTGAATAAA
713446 TTTTATTTTTTACTTTTGAA-AAA
1 TTTTATTTTTTACTTTTGAATAAA
713469 TT
1 TT
713471 AAAAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTATTTTTTACTTTTGAATAAA
Found at i:717013 original size:22 final size:23
Alignment explanation
Indices: 716971--717013 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
716961 TCTAATTATT
* *
716971 TATTGTTTTAAAATATAAAAAAA
1 TATTATTTCAAAATATAAAAAAA
716994 TATTATTTCAAAA-ATAAAAA
1 TATTATTTCAAAATATAAAAA
717014 TCCTACTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TATTATTTCAAAATATAAAAAAA
Found at i:725686 original size:13 final size:13
Alignment explanation
Indices: 725667--725750 Score: 114
Period size: 13 Copynumber: 6.3 Consensus size: 13
725657 AACCCGACCC
725667 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
725680 TACCCGACCAGTT
1 GACCCGACCCGTT
725693 GACCCGACCCGTT
1 GACCCGACCCGTT
*
725706 GACCCGACCCATT
1 GACCCGACCCGTT
725719 GACCCGACCCGTT
1 GACCCGACCCGTT
*
725732 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
725747 GACC
1 GACC
725751 GTTGACCCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
13 50 0.81
15 12 0.19
ACGTcount: A:0.18, C:0.43, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:725709 original size:8 final size:8
Alignment explanation
Indices: 725698--725777 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
725688 CAGTTGACCC
725698 GACCCGTT
1 GACCCGTT
725706 GACCC---
1 GACCCGTT
*
725711 GACCCATT
1 GACCCGTT
725719 GACCC---
1 GACCCGTT
725724 GACCCGTT
1 GACCCGTT
725732 GA-CCGTT
1 GACCCGTT
725739 GACCCGTT
1 GACCCGTT
725747 GA-CCGTT
1 GACCCGTT
725754 GACCCACGTT
1 GA-CC-CGTT
725764 GACCACTGTT
1 GACC-C-GTT
725774 GACC
1 GACC
725778 AAACTTTGAC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
5 10 0.16
7 14 0.23
8 19 0.31
9 5 0.08
10 13 0.21
ACGTcount: A:0.17, C:0.39, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:725739 original size:7 final size:7
Alignment explanation
Indices: 725727--725757 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
725717 TTGACCCGAC
725727 CCGTTGA
1 CCGTTGA
725734 CCGTTGA
1 CCGTTGA
725741 CCCGTTGA
1 -CCGTTGA
725749 CCGTTGA
1 CCGTTGA
725756 CC
1 CC
725758 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:725744 original size:15 final size:15
Alignment explanation
Indices: 725724--725758 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
725714 CCATTGACCC
725724 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
725739 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
725754 GACCC
1 GACCC
725759 ACGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:725778 original size:10 final size:9
Alignment explanation
Indices: 725724--725778 Score: 50
Period size: 7 Copynumber: 6.6 Consensus size: 9
725714 CCATTGACCC
725724 GACC-CGTT
1 GACCACGTT
725732 GA-C-CGTT
1 GACCACGTT
725739 GACC-CGTT
1 GACCACGTT
725747 GA-C-CGTT
1 GACCACGTT
725754 GACCCACGTT
1 GA-CCACGTT
725764 GACCACTGTT
1 GACCAC-GTT
725774 GACCA
1 GACCA
725779 AACTTTGACC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 9 0.21
9 5 0.12
10 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (9 bp):
GACCACGTT
Found at i:727078 original size:18 final size:18
Alignment explanation
Indices: 727052--727087 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
727042 TCGAAAGGAC
*
727052 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
727070 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
727088 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:728253 original size:24 final size:24
Alignment explanation
Indices: 728226--728320 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
728216 ATTTCCGACT
** *
728226 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
728250 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
728274 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
728298 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
728321 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:728264 original size:12 final size:12
Alignment explanation
Indices: 728249--728318 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
728239 GATAAATGAC
728249 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
728261 CTGATTTCTGAT
1 CTGAATTCTGTT
*
728273 CTGGATTCTGTT
1 CTGAATTCTGTT
728285 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
728297 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
728309 TTGATTTCTG
1 CTGAATTCTG
728319 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:728317 original size:48 final size:48
Alignment explanation
Indices: 728212--728320 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
728202 TAAATATTTA
* *
728212 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATAAATGACCTGAATTCTGT
** **
728260 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
*
728308 TTTGATTTCTGAT
1 TCTGATTTCTGAT
728321 ATCTTCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:730414 original size:13 final size:13
Alignment explanation
Indices: 730395--730478 Score: 114
Period size: 13 Copynumber: 6.3 Consensus size: 13
730385 AACCCGACCC
730395 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
730408 TACCCGACCAGTT
1 GACCCGACCCGTT
730421 GACCCGACCCGTT
1 GACCCGACCCGTT
*
730434 GACCCGACCCATT
1 GACCCGACCCGTT
730447 GACCCGACCCGTT
1 GACCCGACCCGTT
*
730460 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
730475 GACC
1 GACC
730479 GTTGACCCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
13 50 0.81
15 12 0.19
ACGTcount: A:0.18, C:0.43, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:730437 original size:8 final size:8
Alignment explanation
Indices: 730426--730505 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
730416 CAGTTGACCC
730426 GACCCGTT
1 GACCCGTT
730434 GACCC---
1 GACCCGTT
*
730439 GACCCATT
1 GACCCGTT
730447 GACCC---
1 GACCCGTT
730452 GACCCGTT
1 GACCCGTT
730460 GA-CCGTT
1 GACCCGTT
730467 GACCCGTT
1 GACCCGTT
730475 GA-CCGTT
1 GACCCGTT
730482 GACCCACGTT
1 GA-CC-CGTT
730492 GACCACTGTT
1 GACC-C-GTT
730502 GACC
1 GACC
730506 AAAACTTTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
5 10 0.16
7 14 0.23
8 19 0.31
9 5 0.08
10 13 0.21
ACGTcount: A:0.17, C:0.39, G:0.23, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:730467 original size:7 final size:7
Alignment explanation
Indices: 730455--730485 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
730445 TTGACCCGAC
730455 CCGTTGA
1 CCGTTGA
730462 CCGTTGA
1 CCGTTGA
730469 CCCGTTGA
1 -CCGTTGA
730477 CCGTTGA
1 CCGTTGA
730484 CC
1 CC
730486 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:730472 original size:15 final size:15
Alignment explanation
Indices: 730452--730486 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
730442 CCATTGACCC
730452 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
730467 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
730482 GACCC
1 GACCC
730487 ACGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:730506 original size:10 final size:9
Alignment explanation
Indices: 730452--730506 Score: 50
Period size: 7 Copynumber: 6.6 Consensus size: 9
730442 CCATTGACCC
730452 GACC-CGTT
1 GACCACGTT
730460 GA-C-CGTT
1 GACCACGTT
730467 GACC-CGTT
1 GACCACGTT
730475 GA-C-CGTT
1 GACCACGTT
730482 GACCCACGTT
1 GA-CCACGTT
730492 GACCACTGTT
1 GACCAC-GTT
730502 GACCA
1 GACCA
730507 AAACTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 9 0.21
9 5 0.12
10 14 0.33
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (9 bp):
GACCACGTT
Found at i:731806 original size:18 final size:18
Alignment explanation
Indices: 731780--731815 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
731770 TCGAAAGGAC
*
731780 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
731798 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
731816 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:732982 original size:24 final size:24
Alignment explanation
Indices: 732955--733048 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
732945 ATTTCCGACT
** *
732955 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
732979 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
733003 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
*
733027 TGAATTCTGTT-TGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
733049 ATCTTCGTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 9 0.15
24 51 0.85
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:732993 original size:12 final size:12
Alignment explanation
Indices: 732978--733046 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
732968 GATAAATGAC
732978 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
732990 CTGATTTCTGAT
1 CTGAATTCTGTT
*
733002 CTGGATTCTGTT
1 CTGAATTCTGTT
733014 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
733026 CTGAATTCTGTT
1 CTGAATTCTGTT
*
733038 -TGATTTCTG
1 CTGAATTCTG
733047 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
11 10 0.20
12 37 0.76
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:732997 original size:48 final size:48
Alignment explanation
Indices: 732941--733044 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
732931 AAATATTTTA
732941 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* * ** **
732989 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
733037 T-TGATTTC
1 TCTGATTTC
733045 TGATATCTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
47 7 0.14
48 41 0.84
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.47
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:735141 original size:13 final size:13
Alignment explanation
Indices: 735122--735190 Score: 111
Period size: 13 Copynumber: 5.3 Consensus size: 13
735112 AACCCGACCC
735122 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
735135 TACCCGACCAGTT
1 GACCCGACCCGTT
735148 GACCCGACCCGTT
1 GACCCGACCCGTT
*
735161 GACCCGACCCATT
1 GACCCGACCCGTT
735174 GACCCGACCCGTT
1 GACCCGACCCGTT
735187 GACC
1 GACC
735191 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.19, C:0.45, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:735194 original size:7 final size:7
Alignment explanation
Indices: 735182--735211 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
735172 TTGACCCGAC
735182 CCGTTGA
1 CCGTTGA
735189 CCGTTGA
1 CCGTTGA
735196 CCGTTGA
1 CCGTTGA
735203 CCGTTGA
1 CCGTTGA
735210 CC
1 CC
735212 CACGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:736532 original size:18 final size:18
Alignment explanation
Indices: 736506--736541 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
736496 TCGAAAGGAC
*
736506 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
736524 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
736542 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:737709 original size:24 final size:24
Alignment explanation
Indices: 737682--737776 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
737672 ATTTCCGACT
** *
737682 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
737706 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
737730 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
737754 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
737777 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:737720 original size:12 final size:12
Alignment explanation
Indices: 737705--737774 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
737695 GATAAATGAC
737705 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
737717 CTGATTTCTGAT
1 CTGAATTCTGTT
*
737729 CTGGATTCTGTT
1 CTGAATTCTGTT
737741 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
737753 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
737765 TTGATTTCTG
1 CTGAATTCTG
737775 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Done.