Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005165.1 Hibiscus syriacus cultivar Beakdansim tig00011653_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: 156465
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3711 original size:19 final size:19
Alignment explanation
Indices: 3677--3721 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3667 AATAAGCACC
**
3677 TTGCATTTTATTTTTCACA
1 TTGCATTTTACCTTTCACA
*
3696 TTGCATTTTACCTTTCGCA
1 TTGCATTTTACCTTTCACA
*
3715 TTACATT
1 TTGCATT
3722 ATATTCATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGCATTTTACCTTTCACA
Found at i:10770 original size:12 final size:12
Alignment explanation
Indices: 10750--10782 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
10740 CTTTGTCTGA
10750 AAGAAAAAAAA-
1 AAGAAAAAAAAT
*
10761 AGGAAAAAAAAT
1 AAGAAAAAAAAT
10773 AAGAAAAAAA
1 AAGAAAAAAA
10783 GTTAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAGAAAAAAAAT
Found at i:10803 original size:15 final size:14
Alignment explanation
Indices: 10748--10805 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
10738 TACTTTGTCT
10748 GAAAGAAAAA-AAAA
1 GAAA-AAAAATAAAA
10762 GGAAAAAAAAT--AA
1 -GAAAAAAAATAAAA
*
10775 GAAAAAAAGTTAAAA
1 GAAAAAAA-ATAAAA
10790 GTAAAAAAAATAAAA
1 G-AAAAAAAATAAAA
10805 G
1 G
10806 GGGTTCAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 5 0.14
15 13 0.36
16 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (14 bp):
GAAAAAAAATAAAA
Found at i:14118 original size:13 final size:13
Alignment explanation
Indices: 14100--14133 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
14090 GATGATGGTC
14100 TTGATGAAGGATG
1 TTGATGAAGGATG
*
14113 TTGATGATGGATG
1 TTGATGAAGGATG
*
14126 ATGATGAA
1 TTGATGAA
14134 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:19639 original size:13 final size:13
Alignment explanation
Indices: 19621--19654 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19611 GATGATGGTC
19621 TTGATGAAGGATG
1 TTGATGAAGGATG
*
19634 TTGATGATGGATG
1 TTGATGAAGGATG
*
19647 ATGATGAA
1 TTGATGAA
19655 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:30478 original size:33 final size:33
Alignment explanation
Indices: 30404--30480 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
30394 ACTGTGACTA
* **
30404 AATAAT-TTTGTTACAATTTTTTATTGTGGAAG
1 AATAATATTTGTCACAATTTTTTATAATGGAAG
*
30436 AATATTATTTGTCACAATTTTTTATAATGAGAA-
1 AATAATATTTGTCACAATTTTTTATAATG-GAAG
*
30469 ATTAATATTTGT
1 AATAATATTTGT
30481 TATAAATTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATGGAAG
Found at i:30731 original size:197 final size:196
Alignment explanation
Indices: 30396--30820 Score: 550
Period size: 197 Copynumber: 2.2 Consensus size: 196
30386 ACTTTTTGAC
* * *
30396 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGGAAGAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
* ****
30461 AATGAGAAATTAATATTTGTTATAAATTCCTATTTTGATTAAAAAAATGTCACAAATTTTTATTT
66 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAAAAAATGTCACAAATAAAAATTT
* * * * * *
30526 TAACAAAATATTGGGACGAAGTAAATTTGACAT-AATTGTTTACTTTGACTAAATTTAACGTGTT
131 TAACAAAATATTAGGACAAAATAAATTTGAAATAAATT-TTTACTTTGACTAAATGTAACATGTT
30590 AT
195 AT
* * *
30592 TGTGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAATAATATTACTTGTCACAATTTTTTTA
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAA-TTTTTTA
* *
30657 TAATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCA-AAA-AAAAA
65 TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAA-AAA-ATGTCACAAATAAAAA
* * * **
30720 TTTTGACAAAATATTATGACAAAATAAATTTGAAATAAATTTTTATTTTGACTAAATGTATTATG
128 TTTTAACAAAATATTAGGACAAAATAAATTTGAAATAAATTTTTACTTTGACTAAATGTAACATG
30785 TTAT
193 TTAT
* * *
30789 TGTAACTAAATAAATTTGTTACAATTAGTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTAT
30821 CGTAATGTTC
Statistics
Matches: 196, Mismatches: 29, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
196 51 0.26
197 130 0.66
198 10 0.05
199 5 0.03
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.45
Consensus pattern (196 bp):
TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAAAAAATGTCACAAATAAAAATTT
TAACAAAATATTAGGACAAAATAAATTTGAAATAAATTTTTACTTTGACTAAATGTAACATGTTA
T
Found at i:32781 original size:33 final size:33
Alignment explanation
Indices: 32707--32783 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
32697 ACTGTGACTA
* **
32707 AATAAT-TTTGTTACAATTTTTTATTGTGGAAG
1 AATAATATTTGTCACAATTTTTTATAATGGAAG
*
32739 AATATTATTTGTCACAATTTTTTATAATGAGAA-
1 AATAATATTTGTCACAATTTTTTATAATG-GAAG
*
32772 ATTAATATTTGT
1 AATAATATTTGT
32784 TATAAATTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATGGAAG
Found at i:32930 original size:197 final size:196
Alignment explanation
Indices: 32699--33123 Score: 566
Period size: 197 Copynumber: 2.2 Consensus size: 196
32689 ACTTTTTGAC
* * *
32699 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGGAAGAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
* ****
32764 AATGAGAAATTAATATTTGTTATAAATTGCTATTTTGATTAAA-AAAAATGTCACAAATTTTTAT
66 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCA-AAA-AAAAAT
* * * *
32828 TTTAACAAAATATTAGGACGAAGTAAATTTGACAT-AATTGCTTACTTTGACTAAATTTAACGTG
129 TTTAACAAAATATTAGGACAAAATAAATTTGACATAAATT-CTTACTTTGACTAAATGTAACATG
32892 TTAT
193 TTAT
* * *
32896 TGTGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAATAATATTACTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
* **
32961 AATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAAAAAAAAATTT
66 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCAAAAAAAAATTT
* * * * **
33026 TGACAAAATATTATGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATGTATTATGTTA
131 TAACAAAATATTAGGACAAAATAAATTTGACATAAATTCTTACTTTGACTAAATGTAACATGTTA
33091 T
196 T
* * *
33092 TGTAACTAAATAAATTTGTTACAATTAGTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTAT
33124 CGTAATGTTC
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
196 82 0.42
197 107 0.54
198 8 0.04
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (196 bp):
TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCAAAAAAAAATTT
TAACAAAATATTAGGACAAAATAAATTTGACATAAATTCTTACTTTGACTAAATGTAACATGTTA
T
Found at i:35084 original size:33 final size:33
Alignment explanation
Indices: 35010--35086 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
35000 ACTGTGACTA
* **
35010 AATAAT-TTTGTTACAATTTTTTATTGTGGAAG
1 AATAATATTTGTCACAATTTTTTATAATGGAAG
*
35042 AATATTATTTGTCACAATTTTTTATAATGAGAA-
1 AATAATATTTGTCACAATTTTTTATAATG-GAAG
*
35075 ATTAATATTTGT
1 AATAATATTTGT
35087 TATAAATTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATGGAAG
Found at i:35232 original size:196 final size:195
Alignment explanation
Indices: 35002--35424 Score: 564
Period size: 195 Copynumber: 2.2 Consensus size: 195
34992 ACTTTTTGAC
* * *
35002 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGGAAGAATATTATTTGTCACAA-TTTTTTA
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
* ***
35066 TAATGAGAAATTAATATTTGTTATAAATTCCTATTTTGATTAAA-AAAATGTCACAAATTTTTAT
66 TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAATGTCA-AAA--AAAAT
* * * *
35130 TTTAACAAAATATTGGGACAAAGTAAATTTGACAT-AATTGTTTACTTTGACTAAATTTAACGTG
128 TTTAACAAAATATTAGGACAAAATAAATTTGACATAAATT-TTTACTTTGACTAAATGTAACATG
35194 TTAT
192 TTAT
* * *
35198 TGTGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAATAATATTACTTGTCACAATTTTTTTA
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
* **
35263 TAATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAATTTGTCAAAAAAAATTTT
66 TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAATGTCAAAAAAAATTTT
* * * **
35328 GACAAAATATTATGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATGTATTATGTTAT
131 AACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTTAT
* * *
35393 TGTAACTAAATAAATTTGTTACAATTAGTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTAT
35425 CGTAATGTTC
Statistics
Matches: 197, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
195 83 0.42
196 55 0.28
197 52 0.26
198 7 0.04
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.45
Consensus pattern (195 bp):
TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAATGTCAAAAAAAATTTT
AACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTTAT
Found at i:37384 original size:33 final size:33
Alignment explanation
Indices: 37310--37386 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
37300 ACTGTGACTA
* **
37310 AATAAT-TTTGTTACAATTTTTTATTGTGGAAG
1 AATAATATTTGTCACAATTTTTTATAATGGAAG
*
37342 AATATTATTTGTCACAATTTTTTATAATGAGAA-
1 AATAATATTTGTCACAATTTTTTATAATG-GAAG
*
37375 ATTAATATTTGT
1 AATAATATTTGT
37387 TATAAATTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATGGAAG
Found at i:37533 original size:197 final size:197
Alignment explanation
Indices: 37302--37727 Score: 577
Period size: 197 Copynumber: 2.2 Consensus size: 197
37292 ACTTTTTGAC
* * *
37302 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGGAAGAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
* * ****
37367 AATGAGAAATTAATATTTGTTATAAATTGCTATTTTGATTAAA-AAAAATGTCACAAATTTTTAT
66 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCAAAAAAAAAT-T
* * * *
37431 TTTAACAAAATATTAGGACGAAGTAAATTTGACAT-AATTGTTTACTTTGACTAAATTTAACGTG
130 TTTAACAAAATATTAGGACAAAATAAATTTGACATAAATT-TTTACTTTGACTAAATGTAACATG
37495 TTAT
194 TTAT
* * *
37499 TGTGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAATAATATTACTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
* **
37564 AATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAAAAAAAAATTT
66 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCAAAAAAAAATTT
* * * **
37629 TTGACAAAATATTATGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATGTATTATGTT
131 TTAACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTT
37694 AT
196 AT
* * *
37696 TGTAACTAAATAAATTTGTTACAATTAGTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTAT
37728 CGTAATGTTC
Statistics
Matches: 198, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
197 182 0.92
198 16 0.08
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.45
Consensus pattern (197 bp):
TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAAAATGTCAAAAAAAAATTT
TTAACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTT
AT
Found at i:39689 original size:33 final size:33
Alignment explanation
Indices: 39615--39691 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
39605 ACTGTGACTA
* **
39615 AATAAT-TTTGTTACAATTTTTTATTGTGGAAG
1 AATAATATTTGTCACAATTTTTTATAATGGAAG
*
39647 AATATTATTTGTCACAATTTTTTATAATGAGAA-
1 AATAATATTTGTCACAATTTTTTATAATG-GAAG
*
39680 ATTAATATTTGT
1 AATAATATTTGT
39692 TATAAATTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATGGAAG
Found at i:39837 original size:196 final size:197
Alignment explanation
Indices: 39607--40031 Score: 561
Period size: 197 Copynumber: 2.2 Consensus size: 197
39597 ACTTTTTGAC
* * *
39607 TGTGACTAAATAATTTTGTTACAATTTTTTATTGTGGAAGAATATTATTTGTCACAA-TTTTTTA
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
* ****
39671 TAATGAGAAATTAATATTTGTTATAAATTCCTATTTTGATTAAA-AAA-ATGTCACAAATTTTTA
66 TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAATATGTCA-AAA-AAAAA
* * * * *
39734 TTTTAACAAAATATTGGGACGAAGTAAATTTGACAT-AATTGTTTACTTTGACTAAATTTAACGT
129 TTTTAACAAAATATTAGGACAAAATAAATTTGACATAAATT-TTTACTTTGACTAAATGTAACAT
39798 GTTAT
193 GTTAT
* * *
39803 TGTGACTAAATCATTTTGTTGCAATTTGTTATTGTGAAATAATATTACTTGTCACAATTTTTTTA
1 TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
* *
39868 TAATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAAAAAAAAATT
66 TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAATATGTCAAAAAAAAATT
* * * **
39933 TTGACAAAATATTATGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATGTATTATGTT
131 TTAACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTT
39998 AT
196 AT
* * *
40000 TGTAACTAAATAAATTTGTTACAATTAGTTAT
1 TGTGACTAAATAATTTTGTTACAATTTGTTAT
40032 CGTAATGTTC
Statistics
Matches: 197, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
196 51 0.26
197 131 0.66
198 10 0.05
199 5 0.03
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (197 bp):
TGTGACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTTA
TAATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAATATGTCAAAAAAAAATT
TTAACAAAATATTAGGACAAAATAAATTTGACATAAATTTTTACTTTGACTAAATGTAACATGTT
AT
Found at i:46861 original size:20 final size:20
Alignment explanation
Indices: 46836--46878 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
46826 TATATTGGGC
* *
46836 TATTGTATATTGTTTATGGT
1 TATTGTATATGGTATATGGT
*
46856 TATTGTCTATGGTATATGGT
1 TATTGTATATGGTATATGGT
46876 TAT
1 TAT
46879 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTATATGGTATATGGT
Found at i:46945 original size:46 final size:46
Alignment explanation
Indices: 46884--46976 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
46874 GTTATGGAAT
* * * * *
46884 AATGGCAAGTGTATTGGTAAAATAAGCTTATGAGCTTATGGTATTA
1 AATGGAAAGTATATTGGTAAAATAAACTTACGAGCTTATGGGATTA
46930 AATGGAAAGTATATTGGTAAAATAAACTTACGAGCTTATGGGATTA
1 AATGGAAAGTATATTGGTAAAATAAACTTACGAGCTTATGGGATTA
46976 A
1 A
46977 TAGTAAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (46 bp):
AATGGAAAGTATATTGGTAAAATAAACTTACGAGCTTATGGGATTA
Found at i:49135 original size:16 final size:16
Alignment explanation
Indices: 49114--49144 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49104 GCCCAATCGG
49114 TTAGGGCTTTGGATGA
1 TTAGGGCTTTGGATGA
*
49130 TTAGGGTTTTGGATG
1 TTAGGGCTTTGGATG
49145 GAGCCTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.39, T:0.42
Consensus pattern (16 bp):
TTAGGGCTTTGGATGA
Found at i:51966 original size:21 final size:23
Alignment explanation
Indices: 51936--52084 Score: 102
Period size: 22 Copynumber: 6.6 Consensus size: 23
51926 CATATAATAT
51936 ATATAATATAGT-TTTTTGAAAAC
1 ATAT-ATATAGTATTTTTGAAAAC
*
51959 ATATTATATAATATAGTTTTGAAAAC
1 ATA-TATATAGTAT--TTTTGAAAAC
* *
51985 ATAT-TATA-TAATTTTTTAAAAT
1 ATATATATAGT-ATTTTTGAAAAC
*
52007 ATATA-ATA-TAGTTTTGAAAAC
1 ATATATATAGTATTTTTGAAAAC
* *
52028 ATAT-TATA-TAATTTTTTAAAAT
1 ATATATATAGT-ATTTTTGAAAAC
*
52050 ATATA-ATA-TAGTTTTGAAAAC
1 ATATATATAGTATTTTTGAAAAC
52071 ATATTATATA-TATT
1 ATA-TATATAGTATT
52085 ATTATTGATA
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
21 29 0.28
22 35 0.34
23 16 0.16
24 8 0.08
25 1 0.01
26 13 0.13
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (23 bp):
ATATATATAGTATTTTTGAAAAC
Found at i:51966 original size:28 final size:26
Alignment explanation
Indices: 51935--52080 Score: 148
Period size: 26 Copynumber: 6.2 Consensus size: 26
51925 GCATATAATA
51935 TATATAATATAGTTTTTTGAAAACATAT
1 TATATAATATAG--TTTTGAAAACATAT
51963 TATATAATATAGTTTTGAAAACATAT
1 TATATAATATAGTTTTGAAAACATAT
51989 TATATAAT-T--TTTT---AA-A-AT
1 TATATAATATAGTTTTGAAAACATAT
52007 -ATATAATATAGTTTTGAAAACATAT
1 TATATAATATAGTTTTGAAAACATAT
52032 TATATAAT-T--TTTT---AA-A-AT
1 TATATAATATAGTTTTGAAAACATAT
52050 -ATATAATATAGTTTTGAAAACATAT
1 TATATAATATAGTTTTGAAAACATAT
52075 TATATA
1 TATATA
52081 TATTATTATT
Statistics
Matches: 100, Mismatches: 0, Indels: 38
0.72 0.00 0.28
Matches are distributed among these distances:
17 14 0.14
18 6 0.06
19 2 0.02
20 12 0.12
23 12 0.12
24 2 0.02
25 6 0.06
26 34 0.34
28 12 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (26 bp):
TATATAATATAGTTTTGAAAACATAT
Found at i:52010 original size:43 final size:43
Alignment explanation
Indices: 51963--52080 Score: 236
Period size: 43 Copynumber: 2.7 Consensus size: 43
51953 GAAAACATAT
51963 TATATAATATAGTTTTGAAAACATATTATATAATTTTTTAAAA
1 TATATAATATAGTTTTGAAAACATATTATATAATTTTTTAAAA
52006 TATATAATATAGTTTTGAAAACATATTATATAATTTTTTAAAA
1 TATATAATATAGTTTTGAAAACATATTATATAATTTTTTAAAA
52049 TATATAATATAGTTTTGAAAACATATTATATA
1 TATATAATATAGTTTTGAAAACATATTATATA
52081 TATTATTATT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (43 bp):
TATATAATATAGTTTTGAAAACATATTATATAATTTTTTAAAA
Found at i:62280 original size:80 final size:77
Alignment explanation
Indices: 62150--62302 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 77
62140 CAATAAAATA
* *
62150 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TTTAATGT
1 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTAGAATCTTTTAATGT
*
62214 TTATTTAAAAAC
66 TTACTTAAAAAC
* * * *
62226 TTATTTAATT-ATTCCGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTAGATTCTTTT
1 TTATTTAATTAATT-C-AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTAGAATCTTTT
62290 AATGTTTACTTAA
61 AATGTTTACTTAA
62303 TATATTCGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
75 3 0.05
76 11 0.17
77 10 0.16
78 1 0.02
79 3 0.05
80 21 0.33
81 15 0.23
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (77 bp):
TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTAGAATCTTTTAATGT
TTACTTAAAAAC
Found at i:67138 original size:18 final size:18
Alignment explanation
Indices: 67115--67191 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
67105 GTCACAACCC
67115 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
67133 GACCCGACCCGACCCATT
1 GACCCGACCCGACCCGTT
*
67151 GACCCGA-CCGACCCTTT
1 GACCCGACCCGACCCGTT
*
67168 GACCTGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
67186 GACCCG
1 GACCCG
67192 TTGACCGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
17 15 0.28
18 38 0.72
ACGTcount: A:0.18, C:0.48, G:0.21, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:67170 original size:35 final size:36
Alignment explanation
Indices: 67115--67191 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
67105 GTCACAACCC
67115 GACCCGACCCGACCCGTTGACCCGACCCGACCCATT
1 GACCCGACCCGACCCGTTGACCCGACCCGACCCATT
* * *
67151 GACCCGA-CCGACCCTTTGACCTGACCCGACCCGTT
1 GACCCGACCCGACCCGTTGACCCGACCCGACCCATT
67186 GACCCG
1 GACCCG
67192 TTGACCGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 31 0.82
36 7 0.18
ACGTcount: A:0.18, C:0.48, G:0.21, T:0.13
Consensus pattern (36 bp):
GACCCGACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:67201 original size:15 final size:16
Alignment explanation
Indices: 67181--67214 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
67171 CTGACCCGAC
67181 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
67196 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
67213 CC
1 CC
67215 AATGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:68520 original size:18 final size:18
Alignment explanation
Indices: 68494--68528 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68484 TCGAAAGGAC
*
68494 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
68512 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
68529 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:72326 original size:18 final size:18
Alignment explanation
Indices: 72303--72361 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
72293 ACCGGTCACA
72303 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
72321 ACCCGAACCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
72339 ACCTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
72357 ACCCG
1 ACCCG
72362 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:72371 original size:15 final size:15
Alignment explanation
Indices: 72351--72383 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
72341 CTGACCCGAC
72351 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
72366 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
72381 CCG
1 CCG
72384 GCGTTGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.36, G:0.27, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:72390 original size:10 final size:8
Alignment explanation
Indices: 72348--72392 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
72338 GACCTGACCC
72348 GACCCGTT
1 GACCCGTT
72356 GACCCGTT
1 GACCCGTT
72364 GA-CCGTT
1 GACCCGTT
72371 GACCCGTT
1 GACCCGTT
72379 GACCGGCGTT
1 GACC--CGTT
72389 GACC
1 GACC
72393 AATGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.21
8 19 0.56
10 8 0.24
ACGTcount: A:0.13, C:0.36, G:0.29, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:73691 original size:18 final size:18
Alignment explanation
Indices: 73665--73699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73655 TTCGAAGGAC
*
73665 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
73683 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
73700 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:79074 original size:20 final size:20
Alignment explanation
Indices: 79051--79121 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
79041 ATAAGCGATG
79051 GATCCCTTTTCCAATGGATT
1 GATCCCTTTTCCAATGGATT
** * * *
79071 GATCTTTTTTCAAAAGGGATA
1 GATCCCTTTTC-CAATGGATT
*
79092 GATCCCTTTTCCAATTGATT
1 GATCCCTTTTCCAATGGATT
79112 GAT-CCTTTTC
1 GATCCCTTTTC
79122 AAAAGGGATC
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 7 0.18
20 17 0.44
21 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (20 bp):
GATCCCTTTTCCAATGGATT
Found at i:79082 original size:41 final size:41
Alignment explanation
Indices: 79037--79135 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
79027 GTAGCTAAAC
* * *
79037 TTTCATAAGCGATGGATCCCTTTTCCAATGGATTGATCTTT
1 TTTCAAAAGCGATAGATCCCTTTTCCAATGGATTGATCCTT
* *
79078 TTTCAAAAGGGATAGATCCCTTTTCCAATTGATTGATCC-T
1 TTTCAAAAGCGATAGATCCCTTTTCCAATGGATTGATCCTT
* *
79118 TTTCAAAAGGGATCGATC
1 TTTCAAAAGCGATAGATC
79136 ATTTTCTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 18 0.35
41 34 0.65
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (41 bp):
TTTCAAAAGCGATAGATCCCTTTTCCAATGGATTGATCCTT
Found at i:79135 original size:20 final size:20
Alignment explanation
Indices: 79077--79141 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
79067 GATTGATCTT
79077 TTTTCAAAAGGGATAGATCCC
1 TTTTCAAAAGGGATAGAT-CC
* ** *
79098 TTTTC-CAATTGATTGATCC
1 TTTTCAAAAGGGATAGATCC
* *
79117 TTTTCAAAAGGGATCGATCA
1 TTTTCAAAAGGGATAGATCC
79137 TTTTC
1 TTTTC
79142 TTGAAAATTC
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
19 7 0.21
20 22 0.65
21 5 0.15
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTTCAAAAGGGATAGATCC
Found at i:89973 original size:6 final size:6
Alignment explanation
Indices: 89962--89992 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
89952 AAGACCTATG
89962 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
89993 ATACAAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (6 bp):
GGTCAT
Found at i:91102 original size:17 final size:17
Alignment explanation
Indices: 91080--91160 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
91070 CATATATTAT
91080 AAGAAGAAAAAAAACAG
1 AAGAAGAAAAAAAACAG
*
91097 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAACAG
* * *
91114 AA-AA-AGAAAATATAG
1 AAGAAGAAAAAAAACAG
*
91129 AAAAAGAAAATGAAAAC-G
1 AAGAAGAAAA--AAAACAG
91147 AAGAAGAAAAAAAA
1 AAGAAGAAAAAAAA
91161 TGAAAACGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.21
16 8 0.15
17 21 0.40
18 10 0.19
19 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAAAAAACAG
Found at i:91108 original size:15 final size:15
Alignment explanation
Indices: 91081--91158 Score: 59
Period size: 15 Copynumber: 4.9 Consensus size: 15
91071 ATATATTATA
*
91081 AGAAGAA-AAAAAAC
1 AGAAGAAGAAAAAAT
91095 AGAAGAAGAAAAAAAAT
1 AGAAGAAG--AAAAAAT
* *
91112 AGAAAAAGAAAATAT
1 AGAAGAAGAAAAAAT
* *
91127 AGAAAAAGAAAATGAAA
1 AGAAGAAGAAAA--AAT
91144 ACGAAGAAGAAAAAA
1 A-GAAGAAGAAAAAA
91159 AATGAAAACG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 7 0.13
15 18 0.35
16 2 0.04
17 15 0.29
18 10 0.19
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (15 bp):
AGAAGAAGAAAAAAT
Found at i:91163 original size:22 final size:22
Alignment explanation
Indices: 91130--91182 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
91120 AAAATATAGA
91130 AAAAGAAAATGAAAACGAAGAAG
1 AAAAGAAAATGAAAACG-AGAAG
91153 AAAA-AAAATGAAAACGAGAAG
1 AAAAGAAAATGAAAACGAGAAG
91174 AAAAGAAAA
1 AAAAGAAAA
91183 ATAGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.31
22 16 0.55
23 4 0.14
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (22 bp):
AAAAGAAAATGAAAACGAGAAG
Found at i:91183 original size:6 final size:6
Alignment explanation
Indices: 91083--91157 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
91073 ATATTATAAG
* * *
91083 AAGAAA AA-AAA CAGAAG AAGAAA AA-AAA TAGAAA AAGAAAA TATAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA -A-AGAAA
* * *
91132 AAGAAA ATGAAA ACGAAG AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
91158 AAATGAAAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
5 8 0.15
6 35 0.66
7 4 0.08
8 4 0.08
9 2 0.04
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:91193 original size:16 final size:17
Alignment explanation
Indices: 91100--91196 Score: 62
Period size: 16 Copynumber: 5.9 Consensus size: 17
91090 AAAACAGAAG
91100 AAGA-AAAAAAATAGAAA
1 AAGAGAAAAAAAT-GAAA
* *
91117 AAGA-AAATATA-GAAA
1 AAGAGAAAAAAATGAAA
* *
91132 AAGA-AAATGAAAACGAAG
1 AAGAGAAA--AAAATGAAA
91150 AAGA-AAAAAAATGAAA
1 AAGAGAAAAAAATGAAA
* *
91166 ACGAGAAGAAAA-GAAA
1 AAGAGAAAAAAATGAAA
*
91182 AATAGAAAAAAATGA
1 AAGAGAAAAAAATGA
91197 GAGATGAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.17
16 23 0.37
17 19 0.30
18 10 0.16
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (17 bp):
AAGAGAAAAAAATGAAA
Found at i:99104 original size:44 final size:44
Alignment explanation
Indices: 99054--99318 Score: 354
Period size: 44 Copynumber: 6.0 Consensus size: 44
99044 TGTTACCGAA
* ** *
99054 ATAAATGAAAATGCATAACGGTGCATGATTGGCAGAAATATACC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
99098 ATAAATGAAAATGCATTACGATGTATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
**
99142 ATAAATGAAAGCGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
99186 ATAAATGAAAATGCATAACTGTGTATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
99230 ATAAATGAAAATGCA-AAGCGGTGCATTATTGG-ATGAAAGGTGCC
1 ATAAATGAAAATGCATAA-CGGTGCATTATTGGCA-GAAAGGTGCC
* * *
99274 ATAAATAAAAATGCATAACGGTGCATTATTGGCCGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
99318 A
1 A
99319 CTCATGGTAT
Statistics
Matches: 194, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.02
44 189 0.97
45 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:104720 original size:32 final size:32
Alignment explanation
Indices: 104684--104772 Score: 169
Period size: 32 Copynumber: 2.8 Consensus size: 32
104674 TTGGAAAGGG
*
104684 TAATGTAGTGGCGATGCACTTAACTGAAAGAC
1 TAATGTAGTAGCGATGCACTTAACTGAAAGAC
104716 TAATGTAGTAGCGATGCACTTAACTGAAAGAC
1 TAATGTAGTAGCGATGCACTTAACTGAAAGAC
104748 TAATGTAGTAGCGATGCACTTAACT
1 TAATGTAGTAGCGATGCACTTAACT
104773 AACTCAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (32 bp):
TAATGTAGTAGCGATGCACTTAACTGAAAGAC
Found at i:107880 original size:44 final size:44
Alignment explanation
Indices: 107827--108036 Score: 259
Period size: 44 Copynumber: 4.8 Consensus size: 44
107817 GTTGTGTTAT
*
107827 GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGTATAAC
1 GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAAC
* * * *
107871 AGTGCATTATT-GCTAGAAATGTTCCATAAA-GCAAAATGCATAAG
1 GGTGCATTATTGGC-AGAAAGGTGCCATAAATG-AAAATGCATAAC
* * * *
107915 GGTGCATTATTGGAACAAGGGTGGCATAAATGAAAATGCATAAC
1 GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAAC
* *
107959 GGTGCATTATTGCCAGAAATGTGCCATAAATGAAAATGCATAAC
1 GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAAC
*
108003 GGTGCATTA-TGGCAGAAA--TGTCATAAATGAAAAT
1 GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAAT
108037 TCATTGTAAT
Statistics
Matches: 141, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
41 15 0.11
43 11 0.08
44 113 0.80
45 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (44 bp):
GGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAAC
Found at i:109398 original size:53 final size:54
Alignment explanation
Indices: 109285--109559 Score: 253
Period size: 53 Copynumber: 5.2 Consensus size: 54
109275 GAATGAGCAC
* * * ** *
109285 TGTGTGCAACCTAATAAA-TCAT-TTATGTTTATG-AATATCCATATTGACACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAAT-TCTGTATTGGCACTG
* * * *
109337 CGTGTGCAACCTAAGAAATTCAAAAAAAGTTTAT-AAATTCTGTATTGGCAATG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAATTCTGTATTGGCACTG
* * * *
109390 TGTGTGCAA-CTAAAGAAA-TCATAATAAGTTTGTGAATTTCCGTATTGGTACTG
1 TGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAAATTCTGTATTGGCACTG
* * * *
109443 TGTGTGCAACCTAAGAAATTCATAATATG-TTATGAATTTGTGTATTGGCCCTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAATTCTGTATTGGCACTG
* * * *
109496 TGTGTGCAACCGAAGAAATTCATAACAAGTTTATG-AATTTTGTTATT-GCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAATTCTG-TATTGGCACTG
*
109549 AGTGTGCAACC
1 TGTGTGCAACC
109560 CCATGTAATT
Statistics
Matches: 182, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
52 30 0.16
53 122 0.67
54 30 0.16
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (54 bp):
TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAATTCTGTATTGGCACTG
Found at i:109487 original size:106 final size:105
Alignment explanation
Indices: 109285--109535 Score: 281
Period size: 106 Copynumber: 2.4 Consensus size: 105
109275 GAATGAGCAC
* * * *
109285 TGTGTGCAACCTAATAAATCAT-TTATGTTTATGAATATCCATATTGACACTGCGTGTGCAACCT
1 TGTGTGCAA-CTAAGAAATCATAATAAGTTTATGAATTTCCATATTGACACTGCGTGTGCAACCT
109349 AAGAAATTCAAAAAAAGTTTATAAATTCTGTATTGGCAATG
65 AAGAAATTCAAAAAAAGTTTATAAATTCTGTATTGGCAATG
* * ** *
109390 TGTGTGCAACTAAAGAAATCATAATAAGTTTGTGAATTTCCGTATTGGTACTGTGTGTGCAACCT
1 TGTGTGCAACT-AAGAAATCATAATAAGTTTATGAATTTCCATATTGACACTGCGTGTGCAACCT
* * * * * **
109455 AAGAAATTCATAATATG-TTATGAATTTGTGTATTGGCCCTG
65 AAGAAATTCAAAAAAAGTTTAT-AAATTCTGTATTGGCAATG
* *
109496 TGTGTGCAACCGAAGAAATTCATAACAAGTTTATGAATTT
1 TGTGTGCAA-CTAAGAAA-TCATAATAAGTTTATGAATTT
109536 TGTTATTGCA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
104 2 0.02
105 22 0.18
106 78 0.64
107 20 0.16
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (105 bp):
TGTGTGCAACTAAGAAATCATAATAAGTTTATGAATTTCCATATTGACACTGCGTGTGCAACCTA
AGAAATTCAAAAAAAGTTTATAAATTCTGTATTGGCAATG
Found at i:114260 original size:261 final size:252
Alignment explanation
Indices: 113779--114288 Score: 939
Period size: 261 Copynumber: 2.0 Consensus size: 252
113769 AGATTTTAGA
113779 GTCTTTACATGAGGTATTGGGTACTCGATTAAACTTCAGCACAACTTTTCATCCCTAGACAGAGG
1 GTCTTTACATGAGGTATTGGGTACTCGATTAAACTTCAGCACAACTTTTCATCCCTAGACAGAGG
113844 GCAATCAAAAAACTATTTAGATATATAGAGGATATGCTAAGGGCATGTGTGATTGAATTTAAAAG
66 GCAATCAAAAAACTATTTAGATATATAGAGGATATGCTAAGGGCATGTGTGATTGAATTTAAAAG
113909 ATCATGGAAGGTATTTTCCTTAGCGGAATTGCTTATAATAATAGTTATCAATAAAGTATTAAGAT
131 ATCATGGAAGGTATTTTCCTTAGCGGAATTGCTTATAATAATAGTTATCAATAAAGTATTAAGAT
113974 GGCCCCATATGAAGCTTTGTATGGGAGGAAGTACAAAACACCATTAAATTGGTTAAG
196 GGCCCCATATGAAGCTTTGTATGGGAGGAAGTACAAAACACCATTAAATTGGTTAAG
114031 GTCTTTACATGAGGTATTGGGTACTCGATTAAACTTCAGCACAACTTTTCATCCCTAGACAGATG
1 GTCTTTACATGAGGTATTGGGTACTCGATTAAACTTCAGCACAACTTTTCATCCCTAGACAGA-G
114096 GGCAATCAAAACAAACTATTTAGATAAATATTAGAGGATATGCTAAGGGCATGTGTGATTGAATT
65 GGCAATC-AAA-AAACTATTTAGAT--ATA-TAGAGGATATGCTAAGGGCATGTGTGATTGAATT
114161 TAAAAGATCATGGGAAGGTATTTTCCATTAGCGGAATTTGCTTATAATAATAGTTATCAATAAAG
125 TAAAAGATCAT-GGAAGGTATTTTCC-TTAGCGGAA-TTGCTTATAATAATAGTTATCAATAAAG
114226 TATTAAGATGGCCCCATATGAAGCTTTGTATGGGAGGAAGTACAAAACACCATTAAATTGGTT
187 TATTAAGATGGCCCCATATGAAGCTTTGTATGGGAGGAAGTACAAAACACCATTAAATTGGTT
114289 TGAACTAAAA
Statistics
Matches: 249, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
252 63 0.25
253 8 0.03
254 3 0.01
255 13 0.05
257 3 0.01
258 45 0.18
259 14 0.06
260 9 0.04
261 91 0.37
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (252 bp):
GTCTTTACATGAGGTATTGGGTACTCGATTAAACTTCAGCACAACTTTTCATCCCTAGACAGAGG
GCAATCAAAAAACTATTTAGATATATAGAGGATATGCTAAGGGCATGTGTGATTGAATTTAAAAG
ATCATGGAAGGTATTTTCCTTAGCGGAATTGCTTATAATAATAGTTATCAATAAAGTATTAAGAT
GGCCCCATATGAAGCTTTGTATGGGAGGAAGTACAAAACACCATTAAATTGGTTAAG
Found at i:115261 original size:11 final size:11
Alignment explanation
Indices: 115245--115271 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
115235 TTTCCTTGTT
115245 AGGGATTTAAG
1 AGGGATTTAAG
115256 AGGGATTTAAG
1 AGGGATTTAAG
115267 AGGGA
1 AGGGA
115272 AAAGGGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (11 bp):
AGGGATTTAAG
Found at i:116337 original size:53 final size:51
Alignment explanation
Indices: 116261--116515 Score: 209
Period size: 53 Copynumber: 5.0 Consensus size: 51
116251 ATGATCAGTT
* *
116261 TGTGTGCAACTTAAGAAA--CATAATATATTTATGAGTTTTCGTATTGGCATTG
1 TGTGTGCAACCTAA-AAATTCATAATA-ATTTATGAATTTTCGTATTGGCA-TG
* * * * *
116313 TGTATGCAACCTAAAAATTCATAATAAGTTATGAATTTT-GTATCGACACG
1 TGTGTGCAACCTAAAAATTCATAATAATTTATGAATTTTCGTATTGGCATG
* * * *
116363 TGTGTGCAACCTATGAAATCCATAATAATTTATGAATTTCCATATTGGCACTG
1 TGTGTGCAACCTA-AAAATTCATAATAATTTATGAATTTTCGTATTGGCA-TG
* * * * *
116416 TGTGTGCAGCCTAAGAATTCATAATATGTTTATGAATTTAT-GTTTTGGTCCTG
1 TGTGTGCAACCTAAAAATTCATAATA-ATTTATGAATTT-TCGTATTGG-CATG
* * *
116469 TGTTTGCAACCT---AATTCATAATAAGTTTATGAATTTCCATATTGGCA
1 TGTGTGCAACCTAAAAATTCATAATAA-TTTATGAATTTTCGTATTGGCA
116516 CTAATGTGCA
Statistics
Matches: 161, Mismatches: 32, Indels: 23
0.75 0.15 0.11
Matches are distributed among these distances:
49 1 0.01
50 40 0.25
51 32 0.20
52 39 0.24
53 48 0.30
54 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (51 bp):
TGTGTGCAACCTAAAAATTCATAATAATTTATGAATTTTCGTATTGGCATG
Found at i:116409 original size:103 final size:105
Alignment explanation
Indices: 116261--116517 Score: 287
Period size: 103 Copynumber: 2.5 Consensus size: 105
116251 ATGATCAGTT
* * * * * *
116261 TGTGTGCAACTTAAGAAA-CATAATATATTTATGAGTTTTCGTATTGGCATTGTGTATGCAACCT
1 TGTGTGCAACCTATGAAATCATAATA-ATTTATGAATTTCCATATTGGCACTGTGTATGCAACCT
116325 AAAAATTCATAATAAG-TTATGAATTT-TG-TATCGACAC-G
65 AAAAATTCATAATAAGTTTATGAATTTATGTTATCGAC-CTG
* *
116363 TGTGTGCAACCTATGAAATCCATAATAATTTATGAATTTCCATATTGGCACTGTGTGTGCAGCCT
1 TGTGTGCAACCTATGAAAT-CATAATAATTTATGAATTTCCATATTGGCACTGTGTATGCAACCT
* * * * *
116428 AAGAATTCATAATATGTTTATGAATTTATGTTTTGGTCCTG
65 AAAAATTCATAATAAGTTTATGAATTTATGTTATCGACCTG
* *
116469 TGTTTGCAACC--T-AATTCATAATAAGTTTATGAATTTCCATATTGGCACT
1 TGTGTGCAACCTATGAAATCATAATAA-TTTATGAATTTCCATATTGGCACT
116518 AATGTGCAAC
Statistics
Matches: 133, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
102 24 0.18
103 73 0.55
104 18 0.14
105 3 0.02
106 15 0.11
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (105 bp):
TGTGTGCAACCTATGAAATCATAATAATTTATGAATTTCCATATTGGCACTGTGTATGCAACCTA
AAAATTCATAATAAGTTTATGAATTTATGTTATCGACCTG
Found at i:123336 original size:89 final size:88
Alignment explanation
Indices: 123221--123396 Score: 253
Period size: 89 Copynumber: 2.0 Consensus size: 88
123211 TTACCGAAAA
* * * * *
123221 AAATGAAAATACATAACAGTGCATTATTGGCAGAAATGTGCCATTAATGAAAAATGCATAACGGT
1 AAATGAAAATACATAACAATGAATTATTGGCAGAAAGGTGCCATAAATG-AAAATGCATAACGAT
* *
123286 GCATTACTGGTAGAAATGTGCCAT
65 GCATTACTGGCAGAAAGGTGCCAT
* *
123310 AAATGAAAATGCATAACAATGAATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAATGATG
1 AAATGAAAATACATAACAATGAATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGATG
*
123375 CATTATTGGCAGAAAGGTGCCA
66 CATTACTGGCAGAAAGGTGCCA
123397 CTCATGGTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 33 0.43
89 44 0.57
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (88 bp):
AAATGAAAATACATAACAATGAATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGATG
CATTACTGGCAGAAAGGTGCCAT
Found at i:123345 original size:44 final size:44
Alignment explanation
Indices: 123221--123396 Score: 235
Period size: 44 Copynumber: 4.0 Consensus size: 44
123211 TTACCGAAAA
* * *
123221 AAATGAAAATACATAACAGTGCATTATTGGCAGAAATGTGCCAT
1 AAATGAAAATGCATAACAATGCATTATTGGCAGAAAGGTGCCAT
* ** * * *
123265 TAATGAAAAATGCATAACGGTGCATTACTGGTAGAAATGTGCCAT
1 AAATG-AAAATGCATAACAATGCATTATTGGCAGAAAGGTGCCAT
*
123310 AAATGAAAATGCATAACAATGAATTATTGGCAGAAAGGTGCCAT
1 AAATGAAAATGCATAACAATGCATTATTGGCAGAAAGGTGCCAT
**
123354 AAATGAAAATGCATAATGATGCATTATTGGCAGAAAGGTGCCA
1 AAATGAAAATGCATAACAATGCATTATTGGCAGAAAGGTGCCA
123397 CTCATGGTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 77 0.66
45 39 0.34
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (44 bp):
AAATGAAAATGCATAACAATGCATTATTGGCAGAAAGGTGCCAT
Found at i:124324 original size:21 final size:21
Alignment explanation
Indices: 124298--124438 Score: 164
Period size: 21 Copynumber: 6.7 Consensus size: 21
124288 AGTGTGTCAA
124298 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
124319 AGTGCATCCATGCACCCCGGC
1 AGTGCATCCATGCACCCCTGC
* *
124340 AGTCCATCCATGCACCCCAGC
1 AGTGCATCCATGCACCCCTGC
124361 AGTGCATCCATGCACCCC-GAC
1 AGTGCATCCATGCACCCCTG-C
124382 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* * *
124403 TAGTGCATCGATGCA-CCATAC
1 -AGTGCATCCATGCACCCCTGC
124424 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
124439 TCAAACACCG
Statistics
Matches: 106, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.02
20 15 0.14
21 74 0.70
22 13 0.12
23 2 0.02
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.18
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:124487 original size:20 final size:20
Alignment explanation
Indices: 124462--124571 Score: 139
Period size: 20 Copynumber: 5.5 Consensus size: 20
124452 ACAATTAGTA
* *
124462 CATCGATGCATCCTCCTGTG
1 CATCGATGCACCCTGCTGTG
*
124482 CATCGATGCACCCTGCTATG
1 CATCGATGCACCCTGCTGTG
* *
124502 CATTGATGCACCCTCCTGTG
1 CATCGATGCACCCTGCTGTG
* *
124522 CATCGATACACCCTGCTATG
1 CATCGATGCACCCTGCTGTG
124542 CATCGATGCACCCTGCTGTG
1 CATCGATGCACCCTGCTGTG
* *
124562 TATCCATGCA
1 CATCGATGCA
124572 TGAAGGCTAC
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (20 bp):
CATCGATGCACCCTGCTGTG
Found at i:124521 original size:40 final size:40
Alignment explanation
Indices: 124462--124571 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
124452 ACAATTAGTA
*
124462 CATCGATGCATCCTCCTGTGCATCGATGCACCCTGCTATG
1 CATCGATGCACCCTCCTGTGCATCGATGCACCCTGCTATG
* *
124502 CATTGATGCACCCTCCTGTGCATCGATACACCCTGCTATG
1 CATCGATGCACCCTCCTGTGCATCGATGCACCCTGCTATG
* * *
124542 CATCGATGCACCCTGCTGTGTATCCATGCA
1 CATCGATGCACCCTCCTGTGCATCGATGCA
124572 TGAAGGCTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (40 bp):
CATCGATGCACCCTCCTGTGCATCGATGCACCCTGCTATG
Found at i:125005 original size:32 final size:34
Alignment explanation
Indices: 124938--125007 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
124928 TTTTGTAAAG
* *
124938 GGGAAAGGTTCTAGCTTATCCCCTATAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCCTATAAAAGCTA
* *
124972 GGGAAAGGTTATAGTTTAGCCCGTA-AAAA-CTA
1 GGGAAAGGTTATAGCTTAGCCCCTATAAAAGCTA
125004 GGGA
1 GGGA
125008 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (34 bp):
GGGAAAGGTTATAGCTTAGCCCCTATAAAAGCTA
Found at i:127947 original size:21 final size:20
Alignment explanation
Indices: 127918--128016 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
127908 AGGGTGTCAA
*
127918 AGTGAATCCATGCACCAATGC
1 AGTGCATCCATGCACC-ATGC
**
127939 AGTGCATCCATGCACCCCGGC
1 AGTGCATCCATGCA-CCATGC
127960 AGTGCATCCATGCACC-TGCAC
1 AGTGCATCCATGCACCATG--C
*
127981 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCATGC
128002 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
128017 TCAAACACCG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.01
20 16 0.24
21 31 0.46
22 17 0.25
23 2 0.03
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.19
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:128007 original size:20 final size:20
Alignment explanation
Indices: 127927--128114 Score: 106
Period size: 20 Copynumber: 9.5 Consensus size: 20
127917 AAGTGAATCC
*
127927 ATGCACCAATGCAGTGCATCC
1 ATGCACC-ATGCAGTGCATCG
** *
127948 ATGCACCCCGGCAGTGCATCC
1 ATGCA-CCATGCAGTGCATCG
127969 ATGCACC-TGCACTAGTGCATCG
1 ATGCACCATG--C-AGTGCATCG
*
127991 ATGCACCATGCAGTGCATCC
1 ATGCACCATGCAGTGCATCG
** *
128011 ATGCA-C-T-CA-AACACCG
1 ATGCACCATGCAGTGCATCG
*
128027 AATGCA--AT-TAGTGCATCG
1 -ATGCACCATGCAGTGCATCG
* * *
128045 ATGCACCCTCCTGTGCATCG
1 ATGCACCATGCAGTGCATCG
* * *
128065 ATGCACCTTCCTGTGCATCG
1 ATGCACCATGCAGTGCATCG
*
128085 ATGCATCATG-ATGTGCATCG
1 ATGCACCATGCA-GTGCATCG
128105 ATGCACCATG
1 ATGCACCATG
128115 TTGTGCATCC
Statistics
Matches: 133, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.02
17 14 0.11
18 5 0.04
19 3 0.02
20 66 0.50
21 23 0.17
22 17 0.13
23 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.22
Consensus pattern (20 bp):
ATGCACCATGCAGTGCATCG
Found at i:128119 original size:20 final size:20
Alignment explanation
Indices: 128037--128123 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
128027 AATGCAATTA
*
128037 GTGCATCGATGCACCCTCCT
1 GTGCATCGATGCACCATCCT
*
128057 GTGCATCGATGCACCTTCCT
1 GTGCATCGATGCACCATCCT
* **
128077 GTGCATCGATGCATCATGAT
1 GTGCATCGATGCACCATCCT
**
128097 GTGCATCGATGCACCATGTT
1 GTGCATCGATGCACCATCCT
128117 GTGCATC
1 GTGCATC
128124 CATACACGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCACCATCCT
Found at i:129572 original size:23 final size:24
Alignment explanation
Indices: 129521--129581 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
129511 GATTCGTCCC
* * *
129521 GAAGGACCACATAGAAAATTTTCCC
1 GAAGGACCACTTAG-AAATTATCCA
129546 GAAGGACCACTTAG-AATTATCCA
1 GAAGGACCACTTAGAAATTATCCA
*
129569 GAAGAACCACTTA
1 GAAGGACCACTTA
129582 TAGTTGTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 19 0.59
25 13 0.41
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (24 bp):
GAAGGACCACTTAGAAATTATCCA
Found at i:135631 original size:23 final size:23
Alignment explanation
Indices: 135578--135634 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
135568 TAGAAAATTT
* *
135578 TCTCGAAGGACCACGTAGAATTG
1 TCTCGAAGGACCACGTAGAAATA
* *
135601 TCAT-GAAGGAGCACTTAGAAATA
1 TC-TCGAAGGACCACGTAGAAATA
135624 TCTCGAAGGAC
1 TCTCGAAGGAC
135635 GACATAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (23 bp):
TCTCGAAGGACCACGTAGAAATA
Found at i:137512 original size:40 final size:40
Alignment explanation
Indices: 137468--137588 Score: 206
Period size: 40 Copynumber: 3.0 Consensus size: 40
137458 GTAGTGCTAC
*
137468 ACATAAGGTCGTGCCCATCATATACACCGAAGTGTATTAT
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAT
* *
137508 ACATAAAGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAT
*
137548 ACATAAGGTCGTGCCCACCATATACACCGAAGAGTATTAT
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAT
137588 A
1 A
137589 AACCTGCAGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAT
Found at i:139849 original size:247 final size:247
Alignment explanation
Indices: 139413--139907 Score: 990
Period size: 247 Copynumber: 2.0 Consensus size: 247
139403 TACAACTCTG
139413 TATATTTATCCAATGCATAGTCCATTTACATCGGAATGAAATGTGCCGATCTAATTAACCAGTCC
1 TATATTTATCCAATGCATAGTCCATTTACATCGGAATGAAATGTGCCGATCTAATTAACCAGTCC
139478 CTATTACTCAAATGAAATCCTTTTTATTTGATGTCAAAGGTAGTCCATTAACCAAAATTCATAGT
66 CTATTACTCAAATGAAATCCTTTTTATTTGATGTCAAAGGTAGTCCATTAACCAAAATTCATAGT
139543 GACTCTTTACCACTTCCACTCTGGAATAGAAATCAGTTGTAATAATTCCAAAAGCACTTGATTCT
131 GACTCTTTACCACTTCCACTCTGGAATAGAAATCAGTTGTAATAATTCCAAAAGCACTTGATTCT
139608 CAGGTTTTATTTGTCGACATGTCAAACATGTAACAAAAAACTCAGTAATGTT
196 CAGGTTTTATTTGTCGACATGTCAAACATGTAACAAAAAACTCAGTAATGTT
139660 TATATTTATCCAATGCATAGTCCATTTACATCGGAATGAAATGTGCCGATCTAATTAACCAGTCC
1 TATATTTATCCAATGCATAGTCCATTTACATCGGAATGAAATGTGCCGATCTAATTAACCAGTCC
139725 CTATTACTCAAATGAAATCCTTTTTATTTGATGTCAAAGGTAGTCCATTAACCAAAATTCATAGT
66 CTATTACTCAAATGAAATCCTTTTTATTTGATGTCAAAGGTAGTCCATTAACCAAAATTCATAGT
139790 GACTCTTTACCACTTCCACTCTGGAATAGAAATCAGTTGTAATAATTCCAAAAGCACTTGATTCT
131 GACTCTTTACCACTTCCACTCTGGAATAGAAATCAGTTGTAATAATTCCAAAAGCACTTGATTCT
139855 CAGGTTTTATTTGTCGACATGTCAAACATGTAACAAAAAACTCAGTAATGTT
196 CAGGTTTTATTTGTCGACATGTCAAACATGTAACAAAAAACTCAGTAATGTT
139907 T
1 T
139908 TTTTTCATAC
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 248 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (247 bp):
TATATTTATCCAATGCATAGTCCATTTACATCGGAATGAAATGTGCCGATCTAATTAACCAGTCC
CTATTACTCAAATGAAATCCTTTTTATTTGATGTCAAAGGTAGTCCATTAACCAAAATTCATAGT
GACTCTTTACCACTTCCACTCTGGAATAGAAATCAGTTGTAATAATTCCAAAAGCACTTGATTCT
CAGGTTTTATTTGTCGACATGTCAAACATGTAACAAAAAACTCAGTAATGTT
Found at i:142921 original size:20 final size:20
Alignment explanation
Indices: 142873--142927 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
142863 ATCAGAACGA
* *
142873 GGTATCGATACCATAGTAGG
1 GGTATTGATACTATAGTAGG
*
142893 GTAGTATTGATACTATGGTAGG
1 G--GTATTGATACTATAGTAGG
142915 GGTATTGATACTA
1 GGTATTGATACTA
142928 AAGAGCCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.33
Consensus pattern (20 bp):
GGTATTGATACTATAGTAGG
Found at i:143422 original size:117 final size:116
Alignment explanation
Indices: 143263--143765 Score: 598
Period size: 117 Copynumber: 4.3 Consensus size: 116
143253 TTTGTGTGAA
* * * * * * *
143263 AAAATGTTAATAAATTTATACTACGTGTATGAATTTCGGTATTGGGCACTTCATGTGCAAAAATG
1 AAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCGGTATTAGACACTTCGTGTGC-AAAATG
* ** *
143328 TTAAGAAATTTATACTAAGTGTATGGCTTTCCATATTGGGCACTTCATGTGC
65 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTGTGC
* *
143380 AAAATGTTAAGAAATTCAAAATAAGTGTATGGATTTTC-GTATTAGACACTTCGTGTGCAAAAAT
1 AAAATGTTAAGAAATTCATACTAAGTGTAT-GATTTTCGGTATTAGACACTTCGTGTGC-AAAAT
** * * *
143444 GTTAAGAAATTCATACTAAGTGTATGGCTTTCCGTATTGGCCACTTCGTGTGT
64 GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTGTGC
* * * * *
143497 AAAATGTTAAGAAATTCATACTAAGTGTATGACTTTCTGTATTGGGCACTTTGTGTGCAAAATGT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCGGTATTAGACACTTCGTGTGCAAAATGT
** * * *
143562 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATTAGGCACTTTGTGTGAA
66 TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTGTG-C
* * *
143614 AAAATGTTAAGAAATTCATACCAAGTGTATGAATTTCCGTATTAGACACTTCGTGTGCAAAA-GT
1 AAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCGGTATTAGACACTTCGTGTGCAAAATGT
* *
143678 TAAGAAATTCATACAAAGTGTATGAATTTCCATATTGGGCACTTTGTGTGC
66 TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTGTGC
* * * * *
143729 -AAATCATTAAGAGATTAATACTAATTGTATGAATTTC
1 AAAAT-GTTAAGAAATTCATACTAAGTGTATGATTTTC
143766 CATATGGGAA
Statistics
Matches: 339, Mismatches: 43, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
114 4 0.01
115 27 0.08
116 105 0.31
117 197 0.58
118 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (116 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGATTTTCGGTATTAGACACTTCGTGTGCAAAATGT
TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTCGTGTGC
Found at i:143770 original size:58 final size:58
Alignment explanation
Indices: 143263--143766 Score: 625
Period size: 58 Copynumber: 8.7 Consensus size: 58
143253 TTTGTGTGAA
* * * * *
143263 AAAATGTTAATAAATTTATACTACGTGTATGAATTTCGGTATTGGGCACTTCATGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* ** * *
143321 AAAAATGTTAAGAAATTTATACTAAGTGTATGGCTTTCCATATTGGGCACTTCATGTGC
1 -AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * * * * *
143380 AAAATGTTAAGAAATTCAAAATAAGTGTATGGATTTTCGTATTAGACACTTCGTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
** * *
143438 AAAAATGTTAAGAAATTCATACTAAGTGTATGGCTTTCCGTATTGGCCACTTCGTGTGT
1 -AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * *
143497 AAAATGTTAAGAAATTCATACTAAGTGTATGACTTTCTGTATTGGGCACTTTGTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * * *
143555 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTAGGCACTTTGTGTGAA
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG-C
* * *
143614 AAAATGTTAAGAAATTCATACCAAGTGTATGAATTTCCGTATTAGACACTTCGTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * *
143672 AAAA-GTTAAGAAATTCATACAAAGTGTATGAATTTCCATATTGGGCACTTTGTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * * *
143729 -AAATCATTAAGAGATTAATACTAATTGTATGAATTTCC
1 AAAAT-GTTAAGAAATTCATACTAAGTGTATGAATTTCC
143767 ATATGGGAAA
Statistics
Matches: 396, Mismatches: 45, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
56 3 0.01
57 48 0.12
58 189 0.48
59 156 0.39
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (58 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
Found at i:150545 original size:58 final size:58
Alignment explanation
Indices: 150307--150703 Score: 479
Period size: 57 Copynumber: 6.9 Consensus size: 58
150297 ATTACCAAAT
*
150307 GGCACTTTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC--ATTG
1 GGCACTTAGTGTG-AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
150364 GGCACTTCGTGTGTAAAAATGTTAAG-AATACATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTAGTGTG-AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
150422 GGCACTTTAG-GCGCAAAATATTAAGAAATTCATAC-AA-TGTATGAATTTCCGTATTG
1 GGCAC-TTAGTGTGAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
150478 GGCACTTAGTGTGAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTG
1 GGCACTTAGTGTGAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
150536 GGCAATTAGTGTGAAAAAATGTTAAGAAATTCATAGTAAGTGTATGAATTACCATATTG
1 GGCACTTAGTGTG-AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
** * *
150595 GGCACTTCTTGT-ACAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTT
1 GGCACTTAGTGTGA-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * * * *
150652 GGTACTTTGTGT-ACAAATCATTAAGAGATTCATTCTAAGTGCATGAATTTCC
1 GGCACTTAGTGTGAAAAAT-GTTAAGAAATTCATACTAAGTGTATGAATTTCC
150704 ATATGGGAAA
Statistics
Matches: 298, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
55 4 0.01
56 74 0.25
57 85 0.29
58 82 0.28
59 53 0.18
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (58 bp):
GGCACTTAGTGTGAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:152057 original size:15 final size:16
Alignment explanation
Indices: 152037--152078 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
152027 GATTAGAATA
152037 AAATAAATAAAAGAT-
1 AAATAAATAAAAGATG
*
152052 AAATAAATGAAAGATG
1 AAATAAATAAAAGATG
152068 AAATAAGATAA
1 AAATAA-ATAA
152079 TAAAGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 6 0.26
17 3 0.13
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (16 bp):
AAATAAATAAAAGATG
Found at i:156353 original size:21 final size:21
Alignment explanation
Indices: 156329--156395 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
156319 TTTTTTGAAA
156329 TTTTGTTTTTTGTTTTTGTTT
1 TTTTGTTTTTTGTTTTTGTTT
** *
156350 TTTTGCCTTTTG-TTTTGCCTT
1 TTTTGTTTTTTGTTTTTG-TTT
* *
156371 TTTTGTTTTTT-TATTGGTTT
1 TTTTGTTTTTTGTTTTTGTTT
156391 TTTTG
1 TTTTG
156396 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 12 0.33
21 24 0.67
ACGTcount: A:0.01, C:0.06, G:0.15, T:0.78
Consensus pattern (21 bp):
TTTTGTTTTTTGTTTTTGTTT
Done.