Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold85
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: 1350895
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 487514 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:143939 original size:18 final size:18
Alignment explanation
Indices: 143918--143955 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
143908 ATGGCGTTTA
*
143918 ATGGGTATTGTTTCCCAC
1 ATGGATATTGTTTCCCAC
143936 ATGGATATTGTTTCCCAC
1 ATGGATATTGTTTCCCAC
143954 AT
1 AT
143956 TTATTATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (18 bp):
ATGGATATTGTTTCCCAC
Found at i:144197 original size:31 final size:31
Alignment explanation
Indices: 144159--144223 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
144149 AGTGGAGTCG
* *
144159 GCTCATTTTGTGGTGCTTGAGGTTGTTTCTC
1 GCTCATTTTGTGGTGCTCGAGGCTGTTTCTC
*
144190 GCTCATTTTGTGGTGCTCGAGGCTGTTTGTC
1 GCTCATTTTGTGGTGCTCGAGGCTGTTTCTC
144221 GCT
1 GCT
144224 GGGTTTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.06, C:0.18, G:0.31, T:0.45
Consensus pattern (31 bp):
GCTCATTTTGTGGTGCTCGAGGCTGTTTCTC
Found at i:144274 original size:21 final size:21
Alignment explanation
Indices: 144245--144284 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
144235 CTACCTGTGG
144245 TATTATTTGCACTGTTCACTT
1 TATTATTTGCACTGTTCACTT
* *
144266 TATTTTTTGCAGTGTTCAC
1 TATTATTTGCACTGTTCAC
144285 GTTACTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.53
Consensus pattern (21 bp):
TATTATTTGCACTGTTCACTT
Found at i:144477 original size:22 final size:21
Alignment explanation
Indices: 144449--144568 Score: 123
Period size: 22 Copynumber: 5.4 Consensus size: 21
144439 AAACATTATA
144449 AAAAATAATATTATCATAATAT
1 AAAAATAATATTAT-ATAATAT
* *
144471 AAAAATAATATTAAAATATTAT
1 AAAAATAATATT-ATATAATAT
*
144493 AAAAATAATATTAATATGATAT
1 AAAAATAATATT-ATATAATAT
*
144515 AAAAATAATATTAATATTATAT
1 AAAAATAATATT-ATATAATAT
* *
144537 AAAAAATAATATTAACATAATGT
1 -AAAAATAATATT-ATATAATAT
144560 AAAATATAA
1 AAAA-ATAA
144569 AAATGTTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
22 62 0.72
23 24 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATAATATTATATAATAT
Found at i:144478 original size:11 final size:11
Alignment explanation
Indices: 144449--144568 Score: 96
Period size: 11 Copynumber: 10.7 Consensus size: 11
144439 AAACATTATA
144449 AAAAATAATAT
1 AAAAATAATAT
* **
144460 TATCATAATAT
1 AAAAATAATAT
144471 AAAAATAATAT
1 AAAAATAATAT
* *
144482 TAAAATATTAT
1 AAAAATAATAT
144493 AAAAATAATAT
1 AAAAATAATAT
* * *
144504 TAATATGATAT
1 AAAAATAATAT
144515 AAAAATAATAT
1 AAAAATAATAT
* * *
144526 TAATATTATAT
1 AAAAATAATAT
144537 AAAAAATAATAT
1 -AAAAATAATAT
* * *
144549 TAACATAATGT
1 AAAAATAATAT
144560 AAAATATAA
1 AAAA-ATAA
144569 AAATGTTAAA
Statistics
Matches: 80, Mismatches: 27, Indels: 3
0.73 0.25 0.03
Matches are distributed among these distances:
11 68 0.85
12 12 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:144515 original size:44 final size:46
Alignment explanation
Indices: 144437--144568 Score: 175
Period size: 44 Copynumber: 2.9 Consensus size: 46
144427 AATGTTTGAC
*
144437 TAAAACATTATAAAAAATAATATT-ATCATAATATAAAAATAATAT
1 TAAAATATTATAAAAAATAATATTAATCATAATATAAAAATAATAT
*
144482 TAAAATATTAT-AAAAATAATATTAAT-ATGATATAAAAATAATAT
1 TAAAATATTATAAAAAATAATATTAATCATAATATAAAAATAATAT
* *
144526 TAATAT-TATATAAAAAATAATATTAA-CATAATGTAAAATATAA
1 TAAAATAT-TATAAAAAATAATATTAATCATAATATAAAA-ATAA
144569 AAATGTTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
43 1 0.01
44 37 0.48
45 35 0.45
46 4 0.05
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (46 bp):
TAAAATATTATAAAAAATAATATTAATCATAATATAAAAATAATAT
Found at i:144582 original size:17 final size:17
Alignment explanation
Indices: 144559--144602 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
144549 TAACATAATG
144559 TAAAATATAAAAATGTTA
1 TAAAATATAAAAAT-TTA
*
144577 -AAAATATTAAAATTTA
1 TAAAATATAAAAATTTA
144593 TATAAATATA
1 TA-AAATATA
144603 TAATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAATATAAAAATTTA
Found at i:147893 original size:18 final size:19
Alignment explanation
Indices: 147870--147911 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
147860 ATTTTAAAAA
147870 AAATAAAAATATAAA-AT-T
1 AAATAAAAAT-TAAATATGT
*
147888 AAATAATAATTAAATATGT
1 AAATAAAAATTAAATATGT
147907 AAATA
1 AAATA
147912 GATATTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATAAAAATTAAATATGT
Found at i:148305 original size:3 final size:3
Alignment explanation
Indices: 148297--148321 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
148287 ACTAATTACT
148297 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
148322 AATGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:149738 original size:17 final size:16
Alignment explanation
Indices: 149718--149775 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
149708 ATAAATAAAC
149718 ATATTTAATATATATAT
1 ATATTTAATATAT-TAT
149735 ATATATT-ATATATT-T
1 ATAT-TTAATATATTAT
* *
149750 ATATTTAAAATTTTGAT
1 ATATTTAATATATT-AT
149767 ATATTTAAT
1 ATATTTAAT
149776 CATTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 1 0.03
17 19 0.56
18 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATATTTAATATATTAT
Found at i:150146 original size:14 final size:15
Alignment explanation
Indices: 150124--150186 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 15
150114 AGAGAAATTG
*
150124 AAATGTAAAAAA-AA
1 AAATTTAAAAAATAA
150138 AAATTTAAAACAATAA
1 AAATTTAAAA-AATAA
* *
150154 AAGTTTAAAAATTTAA
1 AAATTTAAAAA-ATAA
*
150170 AAA-TAAAAAAATAA
1 AAATTTAAAAAATAA
150184 AAA
1 AAA
150187 AAATTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 15 0.38
15 9 0.22
16 16 0.40
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (15 bp):
AAATTTAAAAAATAA
Found at i:151895 original size:25 final size:25
Alignment explanation
Indices: 151867--151918 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
151857 AAATTATTAT
151867 TTATATTAATAAAAATATTTAAATA
1 TTATATTAATAAAAATATTTAAATA
* * ** *
151892 TTATTTTTATATTAATATTTATATA
1 TTATATTAATAAAAATATTTAAATA
151917 TT
1 TT
151919 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATATTAATAAAAATATTTAAATA
Found at i:151933 original size:22 final size:22
Alignment explanation
Indices: 151893--151934 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
151883 ATTTAAATAT
*
151893 TATTTTTATATTAATATTTATA
1 TATTTTTAAATTAATATTTATA
151915 TATTTTTAAAATTAA-ATTTA
1 TATTTTT-AAATTAATATTTA
151935 AATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTAAATTAATATTTATA
Found at i:152211 original size:18 final size:18
Alignment explanation
Indices: 152185--152223 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
152175 TTTTAATTTT
*
152185 AAATTAATTAAAAAAATA
1 AAATAAATTAAAAAAATA
* *
152203 AAATAAATTATAAAATTA
1 AAATAAATTAAAAAAATA
152221 AAA
1 AAA
152224 GATAAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAATTAAAAAAATA
Found at i:152973 original size:22 final size:23
Alignment explanation
Indices: 152946--152994 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
152936 AAAGACAAGG
*
152946 GAAAGAGGGAAAGTCT-GAAAGA
1 GAAAGAAGGAAAGTCTAGAAAGA
* *
152968 GAAAGAAGGAATGTTTAGAAAGA
1 GAAAGAAGGAAAGTCTAGAAAGA
152991 GAAA
1 GAAA
152995 CAAAATCCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.33, T:0.12
Consensus pattern (23 bp):
GAAAGAAGGAAAGTCTAGAAAGA
Found at i:154262 original size:15 final size:16
Alignment explanation
Indices: 154235--154277 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
154225 TAATCTAAGT
*
154235 TTTAGATTATTTTAGA
1 TTTAGATTATTTTAAA
154251 TTTAGA-TATTTTAAA
1 TTTAGATTATTTTAAA
154266 TTT-GAATTATTT
1 TTTAG-ATTATTT
154278 CAGGTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTAGATTATTTTAAA
Found at i:155893 original size:13 final size:13
Alignment explanation
Indices: 155875--155931 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
155865 CATAAAGTGT
*
155875 TGTATCGGTACAA
1 TGTATCGATACAA
155888 TGTATCGATACATAA
1 TGTATCGATAC--AA
155903 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
155920 TGTATCGATACA
1 TGTATCGATACA
155932 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:155910 original size:32 final size:32
Alignment explanation
Indices: 155855--155952 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
155845 TTCAACGATT
*
155855 TGTATCGATACATAAAGTGTTGTATCGGTACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
155888 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
155920 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
155952 T
1 T
155953 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:155912 original size:19 final size:18
Alignment explanation
Indices: 155853--155950 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
155843 ATTTCAACGA
155853 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
*
155872 TGTTGTATCGGTAC--AA-
1 T-TTGTATCGATACATAAG
155888 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
155904 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
155920 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
155936 TTTTGTATCGATACA
1 -TTTGTATCGATACA
155951 ATTTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 24 0.38
20 11 0.17
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:156012 original size:13 final size:13
Alignment explanation
Indices: 155994--156018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155984 ATTACTCAAA
155994 TGTATCGATACAT
1 TGTATCGATACAT
156007 TGTATCGATACA
1 TGTATCGATACA
156019 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:156083 original size:52 final size:52
Alignment explanation
Indices: 156027--156151 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
156017 CACTGATCTT
*
156027 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-TTTTATAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTA-AA
156079 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
156131 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
156152 CTTTTCATAT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 67 0.94
53 4 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:309777 original size:13 final size:13
Alignment explanation
Indices: 309759--309787 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
309749 ACAACATTCC
309759 TTGTATCGATACA
1 TTGTATCGATACA
309772 TTGTATCGATACA
1 TTGTATCGATACA
309785 TTG
1 TTG
309788 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:312353 original size:13 final size:13
Alignment explanation
Indices: 312335--312360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312325 CATGGGACAA
312335 TGTATCGATACAT
1 TGTATCGATACAT
312348 TGTATCGATACAT
1 TGTATCGATACAT
312361 GAGGAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312356 original size:33 final size:34
Alignment explanation
Indices: 312314--312382 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
312304 CTATCACTAT
312314 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
312347 TTGTATCGATACATGAGGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
312381 TT
1 TT
312383 ACTTGTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:320396 original size:32 final size:33
Alignment explanation
Indices: 320353--320443 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 33
320343 CAACACTATC
*
320353 TTTCAAGGCTAAAATAGAAACCTC-C-CTAT-TT
1 TTTCAAGGCTAAGATAG-AACCTCTCTCTATCTT
320384 TTTCACAGGCTAAGATAGAACCTTTCTCTCTATCTT
1 TTTCA-AGGCTAAGATAGAACC--TCTCTCTATCTT
320420 TTTCAAAGGCTAAGATAGAACCTC
1 TTTC-AAGGCTAAGATAGAACCTC
320444 ACAATCACTT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
31 9 0.17
32 11 0.21
33 2 0.04
34 3 0.06
35 4 0.08
36 22 0.42
37 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (33 bp):
TTTCAAGGCTAAGATAGAACCTCTCTCTATCTT
Found at i:320992 original size:32 final size:32
Alignment explanation
Indices: 320904--321028 Score: 144
Period size: 32 Copynumber: 3.8 Consensus size: 32
320894 ACTATTCACA
* *
320904 ATGTATTGATACATGAACAGTTATGAACAG-T
1 ATGTATCGATACATGAACAGTGATGAACAGTT
* * *
320935 AGTGAATTGTGATACATAAACAGTGATGAACAGTT
1 A-TGTA-T-CGATACATGAACAGTGATGAACAGTT
* *
320970 ATGTATCGATACATGAATAGTGATGAACAGTG
1 ATGTATCGATACATGAACAGTGATGAACAGTT
*
321002 ATGTATCAATACATGAACAGTGATGAA
1 ATGTATCGATACATGAACAGTGATGAA
321029 TAGTGATTAG
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
31 1 0.01
32 50 0.62
33 2 0.03
34 25 0.31
35 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACATGAACAGTGATGAACAGTT
Found at i:324797 original size:21 final size:21
Alignment explanation
Indices: 324773--324826 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
324763 TTCAATATCT
*
324773 ATAAATGTTTTAGAG-TTATGA
1 ATAAATGTTTTAGAGCTT-TAA
* *
324794 ATAAATCTTTTTGAGCTTTAA
1 ATAAATGTTTTAGAGCTTTAA
324815 ATCAAATGTTTT
1 AT-AAATGTTTT
324827 TAAGTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (21 bp):
ATAAATGTTTTAGAGCTTTAA
Found at i:324979 original size:19 final size:19
Alignment explanation
Indices: 324917--325027 Score: 123
Period size: 20 Copynumber: 5.7 Consensus size: 19
324907 ACCCTTGAAA
* * *
324917 GTATCGATACATATCCAGAT
1 GTATCGATACATGTTCA-TT
* * *
324937 GTATCGATACATAATGCTTT
1 GTATCGATACAT-GTTCATT
324957 GTATCGATACATGTTCATT
1 GTATCGATACATGTTCATT
324976 GTATCGATACATGTTCATT
1 GTATCGATACATGTTCATT
* *
324995 GTATCGATACATGCATAATT
1 GTATCGATACATG-TTCATT
325015 GTATCGATACATG
1 GTATCGATACATG
325028 AAACTGGCAG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 36 0.44
20 42 0.52
21 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
GTATCGATACATGTTCATT
Found at i:324986 original size:39 final size:38
Alignment explanation
Indices: 324917--325026 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
324907 ACCCTTGAAA
* * * *
324917 GTATCGATACATATCCAGATGTATCGATACATAATGCTTT
1 GTATCGATACATGTTCA-TTGTATCGATACAT-ATGCATT
* *
324957 GTATCGATACATGTTCATTGTATCGATACATGTTCATT
1 GTATCGATACATGTTCATTGTATCGATACATATGCATT
* *
324995 GTATCGATACATGCATAATTGTATCGATACAT
1 GTATCGATACATG-TTCATTGTATCGATACAT
325027 GAAACTGGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 17 0.28
39 29 0.48
40 15 0.25
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (38 bp):
GTATCGATACATGTTCATTGTATCGATACATATGCATT
Found at i:325095 original size:13 final size:13
Alignment explanation
Indices: 325077--325101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325067 CTTGGCACAT
325077 TGTATCGATACAA
1 TGTATCGATACAA
325090 TGTATCGATACA
1 TGTATCGATACA
325102 TAACAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331478 original size:20 final size:19
Alignment explanation
Indices: 331453--331492 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
331443 GGAACATGGA
331453 AAGAAAAAAGAAAAAAAATG
1 AAGAAAAAA-AAAAAAAATG
* *
331473 AAGAAAGAAAAAAAAGATG
1 AAGAAAAAAAAAAAAAATG
331492 A
1 A
331493 TGGACGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAGAAAAAAAAAAAAAATG
Found at i:331814 original size:12 final size:12
Alignment explanation
Indices: 331766--331824 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
331756 TTCTCTTACC
331766 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
331778 TCACCTTTCT-TA
1 TC-TCTTTCTCTA
331790 -C-CTTTCCCTCTA
1 TCTCTTT--CTCTA
331802 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
331814 TATCTTTCTCT
1 TCTCTTTCTCT
331825 CTATTCCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 4 0.10
11 3 0.08
12 21 0.54
13 7 0.18
14 4 0.10
ACGTcount: A:0.10, C:0.36, G:0.00, T:0.54
Consensus pattern (12 bp):
TCTCTTTCTCTA
Found at i:332092 original size:10 final size:10
Alignment explanation
Indices: 332077--332270 Score: 87
Period size: 10 Copynumber: 19.4 Consensus size: 10
332067 CTTCCACAAT
332077 ATTCTAGAAC
1 ATTCTAGAAC
332087 ATTCTAGAATC
1 ATTCTAGAA-C
*
332098 -TTCCAGAAC
1 ATTCTAGAAC
* * * *
332107 CTTCCATAAT
1 ATTCTAGAAC
332117 ATTCTAGAAC
1 ATTCTAGAAC
332127 ATTCTAGAATC
1 ATTCTAGAA-C
*
332138 -TTCCAGAAC
1 ATTCTAGAAC
* * * *
332147 CTTCCATAAT
1 ATTCTAGAAC
332157 ATTCTAGAAC
1 ATTCTAGAAC
332167 ATTCTAGAATC
1 ATTCTAGAA-C
* *
332178 -TTCCAGAGC
1 ATTCTAGAAC
* * *
332187 CTTCCACG-AT
1 ATTCTA-GAAC
332197 ATTCTAGAAC
1 ATTCTAGAAC
332207 ATTCTAGAATC
1 ATTCTAGAA-C
* *
332218 -TTCCAGAGC
1 ATTCTAGAAC
* *
332227 CTT-TCACG-AT
1 ATTCT-A-GAAC
*
332237 ATTCTAGAAT
1 ATTCTAGAAC
*
332247 ATTCCAGAAC
1 ATTCTAGAAC
332257 ATTCTAGAAC
1 ATTCTAGAAC
332267 ATTC
1 ATTC
332271 CAAAGTGTTC
Statistics
Matches: 140, Mismatches: 30, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
9 6 0.04
10 127 0.91
11 7 0.05
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.32
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:332121 original size:40 final size:40
Alignment explanation
Indices: 332066--332272 Score: 299
Period size: 40 Copynumber: 5.2 Consensus size: 40
332056 AGTTCTAGAG
332066 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
*
332106 CCTTCCATAATATTCTAGAACATTCTAGAATCTTCCAGAA
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* *
332146 CCTTCCATAATATTCTAGAACATTCTAGAATCTTCCAGAG
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* *
332186 CCTTCCACGATATTCTAGAACATTCTAGAATCTTCCAGAG
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* * * * *
332226 CCTTTCACGATATTCTAGAATATTCCAGAA-CATTCTAGAA
1 CCTTCCACAATATTCTAGAACATTCTAGAATC-TTCCAGAA
*
332266 CATTCCA
1 CCTTCCA
332273 AAGTGTTCTA
Statistics
Matches: 155, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 154 0.99
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.31
Consensus pattern (40 bp):
CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
Found at i:336275 original size:12 final size:12
Alignment explanation
Indices: 336227--336285 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
336217 TTCTCTTACC
336227 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
336239 TCACCTTTCT-TA
1 TC-TCTTTCTCTA
336251 -C-CTTTCCCTCTA
1 TCTCTTT--CTCTA
336263 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
336275 TATCTTTCTCT
1 TCTCTTTCTCT
336286 CTATTCCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 4 0.10
11 3 0.08
12 21 0.54
13 7 0.18
14 4 0.10
ACGTcount: A:0.10, C:0.36, G:0.00, T:0.54
Consensus pattern (12 bp):
TCTCTTTCTCTA
Found at i:336553 original size:10 final size:10
Alignment explanation
Indices: 336538--336691 Score: 68
Period size: 10 Copynumber: 15.4 Consensus size: 10
336528 CTTCCACAAT
336538 ATTCTAGAAC
1 ATTCTAGAAC
336548 ATTCTAGAATC
1 ATTCTAGAA-C
*
336559 -TTCCAGAAC
1 ATTCTAGAAC
* * * *
336568 CTTCCATAAT
1 ATTCTAGAAC
336578 ATTCTAGAAC
1 ATTCTAGAAC
336588 ATTCTAGAATC
1 ATTCTAGAA-C
* *
336599 -TTCCAGAGC
1 ATTCTAGAAC
* * *
336608 CTTCCACG-AT
1 ATTCTA-GAAC
336618 ATTCTAGAAC
1 ATTCTAGAAC
336628 ATTCTAGAATC
1 ATTCTAGAA-C
* *
336639 -TTCCAGAGC
1 ATTCTAGAAC
* *
336648 CTT-TCACG-AT
1 ATTCT-A-GAAC
*
336658 ATTCTAGAAT
1 ATTCTAGAAC
*
336668 ATTCCAGAAC
1 ATTCTAGAAC
336678 ATTCTAGAAC
1 ATTCTAGAAC
336688 ATTC
1 ATTC
336692 CAAAGTGTTC
Statistics
Matches: 109, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
9 5 0.05
10 98 0.90
11 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:336582 original size:40 final size:40
Alignment explanation
Indices: 336527--336693 Score: 228
Period size: 40 Copynumber: 4.2 Consensus size: 40
336517 AGTTCTAGAG
336527 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* *
336567 CCTTCCATAATATTCTAGAACATTCTAGAATCTTCCAGAG
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* *
336607 CCTTCCACGATATTCTAGAACATTCTAGAATCTTCCAGAG
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
* * * * *
336647 CCTTTCACGATATTCTAGAATATTCCAGAA-CATTCTAGAA
1 CCTTCCACAATATTCTAGAACATTCTAGAATC-TTCCAGAA
*
336687 CATTCCA
1 CCTTCCA
336694 AAGTGTTCTA
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 114 0.99
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (40 bp):
CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAGAA
Found at i:341358 original size:22 final size:21
Alignment explanation
Indices: 341333--341380 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
341323 ATGAGCCCTA
* * *
341333 TTGTATACATTTGTTTATATTT
1 TTGTATAAATTT-TGTATATCT
341355 TTGTTATAAATTTTGTATATCT
1 TTG-TATAAATTTTGTATATCT
341377 TTGT
1 TTGT
341381 TTGATATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 13 0.59
23 8 0.36
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.62
Consensus pattern (21 bp):
TTGTATAAATTTTGTATATCT
Found at i:342566 original size:18 final size:18
Alignment explanation
Indices: 342545--342585 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
342535 TTCTCTAAAT
* *
342545 AAAAAATAAAAAAGA-GA
1 AAAAAAGAAAAAACATGA
342562 AAAAAAGAAAAAACATGA
1 AAAAAAGAAAAAACATGA
342580 AAAAAA
1 AAAAAA
342586 AGATGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAAGAAAAAACATGA
Found at i:342811 original size:15 final size:15
Alignment explanation
Indices: 342791--342829 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
342781 CGATTCCTTA
342791 GGAAAGGTTTTTCTT
1 GGAAAGGTTTTTCTT
342806 GGAAAGGTTTTTCTT
1 GGAAAGGTTTTTCTT
342821 GGAAAGGTT
1 GGAAAGGTT
342830 GTAAGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (15 bp):
GGAAAGGTTTTTCTT
Found at i:350856 original size:89 final size:91
Alignment explanation
Indices: 350745--350925 Score: 303
Period size: 92 Copynumber: 2.0 Consensus size: 91
350735 CAAATCCCAG
350745 GCCACTCCATTTTATTTTTTTTCTTTCATCTTCTTCTTC-T-TTACTTTTTCTTCCTTCTTTCTC
1 GCCACTCCATTTTATTTTTTTTCTTTCATCTTCTTCTTCTTATTACTTTTTCTTCCTTCTTTCTC
*
350808 ACCAATAACCACCCATACCTAGACCA
66 ACCAATAACCACCCATAACTAGACCA
* * *
350834 GCCATTCCATTTTCTTTTTTTTCTTTCATCTTCTTCTTCTTCATTCCTTTTTCTTCCTTCTTTCT
1 GCCACTCCATTTTATTTTTTTTCTTTCATCTTCTTCTTCTT-ATTACTTTTTCTTCCTTCTTTCT
350899 CACCAATAACCACCCATAACTAGACCA
65 CACCAATAACCACCCATAACTAGACCA
350926 TGATAGGAGA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
89 37 0.44
90 1 0.01
92 47 0.55
ACGTcount: A:0.18, C:0.33, G:0.02, T:0.48
Consensus pattern (91 bp):
GCCACTCCATTTTATTTTTTTTCTTTCATCTTCTTCTTCTTATTACTTTTTCTTCCTTCTTTCTC
ACCAATAACCACCCATAACTAGACCA
Found at i:352548 original size:13 final size:13
Alignment explanation
Indices: 352530--352650 Score: 80
Period size: 13 Copynumber: 7.9 Consensus size: 13
352520 TTAGAAGCAA
352530 TGTATCGATACAT
1 TGTATCGATACAT
352543 TGTATCGATACAAT
1 TGTATCGATAC-AT
352557 GCCCATGTATCGATACAT
1 -----TGTATCGATACAT
352575 TGTATCGATACAAT
1 TGTATCGATAC-AT
352589 GCCCATGTATCGATACAT
1 -----TGTATCGATACAT
352607 TGTATCGATACAAT
1 TGTATCGATAC-AT
352621 GCCCATGTATCGATACAT
1 -----TGTATCGATACAT
352639 TGTATCGATACA
1 TGTATCGATACA
352651 ATGCCCATGT
Statistics
Matches: 90, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 45 0.50
14 6 0.07
18 6 0.07
19 33 0.37
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352567 original size:19 final size:19
Alignment explanation
Indices: 352543--352670 Score: 130
Period size: 19 Copynumber: 7.7 Consensus size: 19
352533 ATCGATACAT
352543 TGTATCGATACAATGCCCA
1 TGTATCGATACAATGCCCA
352562 TGTATCGATAC-AT-----
1 TGTATCGATACAATGCCCA
352575 TGTATCGATACAATGCCCA
1 TGTATCGATACAATGCCCA
352594 TGTATCGATAC-AT-----
1 TGTATCGATACAATGCCCA
352607 TGTATCGATACAATGCCCA
1 TGTATCGATACAATGCCCA
352626 TGTATCGATAC-AT-----
1 TGTATCGATACAATGCCCA
352639 TGTATCGATACAATGCCCA
1 TGTATCGATACAATGCCCA
352658 TGTATCGATACAA
1 TGTATCGATACAA
352671 ACAGTGGTAG
Statistics
Matches: 91, Mismatches: 0, Indels: 36
0.72 0.00 0.28
Matches are distributed among these distances:
13 33 0.36
14 6 0.07
18 6 0.07
19 46 0.51
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAATGCCCA
Found at i:352570 original size:32 final size:32
Alignment explanation
Indices: 352529--352669 Score: 282
Period size: 32 Copynumber: 4.4 Consensus size: 32
352519 GTTAGAAGCA
352529 ATGTATCGATACATTGTATCGATACAATGCCC
1 ATGTATCGATACATTGTATCGATACAATGCCC
352561 ATGTATCGATACATTGTATCGATACAATGCCC
1 ATGTATCGATACATTGTATCGATACAATGCCC
352593 ATGTATCGATACATTGTATCGATACAATGCCC
1 ATGTATCGATACATTGTATCGATACAATGCCC
352625 ATGTATCGATACATTGTATCGATACAATGCCC
1 ATGTATCGATACATTGTATCGATACAATGCCC
352657 ATGTATCGATACA
1 ATGTATCGATACA
352670 AACAGTGGTA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 109 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACATTGTATCGATACAATGCCC
Found at i:352754 original size:13 final size:13
Alignment explanation
Indices: 352736--352762 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
352726 CGATACAATG
352736 AAAATGTATCGAT
1 AAAATGTATCGAT
352749 AAAATGTATCGAT
1 AAAATGTATCGAT
352762 A
1 A
352763 CAAAGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
AAAATGTATCGAT
Found at i:353347 original size:30 final size:31
Alignment explanation
Indices: 353311--353368 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
353301 TAAGGTTCTC
*
353311 GTTAAAAA-AATTTCTCCCCCTTGATAATCG
1 GTTAAAAAGAATTTCTCCCCCTAGATAATCG
*
353341 GTTAAAAAGATTTTCTCCCCCTAGATAA
1 GTTAAAAAGAATTTCTCCCCCTAGATAA
353369 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (31 bp):
GTTAAAAAGAATTTCTCCCCCTAGATAATCG
Found at i:362001 original size:89 final size:89
Alignment explanation
Indices: 361818--362519 Score: 877
Period size: 89 Copynumber: 7.9 Consensus size: 89
361808 TTCAAAGAAA
** *
361818 ACACATTTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGTGTCACTAAGCCTA
1 ACACA-TTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTA
*** * *
361883 ATTTTAGTGGGACAAGGTGTAGCCC
65 ATTTCCTTGGGGCAAGGTGCAGCCC
* * ** ** * *
361908 ACACATTCCAAACCATATCCTTTTCATCCAACCACTAGATGGTATTGATGCGCCACTAAGACTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
* *
361973 TTTCCTTGGGGCATGGTGCAGCCT
66 TTTCCTTGGGGCAAGGTGCAGCCC
361997 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
** *
362062 TTTCCTTAAGGTAAGGTGCAGCCC
66 TTTCCTTGGGGCAAGGTGCAGCCC
* * * * * *
362086 ACACATTCCTAATAATATCGCCTTCATCCAACCACTAAATGGTATTGATGCGTTACTAAGCCTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
* * *
362151 TTTCCTTGAGGCAAAGTGCAGCCT
66 TTTCCTTGGGGCAAGGTGCAGCCC
* * * *
362175 ACATATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGAATTGATGCATCACCAAGCCTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
* * *
362240 TTTCTTTGGGGCAAGGTGCAACCAA
66 TTTCCTTGGGGCAAGGTGCAGCC-C
* * * *
362265 ACACCTTTCATAATCATATCCCCTTCATCCAACTACTAGATGGTATTGATGCATTACCAAGCCTA
1 ACA-CATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTA
*
362330 ATTTCCTT-GGGCAAGGTGTAGCCC
65 ATTTCCTTGGGGCAAGGTGCAGCCC
* * *
362354 ACACATTCCCAATCATATCCCCTTCATCCAACTACTAGATGGTATTGATACATCACCAAGCCTAA
1 ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
* *
362419 TTTCCTTAGGGCAAGGTGCAACCC
66 TTTCCTTGGGGCAAGGTGCAGCCC
* * * * *
362443 ACACATT-CTCAATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATTACAAAACCTG
1 ACACATTCCT-AATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTA
*
362507 ATTTTCTTGGGGC
65 ATTTCCTTGGGGC
362520 TAGGACATCT
Statistics
Matches: 527, Mismatches: 81, Indels: 9
0.85 0.13 0.01
Matches are distributed among these distances:
88 65 0.12
89 381 0.72
90 21 0.04
91 60 0.11
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (89 bp):
ACACATTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAA
TTTCCTTGGGGCAAGGTGCAGCCC
Found at i:362487 original size:357 final size:355
Alignment explanation
Indices: 361820--362498 Score: 977
Period size: 357 Copynumber: 1.9 Consensus size: 355
361810 CAAAGAAAAC
* * ** *
361820 ACATTTCCTAATCATATCCCCTTCATCCAACCACTAGATGGTATTGATGTGTCACTAAGCCTAAT
1 ACATTTCCCAATCATATCCCCTTCATCCAACCACTAGATGGAATTGATGCATCACCAAGCCTAAT
* * * **
361885 TTTAGTGGGACAAGGTGTAGCCCACACATTCCAAACCATATCCTTTTCATCCAACCACTAGATGG
66 TTTAGTGGGACAAGGTGCAACCAACACATTCCAAACCATATCCCCTTCATCCAACCACTAGATGG
* * * * *
361950 TATTGATGCGCCACTAAGACTAATTTCCTTGGGGCATGGTGCAGCCTACACATTCCTAATCATAT
131 TATTGATGCACCACCAAGACTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATAT
* *
362015 CCCCTTCATCCAACCACTAGATGGTATTGATGCATCACCAAGCCTAATTTCCTTAAGGTAAGGTG
196 CCCCTTCATCCAACCACTAGATGGTATTGATACATCACCAAGCCTAATTTCCTTAAGGCAAGGTG
* *
362080 CAGCCCACACATTCCTAATAATATCGCCTTCATCCAACCACTAAATGGTATTGATGCGTTACTAA
261 CAACCCACACATTCCTAATAATATCGCCTTCATCCAACCACTAAATGGTATTGATGCATTACTAA
362145 GCCTAATTTCCTTGAGGCAAAGTGCAGCCT
326 GCCTAATTTCCTTGAGGCAAAGTGCAGCCT
*
362175 ACATATTCCCAATCATATCCCCTTTATCCAACCACTAGATGGAATTGATGCATCACCAAGCCTAA
1 ACAT-TTCCCAATCATATCCCCTTCATCCAACCACTAGATGGAATTGATGCATCACCAAGCCTAA
* * * * * *
362240 TTTCT-TTGGGGCAAGGTGCAACCAAACACCTTTCATAATCATATCCCCTTCATCCAACTACTAG
65 TTT-TAGTGGGACAAGGTGCAACC-AACACATTCCA-AACCATATCCCCTTCATCCAACCACTAG
** * *
362304 ATGGTATTGATGCATTACCAAGCCTAATTTCCTT-GGGCAAGGTGTAGCCCACACATTCCCAATC
127 ATGGTATTGATGCACCACCAAGACTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATC
* *
362368 ATATCCCCTTCATCCAACTACTAGATGGTATTGATACATCACCAAGCCTAATTTCCTTAGGGCAA
192 ATATCCCCTTCATCCAACCACTAGATGGTATTGATACATCACCAAGCCTAATTTCCTTAAGGCAA
* * *
362433 GGTGCAACCCACACATT-CTCAATCATATCTCCTTCATCCAACCACTAGATGGTATTGATGCATT
257 GGTGCAACCCACACATTCCT-AATAATATCGCCTTCATCCAACCACTAAATGGTATTGATGCATT
362497 AC
321 AC
362499 AAAACCTGAT
Statistics
Matches: 284, Mismatches: 35, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
355 4 0.01
356 73 0.26
357 154 0.54
358 53 0.19
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (355 bp):
ACATTTCCCAATCATATCCCCTTCATCCAACCACTAGATGGAATTGATGCATCACCAAGCCTAAT
TTTAGTGGGACAAGGTGCAACCAACACATTCCAAACCATATCCCCTTCATCCAACCACTAGATGG
TATTGATGCACCACCAAGACTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATAT
CCCCTTCATCCAACCACTAGATGGTATTGATACATCACCAAGCCTAATTTCCTTAAGGCAAGGTG
CAACCCACACATTCCTAATAATATCGCCTTCATCCAACCACTAAATGGTATTGATGCATTACTAA
GCCTAATTTCCTTGAGGCAAAGTGCAGCCT
Found at i:362955 original size:42 final size:42
Alignment explanation
Indices: 362880--363027 Score: 131
Period size: 42 Copynumber: 3.5 Consensus size: 42
362870 GTCTCACTCT
* * * * *
362880 AGATTCTTT-ATCTTTTATTTGCCCATTGGCTCAGACCTGAG
1 AGATTTTTTCATCTTTTGTTTGCCCATCGACTCAGAACTGAG
* * *
362921 AAATTTTTTCATCTTTTGTTTGCCCGTCGACTCAGATC-GAAG
1 AGATTTTTTCATCTTTTGTTTGCCCATCGACTCAGAACTG-AG
* * * *
362963 AGATTTCTTCATCATTTGTCTGCCCATCGACTC-GAACTTAGG
1 AGATTTTTTCATCTTTTGTTTGCCCATCGACTCAGAACTGA-G
**
363005 AGACATTTTCATCTTTTGTTTGC
1 AGATTTTTTCATCTTTTGTTTGC
363028 TCGTTGCCTC
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
41 12 0.14
42 72 0.86
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (42 bp):
AGATTTTTTCATCTTTTGTTTGCCCATCGACTCAGAACTGAG
Found at i:363206 original size:42 final size:41
Alignment explanation
Indices: 363041--363206 Score: 156
Period size: 42 Copynumber: 4.0 Consensus size: 41
363031 TTGCCTCTAA
* *
363041 TCAAAAGACTCC-TCGACCCTTTGTCTGCCCGTCGACTCTGAC
1 TCAAAAGACTCCTTC-ACCCTTTGTCTG-CCATCGACTTTGAC
** *
363083 TCAAGGGACTCCTTCACCCTTTGTCTGCCCATTGACTTTGAC
1 TCAAAAGACTCCTTCACCCTTTGTCTG-CCATCGACTTTGAC
* * ** *
363125 TCGAGAGACTTTTTCACCCTTTGTCTCCCCATC-AGCTTTGAC
1 TCAAAAGACTCCTTCACCCTTTGTCT-GCCATCGA-CTTTGAC
* *
363167 CCAAAAGACTCCTTCACCCTTAGTCTGCCAGTCGACTTTG
1 TCAAAAGACTCCTTCACCCTTTGTCTGCCA-TCGACTTTG
363207 TGAGCTCAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 4 0.04
42 94 0.93
43 3 0.03
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.31
Consensus pattern (41 bp):
TCAAAAGACTCCTTCACCCTTTGTCTGCCATCGACTTTGAC
Found at i:364132 original size:22 final size:22
Alignment explanation
Indices: 364077--364132 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
364067 ACAGTGACCT
364077 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
364099 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
364120 ATGAACAGTGATG
1 ATGAACAGTGATG
364133 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:364238 original size:53 final size:53
Alignment explanation
Indices: 364174--364310 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
364164 CTACTACCAA
* * *
364174 TGTATCGATACATATTTTGTGTATTGATACAAATTTGGCTACTGCCAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGACAATGACC
* *
364227 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGACAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGACAATGACC
364280 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
364311 TATGCAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 64 0.83
54 13 0.17
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGACAATGACC
Found at i:364343 original size:20 final size:20
Alignment explanation
Indices: 364280--364350 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
364270 GACAATGTCC
**
364280 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
364300 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
364320 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
364340 TGTATCGATAC
1 TGTATCGATAC
364351 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:364416 original size:21 final size:21
Alignment explanation
Indices: 364390--364430 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
364380 GTCAACCTTG
364390 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
364411 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
364431 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:364848 original size:42 final size:42
Alignment explanation
Indices: 364760--365018 Score: 200
Period size: 42 Copynumber: 6.2 Consensus size: 42
364750 TGCCCATTGT
* ** * * **
364760 CTTTGACTCGGGAGACTCTTTCACTTTTTGTCTGTCGGTC-G
1 CTTTGACTCGAGAGACTCTTTCACCATTTGTTTGCCCATCAG
* *
364801 ACTTTGACTCGGGAGACTC-CTCTACCATTTGTTTGCCCATCAG
1 -CTTTGACTCGAGAGACTCTTTC-ACCATTTGTTTGCCCATCAG
* ** * * * *
364844 CTTTGACTCGAGAGACTTTTTCACTTTTTCTCTGCTCGTCAG
1 CTTTGACTCGAGAGACTCTTTCACCATTTGTTTGCCCATCAG
* * * *
364886 CTTTGACTCAAGAGACTGTTTCACCCA-TTGTCTACCCATCAG
1 CTTTGACTCGAGAGACTCTTTCA-CCATTTGTTTGCCCATCAG
* * * * * * * *
364928 CTTTTACTTGGGAGACTTTTTCACCCTTTTTTTGCTCATCAA
1 CTTTGACTCGAGAGACTCTTTCACCATTTGTTTGCCCATCAG
* *
364970 CTTTGACTCGAGAGACTCCTTCACCTTTTGTTTGCCCATCAG
1 CTTTGACTCGAGAGACTCTTTCACCATTTGTTTGCCCATCAG
365012 CTTTGAC
1 CTTTGAC
365019 CTGGGACATC
Statistics
Matches: 168, Mismatches: 44, Indels: 10
0.76 0.20 0.05
Matches are distributed among these distances:
41 4 0.02
42 160 0.95
43 4 0.02
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (42 bp):
CTTTGACTCGAGAGACTCTTTCACCATTTGTTTGCCCATCAG
Found at i:364866 original size:84 final size:82
Alignment explanation
Indices: 364760--365018 Score: 292
Period size: 84 Copynumber: 3.1 Consensus size: 82
364750 TGCCCATTGT
* *
364760 CTTTGACTCGGGAGACTCTTTCACTTTTTGTCTG-TCGGTCGACTTTGACTCGGGAGACTCC-TC
1 CTTTGACTCGGGAGACTTTTTCACTTTTT-TCTGCTC-GTC-ACTTTGACTCGAGAGACTCCTTC
364823 TACCATTTGTTTGCCCATCAG
63 -ACCATTTGTTTGCCCATCAG
* * **
364844 CTTTGACTCGAGAGACTTTTTCACTTTTTCTCTGCTCGTCAGCTTTGACTCAAGAGACTGTTTCA
1 CTTTGACTCGGGAGACTTTTTCACTTTTT-TCTGCTCGTCA-CTTTGACTCGAGAGACTCCTTCA
* *
364909 CCCA-TTGTCTACCCATCAG
64 -CCATTTGTTTGCCCATCAG
* * *
364928 CTTTTACTTGGGAGACTTTTTCACCCTTTTTT-TGCTCATCAACTTTGACTCGAGAGACTCCTTC
1 CTTTGACTCGGGAGACTTTTTCA--CTTTTTTCTGCTCGTC-ACTTTGACTCGAGAGACTCCTTC
*
364992 ACCTTTTGTTTGCCCATCAG
63 ACCATTTGTTTGCCCATCAG
365012 CTTTGAC
1 CTTTGAC
365019 CTGGGACATC
Statistics
Matches: 147, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
83 3 0.02
84 129 0.88
85 9 0.06
86 6 0.04
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (82 bp):
CTTTGACTCGGGAGACTTTTTCACTTTTTTCTGCTCGTCACTTTGACTCGAGAGACTCCTTCACC
ATTTGTTTGCCCATCAG
Found at i:365602 original size:42 final size:42
Alignment explanation
Indices: 364802--365878 Score: 211
Period size: 42 Copynumber: 25.9 Consensus size: 42
364792 TGTCGGTCGA
* * * * *
364802 CTTTGACTCGGGAGACTCCTCTACCATTTGTTTGCCCATCAG
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * ** * * *
364844 CTTTGACTCGAGAGACT-TTTTCACTTTTTCTCTGCTCGTCAG
1 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGCCCATCAG
* * * * *
364886 CTTTGACTCAAGAGACT-GTTTCACCCATTGTCTACCCATCAG
1 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGCCCATCAG
* ** * * * * * *
364928 CTTTTACTTGGGAGACT-TTTTCACCCTTTTTTTGCTCATCAA
1 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGCCCATCAG
* * * *
364970 CTTTGACTCGAGAGACTCCTTCACCTTTTGTTTGCCCATCAG
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * *
365012 CTTTGACCTG-G-GACATCCCTTTACCC--T-TCTACCC-TCAT
1 CTTTGACCCGAGAGAC-T-CCTTTACCCTTTGTCTGCCCATCAG
* * * *
365050 CTTTAACCCGAGAGACT-TTTTCACCATTTATCTGCCCATC-G
1 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGCCCATCAG
* ** * ** *
365091 ATTTTGACCC-AGGAGACTCCTTCCCCCTTTGTCTGTCGGTCAA
1 -CTTTGACCCGA-GAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * * * * *
365134 CTTTGA-CCTAGGAGACTCCTTTATCATCTGTCTTCCTAT-TG
1 CTTTGACCCGA-GAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * ** * * **
365175 ACTTTGACTCGAGAGACT-ATTTCACCCAATATCTACTCC-TTGG
1 -CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGC-CCATCAG
** * * *
365218 CTTTGACTTGGGAGA-TTCTTTCACCCTTCT-TTTGCCCATCAG
1 CTTTGACCCGAGAGACTCCTTT-ACCCTT-TGTCTGCCCATCAG
* * * * * *
365260 CTTTGACCAGAGAGGCTCCTTCACCCTTTATTTGCCCGTCAG
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* *
365302 CTTTGA-CCTAGAAGA-T-CTTGTCACCC--T-TCTGCCCATTAG
1 CTTTGACCCGAG-AGACTCCTT-T-ACCCTTTGTCTGCCCATCAG
* * * * * *
365341 CTTTGACCAGGGAGACTCCTTCACCCTTTGTCT-ACTAGT-TG
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCA-TCAG
* * * * * * **
365382 ACTTTGACTCGGGAGACTTCTTCACTCTTTGTTTGCCTGTCAG
1 -CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * * * ** *
365425 CTTTGACCCAAGAGACTCCTCTACACTTTGTTTACCTGTCGG
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
** * *
365467 CTTTGACCTAAGGGACT-CTTT-CTCCTTTTGTCTGCCCGTC-G
1 CTTTGACCCGAGAGACTCCTTTAC-CC-TTTGTCTGCCCATCAG
* ** ** * * * *
365508 ACATTGAATCGAGAGA-TTTTGTTATCTTTTTTTTGTCCC-TC-G
1 -CTTTGACCCGAGAGACTCCT-TTACCCTTTGTCTG-CCCATCAG
* *
365550 ACTTTTACCCGAGAGACTACTTTACCCTTTGTCTGCCCATCAG
1 -CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * * ** * *
365593 CTTTGACCCGAGAGAGTCTTTTACCTTTTGTTTGCCTGTTAA
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * * * *
365635 CTTTGACCCGAAAGACT-ATTTCACCCATTGTTTACCCCTC-G
1 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTGCCCATCAG
** * * * * *
365676 ACTTTGACTTGGGAGACTCCTTTACCCTTTTTTTTACCCGTCAG
1 -CTTTGACCCGAGAGACTCCTTTACCC-TTTGTCTGCCCATCAG
* * * * *
365720 CTTTGA--CGTAGGAGACTCCTTCACCCTTTGTTTACGCGTCAG
1 CTTTGACCCG-A-GAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * *
365762 CTTTGACCTAGAAAAAC-CCTTTACCC-TT-T-TGCCCGTC-G
1 CTTTGACC-CGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
* * * * **** * *
365800 ACTTTGACCTGGGAAACTCCTTCACCCTTTGTCTGTTGGTTAA
1 -CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
** *
365843 CTTTGATTCGAGAGACTCCTTCACCCTTTGTCTGCC
1 CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCC
365879 TGTCGACTTC
Statistics
Matches: 755, Mismatches: 215, Indels: 130
0.69 0.20 0.12
Matches are distributed among these distances:
37 3 0.00
38 20 0.03
39 51 0.07
40 19 0.03
41 47 0.06
42 550 0.73
43 62 0.08
44 2 0.00
45 1 0.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (42 bp):
CTTTGACCCGAGAGACTCCTTTACCCTTTGTCTGCCCATCAG
Found at i:366432 original size:13 final size:13
Alignment explanation
Indices: 366414--366439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
366404 CATTATTCAA
366414 TGTATCGATACAT
1 TGTATCGATACAT
366427 TGTATCGATACAT
1 TGTATCGATACAT
366440 CTAGGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:369232 original size:22 final size:22
Alignment explanation
Indices: 369207--369251 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
369197 TCTCTCTGGG
369207 TGCATATGAGATTAAAATTTTA
1 TGCATATGAGATTAAAATTTTA
369229 TGCATATGAGATTAAAATTTTA
1 TGCATATGAGATTAAAATTTTA
369251 T
1 T
369252 CAAAACCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TGCATATGAGATTAAAATTTTA
Found at i:380252 original size:16 final size:16
Alignment explanation
Indices: 380193--380244 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
380183 CGTCCTTTGC
380193 AAAAAAAAAG--AAA-
1 AAAAAAAAAGAAAAAT
* *
380206 AAAAAAAGATAAAAAT
1 AAAAAAAAAGAAAAAT
*
380222 AAAAAAAAATAAAAAT
1 AAAAAAAAAGAAAAAT
380238 AAAAAAA
1 AAAAAAA
380245 CAGCAAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 8 0.24
15 3 0.09
16 22 0.67
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAT
Found at i:380253 original size:1 final size:1
Alignment explanation
Indices: 380193--380244 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
380183 CGTCCTTTGC
* * * * * *
380193 AAAAAAAAAGAAAAAAAAAAGATAAAAATAAAAAAAAATAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
380245 CAGCAAAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (1 bp):
A
Found at i:381318 original size:37 final size:37
Alignment explanation
Indices: 381277--381405 Score: 244
Period size: 37 Copynumber: 3.5 Consensus size: 37
381267 TGCCACAATC
381277 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
381314 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
381351 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
381388 ATGCATTTGTG-C-TTCATA
1 ATGCATTTGTGACATTCATA
381406 TTTTCTTTGG
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.07
36 1 0.01
37 85 0.92
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:381805 original size:29 final size:29
Alignment explanation
Indices: 381763--382335 Score: 675
Period size: 29 Copynumber: 20.1 Consensus size: 29
381753 CCTCACCTTC
* *
381763 CAAAA-CCCATAAGTTAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
381791 CAAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* *
381820 C-AAAGCCCACAAGTCAGTGGCAAC-CTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
*
381847 CAAAAGCCCATAAGTCAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* *
381876 CAAAAGCCCACAAGTCAGTGGCACCCTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
*
381905 CAAAAGCCCACAAGTCAGTGGCACCCTTTT
1 CAAAAGCCCACAAGTCAGTGGCA-TCTTTT
*
381935 -TAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
381963 CAAAAGCCCACAAGTCATTGGCAAC-CTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* *
381991 CAAAAGCCCACAAGTTAGTGGCACCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
382020 C-AAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
382048 CAAAAGCCCACAAGTTAGTGGCAAC-CTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
382076 CAAAAGTCCACAAGTTAGTGGCACCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* *
382105 C-AAAGTCCACAAGTCAGTAGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
382133 CAAAAGCCCACAATTTAGTGGCACCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
** *
382162 C-AAAGCGGACAAGTCAGTGGAATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * * *
382190 TAAAAGCGCACAAGTCAGTGGGATATTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
382219 CAAAAGCCCACAAGTCAATGGCAAC-CTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
*
382247 C-AAAGCTCACAAGTCAGTGGCATCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* * * *
382275 CAAAAGCCCACAAGTTAGTGACAAC-CTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
* *
382303 CAAAAGCCCACAAGTTAGTGGCACCTTTT
1 CAAAAGCCCACAAGTCAGTGGCATCTTTT
382332 CAAA
1 CAAA
382336 GCTGACAAGT
Statistics
Matches: 466, Mismatches: 66, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
27 23 0.05
28 205 0.44
29 233 0.50
30 5 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (29 bp):
CAAAAGCCCACAAGTCAGTGGCATCTTTT
Found at i:381867 original size:85 final size:84
Alignment explanation
Indices: 381757--382371 Score: 652
Period size: 85 Copynumber: 7.2 Consensus size: 84
381747 GACATTCCTC
* * *
381757 ACCTTCCAAAA-CCCATAAGTTAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTC
1 ACCTT-CAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-TTTC
381821 AAAGCCCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
* *
381842 ACCTTCAAAAGCCCATAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACTTTC-
381907 AAAGCCCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
* ** * *
381928 CCCTTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCATTGGCAACCTTCA
1 ACC-TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACTTTC-
*
381993 AAAGCCCACAAGTTAGTGGC-
64 AAAGCCCACAAGTCAGTGGCA
* *
382013 ACCTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTC
1 ACC--TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACTTTC
* *
382077 AAAAGTCCACAAGTTAGTGGC-
64 -AAAGCCCACAAGTCAGTGGCA
* * * * *
382098 ACCTTTTC-AAAGTCCACAAGTCAGTAGCATCTTTTCAAAAGCCCACAATTTAGTGGCACCTTTT
1 ACC--TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-TTT
**
382162 CAAAGCGGACAAGTCAGTGG-A
63 CAAAGCCCACAAGTCAGTGGCA
* * * * * * *
382183 ATCTTTTTAAAAGCGCACAAGTCAGTGGGATATTTTCAAAAGCCCACAAGTCAATGGCAACCTTC
1 A-C-CTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACTTTC
*
382248 AAAGCTCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
* * * * * * * *
382269 TCTTTTCAAAAGCCCACAAGTTAGTGACAAC-CTTCAAAAGCCCACAAGTTAGTGGCACCTTTTC
1 AC-CTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-TTTC
** * *
382333 AAAGCTGACAAGTTAATGGCA
64 AAAGCCCACAAGTCAGTGGCA
382354 ACCTTC-AAAGCCCACAAG
1 ACCTTCAAAAGCCCACAAG
382372 GTAGTGGAAA
Statistics
Matches: 462, Mismatches: 56, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
83 12 0.03
84 32 0.07
85 269 0.58
86 99 0.21
87 50 0.11
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (84 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACTTTCAA
AGCCCACAAGTCAGTGGCA
Found at i:382411 original size:56 final size:54
Alignment explanation
Indices: 381789--382428 Score: 289
Period size: 57 Copynumber: 11.3 Consensus size: 54
381779 GTGGCATCTT
* * * * *
381789 TTCAAAAGCCCACAA-GTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGGT-AGTGG-AACCTTTAAAAGCTCACAAGTTAGT-GCAACC
* * * * * *
381845 TTCAAAAGCCCATAA-GTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACCC
1 TTCAAAAGCCCACAAGGT-AGTGG-AACCTTT-AAAAGCTCACAAGTTAGT-GCAACC
* * * * * *
381902 TTTCAAAAGCCCACAA-GTCAGTGGCACCCTTTTTAAAGCCCACAAGTCAGTGGCATCTT
1 -TTCAAAAGCCCACAAGGT-AGTGG-AACC-TTTAAAAGCTCACAAGTTAGT-GCAAC-C
* * *
381961 TTCAAAAGCCCACAA-GTCATTGGCAACCTTCAAAAGCCCACAAGTTAGTGGC-ACC
1 TTCAAAAGCCCACAAGGT-AGTGG-AACCTTTAAAAGCTCACAAGTTAGT-GCAACC
* * *
382016 TTTTC-AAAGCCCACAA-GTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCAACC
1 --TTCAAAAGCCCACAAGGT-AGTGG-AACCTTT-AAAAGCTCACAAGTTAGT-GCAACC
* * * * * * *
382074 TTCAAAAGTCCACAAGTTAGTGGCACCTTTTCAAAG-TCCACAAGTCAGTAGCATCTT
1 TTCAAAAGCCCACAAGGTAGTGGAACC-TTTAAAAGCT-CACAAGTTAGT-GCAAC-C
** * * ** * * *
382131 TTCAAAAGCCCACAATTTAGTGGCACCTTTTCAAAGCGGACAAGTCAGTGGAATCTT
1 TTCAAAAGCCCACAAGGTAGTGGAACC-TTTAAAAGCTCACAAGTTAGTGCAA-C-C
* * * * * *
382188 TTTAAAAGCGCACAA-GTCAGTGGGATA-TTTTCAAAAGCCCACAAGTCAATGGCAACC
1 TTCAAAAGCCCACAAGGT-AGT-GGA-ACCTTT-AAAAGCTCACAAGTTAGT-GCAACC
* * * *
382245 TTC-AAAGCTCACAA-GTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGACAACC
1 TTCAAAAGCCCACAAGGT-AGTGG-AACCTTT-AAAAGCTCACAAGTTAGTG-CAACC
* * * * *
382301 TTCAAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCTGACAAGTTAATGGCAACC
1 TTCAAAAGCCCACAAGGTAGTGGAACC-TTTAAAAGCTCACAAGTTAGT-GCAACC
*
382357 TTC-AAAGCCCACAAGGTAGTGGAAACCTTTAAAAGCATACACAAGTTGGTGCAACCC
1 TTCAAAAGCCCACAAGGTAGTGG-AACCTTTAAAAGC-T-CACAAGTTAGTGCAA-CC
382414 TTTCAAAAGCCCACA
1 -TTCAAAAGCCCACA
382429 TAAGTTGGTG
Statistics
Matches: 483, Mismatches: 68, Indels: 63
0.79 0.11 0.10
Matches are distributed among these distances:
55 29 0.06
56 156 0.32
57 183 0.38
58 98 0.20
59 17 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (54 bp):
TTCAAAAGCCCACAAGGTAGTGGAACCTTTAAAAGCTCACAAGTTAGTGCAACC
Found at i:382511 original size:43 final size:43
Alignment explanation
Indices: 382450--382585 Score: 155
Period size: 49 Copynumber: 3.0 Consensus size: 43
382440 CATCTTCTTC
* * *
382450 TAAGTCTAATATCGCTGGCCTTAAATCAGCATATTAGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * *
382493 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
*
382542 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGGACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
382585 T
1 T
382586 GTCATCTTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
43 37 0.48
45 1 0.01
47 1 0.01
49 38 0.49
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:382562 original size:49 final size:49
Alignment explanation
Indices: 382445--382789 Score: 265
Period size: 52 Copynumber: 7.0 Consensus size: 49
382435 GGTGGCATCT
* * * *
382445 TCTTCTAAGTCTAATATCGCTGGCCTTAAATCAGCATATTAGCA----C-
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
382490 -CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
382538 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGGACCTTTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
* * * *
382590 TCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTAGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
382639 CCTTTAAATCCAAAATCACTGGCCTTGAATCAGCACATTAGCATTCTCCTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--C-CTTCA
* * * * * * **
382691 CCTTCAAGTCTAATGTCGCTGACCATGAATCAGCACATTGATAG-ATTTTACA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG---GCACCTT-CA
* * *
382743 TCTTTAAGCCCAATATCACTGGTCC-TGAATCAGCATATTGGCACCTT
1 TCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCACCTT
382790 TATCACTCTT
Statistics
Matches: 236, Mismatches: 46, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
43 33 0.14
44 3 0.01
47 1 0.00
49 80 0.34
50 4 0.02
51 3 0.01
52 108 0.46
53 2 0.01
54 1 0.00
55 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:382613 original size:52 final size:51
Alignment explanation
Indices: 382490--382799 Score: 270
Period size: 52 Copynumber: 6.1 Consensus size: 51
382480 ATATTAGCAC
* *
382490 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC--TTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* *
382539 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGGACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-TCAT
* * * * *
382591 CTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTAGCACC--TTCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * * * * ** *
382640 CTTTAAATCCAAAATCACTGGCCTTGAATCAGCACATTAGCATTCTCCTCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTTTTCAT
* * * * * ** **
382692 CTTCAAGTCTAATGTCGCTGACCATGAATCAGCACATTGATAGATTTTACAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CAT
* * *
382744 CTTTAAGCCCAATATCACTGGTCC-TGAATCAGCATATTGGCACCTTTATCACT
1 CTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCACCTTT-TCA-T
382797 CTT
1 CTT
382800 CTCATCTTCA
Statistics
Matches: 205, Mismatches: 46, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
49 79 0.39
50 2 0.01
51 3 0.01
52 114 0.56
53 7 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (51 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
Found at i:382700 original size:101 final size:101
Alignment explanation
Indices: 382487--382729 Score: 310
Period size: 101 Copynumber: 2.4 Consensus size: 101
382477 AGCATATTAG
* * * * * *
382487 CACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAATCCAAA
* * * * *
382552 ATCGCTGGCCTTGAATCAGCATATTGGGACCTTTGT
66 ATCACTGGCCTTGAATCAGCACATTGAGACATTTCT
* *
382588 CATCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTAGCACCTTCACCTTTAAATCCAAA
1 CACCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAATCCAAA
382653 ATCACTGGCCTTGAATCAGCACATT-AG-CATTCTCCT
66 ATCACTGGCCTTGAATCAGCACATTGAGACATT-T-CT
* * *
382689 CACCTTCAAGTCTAATGTCGCTGACCATGAATCAGCACATT
1 CACCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATT
382730 GATAGATTTT
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 3 0.02
100 2 0.02
101 117 0.96
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (101 bp):
CACCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAATCCAAA
ATCACTGGCCTTGAATCAGCACATTGAGACATTTCT
Found at i:382772 original size:153 final size:150
Alignment explanation
Indices: 382507--382789 Score: 327
Period size: 153 Copynumber: 1.9 Consensus size: 150
382497 TCCAATGTTG
* * * * * *
382507 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
1 CTGGCCTTGAATCAGCACATTAGCACCCTCACCTTCAAGTCCAATATCGCTGACCATGAATCAGC
* * * * * * * *
382572 ATATTGGGACCTTTGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATTAGCACATTAGCACCTT
66 ACATTGAGACATTTGTCATCTTTAAGCCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTT
382637 CACCTTTAAATCCAAAATCA
131 CACCTTTAAATCCAAAATCA
* *
382657 CTGGCCTTGAATCAGCACATTAGCATTCTCCTCACCTTCAAGTCTAATGTCGCTGACCATGAATC
1 CTGGCCTTGAATCAGCACATTAGCA--C-CCTCACCTTCAAGTCCAATATCGCTGACCATGAATC
* * * *
382722 AGCACATTGATAGATTT-TACATCTTTAAGCCCAATATCACTGGTCC-TGAATCAGCATATTGGC
63 AGCACATTGAGACATTTGT-CATCTTTAAGCCCAATATCACTGG-CCTTGAATCAGCACATTAGC
382785 ACCTT
126 ACCTT
382790 TATCACTCTT
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
150 24 0.22
152 2 0.02
153 80 0.74
154 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (150 bp):
CTGGCCTTGAATCAGCACATTAGCACCCTCACCTTCAAGTCCAATATCGCTGACCATGAATCAGC
ACATTGAGACATTTGTCATCTTTAAGCCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTT
CACCTTTAAATCCAAAATCA
Found at i:386477 original size:144 final size:144
Alignment explanation
Indices: 386252--386535 Score: 532
Period size: 144 Copynumber: 2.0 Consensus size: 144
386242 TCCGTGTTGG
* *
386252 TATCTCTCTAGTGCCTGATACGGACTACCCAATTTTAAAGTGAAATCCAGAGGCAACTTTATATC
1 TATCTCTCCAGTGCCTGATACGGAATACCCAATTTTAAAGTGAAATCCAGAGGCAACTTTATATC
386317 TCTATGTTTCCCATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGGATTTATTT
66 TCTATGTTTCCCATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGGATTTATTT
386382 TTATACAAAAATTT
131 TTATACAAAAATTT
386396 TATCTCTCCAGTGCCTGATACGGAATACCCAATTTTAAAGTGAAATCCAGAGGCAACTTTATATC
1 TATCTCTCCAGTGCCTGATACGGAATACCCAATTTTAAAGTGAAATCCAGAGGCAACTTTATATC
*
386461 TCTATGTTTCCTATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGGATTTATTT
66 TCTATGTTTCCCATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGGATTTATTT
*
386526 TTATATAAAA
131 TTATACAAAA
386536 TTCATGCATT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (144 bp):
TATCTCTCCAGTGCCTGATACGGAATACCCAATTTTAAAGTGAAATCCAGAGGCAACTTTATATC
TCTATGTTTCCCATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGGATTTATTT
TTATACAAAAATTT
Found at i:386529 original size:72 final size:72
Alignment explanation
Indices: 386309--386531 Score: 174
Period size: 72 Copynumber: 3.1 Consensus size: 72
386299 CAGAGGCAAC
*
386309 TTTATATCTCTATGTTTCCCATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGG
1 TTTATATCTCTATGTTTCCTATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGG
386374 ATTTATT
66 ATTTATT
** ** * * * *
386381 TTTATA-C-AAAAATTT--TATCTCTCC--AGTGCCTGAT-ACGGAATACCCAATTTTAAAGTGA
1 TTTATATCTCTATGTTTCCTATCTCTCCGGAGTGCAT-ATGA--GATTA--AAATTTT--A-TCA
* * *** **
386439 AATCC-AGAGGCAAC
58 AAACCTGGATTTATT
386453 TTTATATCTCTATGTTTCCTATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGG
1 TTTATATCTCTATGTTTCCTATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGG
386518 ATTTATT
66 ATTTATT
386525 TTTATAT
1 TTTATAT
386532 AAAATTCATG
Statistics
Matches: 104, Mismatches: 31, Indels: 32
0.62 0.19 0.19
Matches are distributed among these distances:
66 7 0.07
67 2 0.02
68 12 0.12
70 10 0.10
71 7 0.07
72 27 0.26
73 7 0.07
74 10 0.10
76 13 0.12
77 2 0.02
78 7 0.07
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (72 bp):
TTTATATCTCTATGTTTCCTATCTCTCCGGAGTGCATATGAGATTAAAATTTTATCAAAACCTGG
ATTTATT
Found at i:387282 original size:42 final size:42
Alignment explanation
Indices: 387202--390119 Score: 338
Period size: 42 Copynumber: 69.9 Consensus size: 42
387192 TTTGATCTAA
* * * * *
387202 GAGACTCCTTCACCCTTTTTTCTGCCGATCAACTTTGACTTGG
1 GAGACTCTTTCA-CCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
387245 GAGACTTTTTTACCATTTGTCTACCCATCAGCTTTGACTCGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * ** ** *
387287 AAGACTTTTTAACC-TTTAATCTGCCTGTCAGCTTTGACCCGA
1 GAGACTCTTTCACCATTT-GTCTGCCCATCAGCTTTGACTTGG
* * * * *
387329 AAGACTGTTTCACCCA-TTATCTTCCCATCAGCTTTGACTTAG
1 GAGACTCTTTCA-CCATTTGTCTGCCCATCAGCTTTGACTTGG
* * ** * * **
387371 GAGACTCTTTCACCCTTT-TTTGGCCTGTCAACTTTGACCTAA
1 GAGACTCTTTCACCATTTGTCT-GCCCATCAGCTTTGACTTGG
* * * *
387413 GAGACTCTTTCACCTTTTGTTTGCCCATTAGCTTTGACTTAG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * *
387455 GAGA-TCCCTTCACC-TTT-T-TACCC-TCGGTTTTGACCTGA
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
387493 GAGACTCTTTTACCCA-TTGTCTTCCCATCGGCTTTGACCTCG
1 GAGACTCTTTCA-CCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
387535 GAGACTCCTTCACCCTTTGTCTG-CTAGTCAACTTTGACTTAG
1 GAGACTCTTTCACCATTTGTCTGCCCA-TCAGCTTTGACTTGG
* * * * *
387577 GAGACTCTTTTACCATTTGTCTACCTATC-GACTTTGA-TCCGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACT-TGG
* * *
387619 GAGACT-TTTCACCCTTTGTTTGCCCATCAACTTTGACTTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * *
387660 GAGACTATTTCACCCA-TTGTTTGCTCGTCAGCTTTGACTTGG
1 GAGACTCTTTCA-CCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * ** * * ***
387702 GAGACTCTTTCACCCTTTTTTTGCCTGTCAACTTTAACTCAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * *
387744 GAGACTCTTTCACCCTTTGTTTACCCATCAGCTTTGACTTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* ** * **
387786 GAGA-TCCCTTCA-C-TTT-TCTGCCTGTTAGCTTTGACCAGG
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
387825 GAGACTCCTTCACCCTTTGTCTGCCCACCAGCTTTGACCTAG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * *
387867 GAGACCCTTTCACC-CTT-T-TGCCCTTC-GAATTTGACTTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * * * ***
387906 GAGACCCCTTCACC-TTT-T-TGCTCATTAGTTTTGACCCAG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * *
387945 AAGACTCCTTCACCCTTTGTCTGCCCGTC-GACTTTGGCCTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * ** * * * ****
387987 AAGATTCCATCACCCTTTGTCTGCCCATCAGATTTGGCCCAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * ****
388029 GAGACTTTTTTACTC-TTTATCTACCCATCAACTTTAACCCAA
1 GAGACTCTTTCAC-CATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * ** *
388071 GAGATTTTTTTACCTTTTATTTGCCCATTGGCTTTGA-TCTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACT-TGG
* * * * * ****
388113 AAGACTCTTGAAAGACTTCTCTACCTTTTGTCTACCCGTCAG-TTTCAACCCAA
1 GAGA--C-T------CTT-TC-ACCATTTGTCTGCCCATCAGCTTT-GACTTGG
* * * ** * **
388166 GAAACTCCTTCACCTTTTGT-TGCCCATGGGCTTTGACCTAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * ** ** * **
388207 AAGACTCTTTTC-CCCTTTTTCTACCTGTTGGCTTTAACTTCA
1 GAGACTC-TTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * * *
388249 GAGAGTTTTTCACCCTTTGTCAGCTCGTCAACTTTGACTTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * ** ***
388291 GAGACTCTTTTACCCTTTGCCTACTCATTGGCTTTGACTCAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
388333 GAGACT-TCTTCACCATTTGTTTGCTCGTCCA-CTTTGACCTGA
1 GAGACTCT-TTCACCATTTGTCTGCCCAT-CAGCTTTGACTTGG
* * * ** *
388375 GAGACTCCTTT-ACCTTTTGTTTGCCCATTAAATTTGACCTGG
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * ***
388417 GAGACTCCATT-ATC-TTTGGTCTGCTCTTC-GATTTTGACTCAT
1 GAGACT-CTTTCACCATTT-GTCTGCCCATCAG-CTTTGACTTGG
* * * * * * ***
388459 GAGGCTCTTTTACCTTTTGTTTGCCCGTCAACTTTGA-TCAAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACT-TGG
* * *** **
388501 GAGACTCTTTCACCCTTTGTCTACTGGTC-GACTTTGACCCGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * * * *
388543 GAGACTC-CTCTACCATTTGTTTACCCGTC-GAC-TTGAATTAG
1 GAGACTCTTTC-ACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * ** * * * * *
388584 AAGACTCTTTCACCCTTAATTTTCCAATCAGCTTTAACTCGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * *
388626 GATATTGTTTCACCCATTAT-T-TGCCCATC-GACTTTGACTTTG
1 GAGACTCTTTCA-CCATT-TGTCTGCCCATCAG-CTTTGACTTGG
* * * * *** * * *
388668 GAGACGTCTTT-ACCGTTTTTTTACTTGTCAACTTTGACCTGA
1 GAGAC-TCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
388710 GAGACTCCTTCACCCTTTGTTTGCCCATCAGCTTTGACCTAG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * ****
388752 GAGA-TCCCTTCACC-TTT-T-TGCCC-TCAACTTTAACCCAA
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * *
388790 GAGACTCTTTTACCCTTTGTCTTCCCATC-GATTTTGACCCT-A
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGA-CTTGG
* * ** * * ** * *
388832 AAGACTCTTTTACCCCTTATTTGCTGGATGA-CTTTGACTTAG
1 GAGACTCTTTCACCATTTGTCTGC-CCATCAGCTTTGACTTGG
* * ****
388874 GAGACTC-TTCTACCATTTGTCTGCCCATCAACTTTAACACAA
1 GAGACTCTTTC-ACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
388916 GAGACTCTTTTACCCTTTTTCTGCCTATCAGCTTTGACCTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* **
388958 GAGACTGTTTCACCCA-TTGTCTGCCTGTCAGCTTTGACTTGG
1 GAGACTCTTTCA-CCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * ** *
389000 GAGACTCTTTCACCCTTTTTTTGCCCATCAGCTTTGACCCGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
389042 GAGACTCTTTCACCCTTTGTTTACCCGTCAGCTTTGACCTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * ***
389084 GAGA-TCTCTTCACC--TT-TCTGCTCATTAGCTTTGACTCAA
1 GAGACTCT-TTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * **
389123 GAAACTCCTTCACCCTTTGTCTACCCATCAGCTTTGACCTAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * *
389165 GAGACCCTTTCACCCTTT-T-T-CCCGTCAACTTTGACCTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * *
389204 GATACCCCTTT-ACC--TT-TCTGCCTATC-GATTTTGACCTAG
1 GAGA-CTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * * * *
389243 AAAACTCCTTCACCCTTTGTCTGCCCATC-GACTTT-AGCCTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGA-CTTGG
* * * * ** * *
389285 AAGACTCTATCACCCTTTGTCTGCCCATTAAATTTGTCTCGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* ** * * * *
389327 GAGACTCTTTTACTTTTTATCTGCCCATCAACTTTAACTTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * *
389369 GAGATTCCATT-ATCTTTTGTCTGCCCATCAGCTTCGACCTGA
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * *
389411 AAAACTCTTTCACCTTTTGTCT-ACCAGTCAGCTTTAAGTTGG
1 GAGACTCTTTCACCATTTGTCTGCCCA-TCAGCTTTGACTTGG
* * * * * ***
389453 AAGACTTCTTT-ACCCTTTGTCTGCCCGTC-GATTTTAACCCAG
1 GAGAC-TCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * * * ** ****
389495 GAAAATCCTTCACCTTTTG-CTGCCGATTGGCTTTGACCCAA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * ** ** * *
389536 GAGACTCTTTCCCCCTTTTTCTGCCTGTTGGCTTTGACTCGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * ** *
389578 GAGAGTTTTTCACCCTTTGT-TAGCTCATCGGCTTTGACCCGA
1 GAGACTCTTTCACCATTTGTCT-GCCCATCAGCTTTGACTTGG
* * * ** * *
389620 GAGACTCCTTT-ACCCTTTGTCTACTCATTGGGTTTGACTTGA
1 GAGACT-CTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * * **
389662 GAGACTTTTTCACCTTTTTTTTGCTCATTC-GCTTGGACCTAA
1 GAGACTCTTTCACCATTTGTCTGCCCA-TCAGCTTTGACTTGG
* * * *
389704 GAGACTCTTTTACCCTTTGTCTGCCCATC-GAATTTGACTTGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * * ** * * *
389746 GAGACTCCATT-ATC-TTTAGTCTACTC-TTTGACTTTAACTCGA
1 GAGACT-CTTTCACCATTT-GTCTGCCCATCAG-CTTTGACTTGG
* * * ** * ***
389788 GATACTTTTTCACCTTTTGTCTGCTTAT-TGTCTTTGAC-CCC
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* * * **
389829 GAGACTCTTTCACCATTTGTCTACCCATTAACTTTGACCCGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * **
389871 GAGACCCCTTCACCCTTTTTTTGCCCATCAACTTTGACGAGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * ***
389913 GAGACTC-CTCGACCCTTTGTCTGCTTGTCAGCTTTGACTTGG
1 GAGACTCTTTC-ACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * * * *
389955 GGGACTCCTTCACCCTTTGTCTACCTATTAGCTTTGGCCTAG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * ** * *
389997 AAAAATCCTTCACCCCTTGTTTGCCCATCGGCTTTGACTTGG
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
* * * * * * * *
390039 GAGACTCTTTTACCCTTTATTTGCCCAAC-GAATTTGACTCGA
1 GAGACTCTTTCACCATTTGTCTGCCCATCAG-CTTTGACTTGG
* **
390081 GAGACTCTTTCACCCTTTGTCTGCCCATTGGCTTTGACT
1 GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACT
390120 CGAAAGACGT
Statistics
Matches: 2101, Mismatches: 635, Indels: 279
0.70 0.21 0.09
Matches are distributed among these distances:
37 3 0.00
38 44 0.02
39 160 0.08
40 26 0.01
41 243 0.12
42 1523 0.72
43 72 0.03
44 3 0.00
45 1 0.00
50 1 0.00
51 3 0.00
52 4 0.00
53 18 0.01
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (42 bp):
GAGACTCTTTCACCATTTGTCTGCCCATCAGCTTTGACTTGG
Found at i:387715 original size:331 final size:333
Alignment explanation
Indices: 387191--387884 Score: 857
Period size: 331 Copynumber: 2.1 Consensus size: 333
387181 TGTCCCTCGA
* * * * * *
387191 CTTTGATCTAAGAGACTCCTTCACCCTTTTTTCTGCCGATCAACTTTGACTTGGGAGACTTTTTT
1 CTTTGACCTAGGAGACTCCTTCACCC-TTTGTCTGCAGATCAACTTTGACTTAGGAGACTCTTTT
* ** *
387256 ACCATTTGTCTACCCATCAGCTTTGACTCGAAAGACTTTTTAACCTTTAATCTGCCTGTCAGCTT
65 ACCATTTGTCTACCCATCAGCTTTGACTCGAAAGACTTTTCAACCTTTAATCTGCCCATCAACTT
*
387321 TGACCCGAAAGACTGTTTCACCCATTATCTTCCCATCAGCTTTGACTTAGGAGACTCTTTCACCC
130 TGACCCGAAAGACTATTTCACCCATTATCTTCCCATCAGCTTTGACTTAGGAGACTCTTTCACCC
* * * *
387386 TTTTTTGGCCTGTCAACTTTGAC-CTAAGAGACTCTTTCACCTTTTGTTTGCCCATTAGCTTTGA
195 TTTTTTGGCCTGTCAACTTTAACTC-AAGAGACTCTTTCACCCTTTGTTTACCCATCAGCTTTGA
* * * * *
387450 CTTAGGAGATCCCTTCACCTTTT-TACC-CTCGGTTTTGACCTGAGAGACTCTTTTACCCATTGT
259 CTTAGGAGATCCCTTCA-CTTTTCTACCTCTCAGCTTTGACCAGAGAGACTCCTTCACCCATTGT
* * *
387513 CTTCCCATCGG
323 CTGCCCACCAG
*
387524 CTTTGACCTCGGAGACTCCTTCACCCTTTGTCTGCTAG-TCAACTTTGACTTAGGAGACTCTTTT
1 CTTTGACCTAGGAGACTCCTTCACCCTTTGTCTGC-AGATCAACTTTGACTTAGGAGACTCTTTT
* * * * *
387588 ACCATTTGTCTACCTATC-GACTTTGA-TCCGAGAGACTTTTCACCCTTT-GTTTGCCCATCAAC
65 ACCATTTGTCTACCCATCAG-CTTTGACT-CGAAAGACTTTTCAACCTTTAATCTGCCCATCAAC
** ** * * * *
387650 TTTGACTTGGGAGACTATTTCACCCATTGT-TTGCTCGTCAGCTTTGACTTGGGAGACTCTTTCA
128 TTTGACCCGAAAGACTATTTCACCCATTATCTT-CCCATCAGCTTTGACTTAGGAGACTCTTTCA
*
387714 CCCTTTTTTTGCCTGTCAACTTTAACTCAAGAGACTCTTTCACCCTTTGTTTACCCATCAGCTTT
192 CCCTTTTTTGGCCTGTCAACTTTAACTCAAGAGACTCTTTCACCCTTTGTTTACCCATCAGCTTT
* * * * * *
387779 GACTTGGGAGATCCCTTCACTTTTCTGCCTGTTAGCTTTGACCAGGGAGACTCCTTCACCCTTTG
257 GACTTAGGAGATCCCTTCACTTTTCTACCTCTCAGCTTTGACCAGAGAGACTCCTTCACCCATTG
387844 TCTGCCCACCAG
322 TCTGCCCACCAG
387856 CTTTGACCTAGGAGAC-CCTTTCACCCTTT
1 CTTTGACCTAGGAGACTCC-TTCACCCTTT
387885 TGCCCTTCGA
Statistics
Matches: 308, Mismatches: 45, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
330 7 0.02
331 144 0.47
332 133 0.43
333 24 0.08
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.37
Consensus pattern (333 bp):
CTTTGACCTAGGAGACTCCTTCACCCTTTGTCTGCAGATCAACTTTGACTTAGGAGACTCTTTTA
CCATTTGTCTACCCATCAGCTTTGACTCGAAAGACTTTTCAACCTTTAATCTGCCCATCAACTTT
GACCCGAAAGACTATTTCACCCATTATCTTCCCATCAGCTTTGACTTAGGAGACTCTTTCACCCT
TTTTTGGCCTGTCAACTTTAACTCAAGAGACTCTTTCACCCTTTGTTTACCCATCAGCTTTGACT
TAGGAGATCCCTTCACTTTTCTACCTCTCAGCTTTGACCAGAGAGACTCCTTCACCCATTGTCTG
CCCACCAG
Found at i:387939 original size:39 final size:39
Alignment explanation
Indices: 387768--387969 Score: 131
Period size: 39 Copynumber: 5.1 Consensus size: 39
387758 CTTTGTTTAC
* * *
387768 CCATCAGCTTTGACTTGGGAGATCCCTTCA-CTTTTCTG
1 CCATTAGCTTTGACCTGGGAGACCCCTTCACCTTTTCTG
* * *
387806 CCTGTTAGCTTTGACCAGGGAGACTCCTTCACCCTTTGTCTG
1 CC-ATTAGCTTTGACCTGGGAGACCCCTTCA-CCTTT-TCTG
** * * *
387848 CCCACCAGCTTTGACCTAGGAGACCCTTTCACCCTTT-TG
1 -CCATTAGCTTTGACCTGGGAGACCCCTTCACCTTTTCTG
* * * *
387887 CCCTTCGAATTTGACTTGGGAGACCCCTTCACCTTTT-TG
1 CCATTAG-CTTTGACCTGGGAGACCCCTTCACCTTTTCTG
* ** * *
387926 CTCATTAGTTTTGACCCAGAAGACTCCTTCACCCTTTGTCTG
1 C-CATTAGCTTTGACCTGGGAGACCCCTTCA-CCTTT-TCTG
387968 CC
1 CC
387970 CGTCGACTTT
Statistics
Matches: 123, Mismatches: 31, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
38 5 0.04
39 68 0.55
40 10 0.08
41 10 0.08
42 28 0.23
43 2 0.02
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (39 bp):
CCATTAGCTTTGACCTGGGAGACCCCTTCACCTTTTCTG
Found at i:389298 original size:120 final size:121
Alignment explanation
Indices: 389003--389302 Score: 335
Period size: 120 Copynumber: 2.5 Consensus size: 121
388993 GACTTGGGAG
* * * * *
389003 ACTCTTTCACCCTTTTTTTGCCCATCAGCTTTGACCCGAGAGACTCTTTCACCCTTTGTTTACCC
1 ACTCCTTCACCCTTTGTCTGCCCATCAGCTTTGACCTGAAAGACTCTTTCACCC-TT-TTTACCC
* * * *
389068 GTCAGCTTTGACCTGGGAGATCTCTTCACCTTTCTGCTCATTAGCTTTGACTCAAGAA
64 GTCAACTTTGACCTGGGAGACCCCTTCACCTTTCTGCTCATGAGCTTTGACTCAAGAA
* *
389126 ACTCCTTCACCCTTTGTCTACCCATCAGCTTTGACCT-AAGAGACCCTTTCACCCTTTTT-CCCG
1 ACTCCTTCACCCTTTGTCTGCCCATCAGCTTTGACCTGAA-AGACTCTTTCACCCTTTTTACCCG
* * * *
389189 TCAACTTTGACCTGGGATACCCCTTTACCTTTCTGC-CTATCGA-TTTTGAC-CTAGAAA
65 TCAACTTTGACCTGGGAGACCCCTTCACCTTTCTGCTC-AT-GAGCTTTGACTCAAG-AA
*
389246 ACTCCTTCACCCTTTGTCTGCCCATC-GACTTT-AGCCTGAAAGACTCTATCACCCTTT
1 ACTCCTTCACCCTTTGTCTGCCCATCAG-CTTTGA-CCTGAAAGACTCTTTCACCCTTT
389303 GTCTGCCCAT
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
119 6 0.04
120 92 0.61
121 6 0.04
122 3 0.02
123 45 0.30
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (121 bp):
ACTCCTTCACCCTTTGTCTGCCCATCAGCTTTGACCTGAAAGACTCTTTCACCCTTTTTACCCGT
CAACTTTGACCTGGGAGACCCCTTCACCTTTCTGCTCATGAGCTTTGACTCAAGAA
Found at i:390120 original size:42 final size:42
Alignment explanation
Indices: 388699--390127 Score: 494
Period size: 42 Copynumber: 34.4 Consensus size: 42
388689 TACTTGTCAA
* *
388699 CTTTGAC-CTGAGAGACTCCTTCACCCTTTGTTTGCCCATCAG
1 CTTTGACTC-GAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * *
388741 CTTTGAC-CTAGGAGA-TCCCTTCA-CCTTT-T-TGCCC-TCAA
1 CTTTGACTCGA-GAGACT-CTTTCACCCTTTGTCTGCCCATCAG
* * * * *
388779 CTTTAACCCAAGAGACTCTTTTACCCTTTGTCTTCCCATC-G
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * * * * ** *
388820 ATTTTGACCCTAAAGACTCTTTTACCCCTTATTTGCTGGATGA-
1 -CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGC-CCATCAG
* * *
388863 CTTTGACT-TAGGAGACTC-TTCTACCATTTGTCTGCCCATCAA
1 CTTTGACTCGA-GAGACTCTTTC-ACCCTTTGTCTGCCCATCAG
* * * * * *
388905 CTTTAACACAAGAGACTCTTTTACCCTTTTTCTGCCTATCAG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * **
388947 CTTTGAC-CTGGGAGACTGTTTCACCCATTGTCTGCCTGTCAG
1 CTTTGACTC-GAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
388989 CTTTGACTTGGGAGACTCTTTCACCCTTTTTTTGCCCATCAG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
389031 CTTTGACCCGAGAGACTCTTTCACCCTTTGTTTACCCGTCAG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * *
389073 CTTTGAC-CTGGGAGA-TCTCTTCA-CC-TT-TCTGCTCATTAG
1 CTTTGACTC-GAGAGACTCT-TTCACCCTTTGTCTGCCCATCAG
* * * *
389112 CTTTGACTCAAGAAACTCCTTCACCCTTTGTCTACCCATCAG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
389154 CTTTGAC-CTAAGAGACCCTTTCACCCTTT-T-T-CCCGTCAA
1 CTTTGACTC-GAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
389193 CTTTGAC-CTGGGATACCCCTTT-A-CC-TT-TCTGCCTATC-G
1 CTTTGACTC-GAGAGA-CTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
389231 ATTTTGAC-CTAGAAAACTCCTTCACCCTTTGTCTGCCCATC-G
1 -CTTTGACTCGAG-AGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * *
389273 ACTTTAGCCT-GAAAGACTCTATCACCCTTTGTCTGCCCATTAA
1 -CTTT-GACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * ** * *
389316 ATTTGTCTCGGGAGACTCTTTTACTTTTTATCTGCCCATCAA
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * *
389358 CTTTAACTTGAGAGATTCCATT-ATCTTTTGTCTGCCCATCAG
1 CTTTGACTCGAGAGACT-CTTTCACCCTTTGTCTGCCCATCAG
* * * * *
389400 CTTCGAC-CTGAAAAACTCTTTCACCTTTTGTCT-ACCAGTCAG
1 CTTTGACTC-GAGAGACTCTTTCACCCTTTGTCTGCCCA-TCAG
* * * *
389442 CTTTAAGTTG-GAAGACTTCTTT-ACCCTTTGTCTGCCCGTC-G
1 CTTTGACTCGAG-AGAC-TCTTTCACCCTTTGTCTGCCCATCAG
* * * * * * * * **
389483 ATTTTAAC-CCAGGAAAATCCTTCACCTTTTG-CTGCCGATTGG
1 -CTTTGACTCGA-GAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * ** **
389525 CTTTGACCCAAGAGACTCTTTCCCCCTTTTTCTGCCTGTTGG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * *
389567 CTTTGACTCGAGAGAGTTTTTCACCCTTTGT-TAGCTCATCGG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCT-GCCCATCAG
* * * **
389609 CTTTGACCCGAGAGACTCCTTT-ACCCTTTGTCTACTCATTGG
1 CTTTGACTCGAGAGACT-CTTTCACCCTTTGTCTGCCCATCAG
* * * * * * *
389651 GTTTGACTTGAGAGACTTTTTCACCTTTTTTTTGCTCATTC-G
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCA-TCAG
* * *
389693 CTTGGAC-CTAAGAGACTCTTTTACCCTTTGTCTGCCCATC-G
1 CTTTGACTC-GAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * * **
389734 AATTTGACTTGAGAGACTCCATT-A-TCTTTAGTCTACTC-TTTG
1 -CTTTGACTCGAGAGACT-CTTTCACCCTTT-GTCTGCCCATCAG
* * * * ** *
389776 ACTTTAACTCGAGATACTTTTTCACCTTTTGTCTGCTTAT-TG
1 -CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
** * * * *
389818 TCTTTGAC-CCCGAGACTCTTTCACCATTTGTCTACCCATTAA
1 -CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * * *
389860 CTTTGACCCGGGAGACCCCTTCACCCTTTTTTTGCCCATCAA
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
** * * ***
389902 CTTTGACGAGGGAGACTC-CTCGACCCTTTGTCTGCTTGTCAG
1 CTTTGACTCGAGAGACTCTTTC-ACCCTTTGTCTGCCCATCAG
* * * * * * *
389944 CTTTGACTTGGGGGACTCCTTCACCCTTTGTCTACCTATTAG
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * * * *
389986 CTTTGGC-CTAGAAAAATCCTTCACCCCTTGTTTGCCCATCGG
1 CTTTGACTCGAG-AGACTCTTTCACCCTTTGTCTGCCCATCAG
* * * * * *
390028 CTTTGACTTGGGAGACTCTTTTACCCTTTATTTGCCCAAC-G
1 CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
* **
390069 AATTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATTGG
1 -CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
*
390112 CTTTGACTCGAAAGAC
1 CTTTGACTCGAGAGAC
390128 GTTTTTGTGA
Statistics
Matches: 1025, Mismatches: 286, Indels: 152
0.70 0.20 0.10
Matches are distributed among these distances:
37 3 0.00
38 25 0.02
39 67 0.07
40 18 0.02
41 117 0.11
42 760 0.74
43 35 0.03
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (42 bp):
CTTTGACTCGAGAGACTCTTTCACCCTTTGTCTGCCCATCAG
Found at i:393972 original size:18 final size:18
Alignment explanation
Indices: 393938--393973 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
393928 TGATACCAAT
*
393938 TGATACCAATTGATGAAA
1 TGATACCAAATGATGAAA
*
393956 TGATACCAAATGTTGAAA
1 TGATACCAAATGATGAAA
393974 GATTAATGAC
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:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
TGATACCAAATGATGAAA
Found at i:395806 original size:21 final size:21
Alignment explanation
Indices: 395773--395824 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
395763 AGTTAATTCA
**
395773 TCATTTTCATTTTGTAACTCATT
1 TCATTTTC-TTTTCCAACTCA-T
395796 TC-TTTTCTTTTCCAACTCAT
1 TCATTTTCTTTTCCAACTCAT
395816 TCATTTTCT
1 TCATTTTCT
395825 CTTCTAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 5 0.19
23 2 0.08
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (21 bp):
TCATTTTCTTTTCCAACTCAT
Found at i:399329 original size:20 final size:20
Alignment explanation
Indices: 399304--399391 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
399294 ATTTACCTAC
*
399304 ATGTATCAATACATTGAATA
1 ATGTATCGATACATTGAATA
399324 ATGTATCGATACA-T---T-
1 ATGTATCGATACATTGAATA
*
399339 A--TATCGATATATTGAATA
1 ATGTATCGATACATTGAATA
399357 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
399377 ATGTATTGATACATT
1 ATGTATCGATACATT
399392 TCCTTGGCAG
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 42 0.74
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:399353 original size:33 final size:33
Alignment explanation
Indices: 399307--399371 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
399297 TACCTACATG
399307 TATCAATACATTGAATAATGTATCGATACATTA
1 TATCAATACATTGAATAATGTATCGATACATTA
* *
399340 TATCGATATATTGAATAATGTATCGATACATT
1 TATCAATACATTGAATAATGTATCGATACATT
399372 GAATAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (33 bp):
TATCAATACATTGAATAATGTATCGATACATTA
Found at i:401072 original size:36 final size:32
Alignment explanation
Indices: 400988--401082 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 32
400978 CCTTAAAACA
*
400988 CTATC-TTTCAAGGCTAAGATAGAAAC-TTCC
1 CTATCTTTTCAAGGCTAAGATAGAACCTTTCC
*
401018 CTATCTTTTCACGAGCTAAGATAGAACCTTTCTC
1 CTATCTTTTCAAG-GCTAAGATAGAACCTTTC-C
401052 CTTATCTTTTTCAAAGGCTAAGATAGAACCT
1 C-TATC-TTTTC-AAGGCTAAGATAGAACCT
401083 CACAATCACT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 13 0.24
33 3 0.05
34 2 0.04
35 4 0.07
36 20 0.36
37 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (32 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTTTCC
Found at i:401595 original size:24 final size:24
Alignment explanation
Indices: 401562--401607 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
401552 ACTATATCGA
*
401562 TACATGAACAATGATGAACAGTGC
1 TACATAAACAATGATGAACAGTGC
* *
401586 TACATAAACAGTTATGAACAGT
1 TACATAAACAATGATGAACAGT
401608 AATGTATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (24 bp):
TACATAAACAATGATGAACAGTGC
Found at i:413976 original size:44 final size:44
Alignment explanation
Indices: 413844--413994 Score: 127
Period size: 42 Copynumber: 3.5 Consensus size: 44
413834 AGTTTATCTC
*
413844 TTTTTCCTTTGTCTTCAAGGAGCAGGACCCATTTCA--TT-CTT
1 TTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTTTCCTT
* * * * * * * *
413885 TTCTTCCCATTGTGCTTAAGAAGCAGTACGCA-TTCTTTTTCTCTT
1 TT-TTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTTTC-CTT
* *
413930 TTTTTCCTTTGTCCTCGAGGAGTAGGACCCATTTCATTTTCC--
1 TTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTTTCCTT
*
413972 TTTTT-CTTTGTCCTCAAAGAGCA
1 TTTTTCCTTTGTCCTCAAGGAGCA
413995 AAACTCTCAC
Statistics
Matches: 82, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
41 20 0.24
42 26 0.32
43 2 0.02
44 21 0.26
45 13 0.16
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.44
Consensus pattern (44 bp):
TTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATTTTCCTT
Found at i:414378 original size:62 final size:62
Alignment explanation
Indices: 414100--414397 Score: 307
Period size: 62 Copynumber: 4.8 Consensus size: 62
414090 TAGAATGTCA
* * * *
414100 AAGCCCACATGAGTTGGTGGCACCCTAATCAAAGCCCGAACAAGTTGGCGACACTTGAGTCT
1 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGTTGGCGACACCTGAGTCT
** * * * *
414162 AAGCCTGCACGAGTTGTTGGCACCATAGTCGAAGCCCGCACAAGCTGGCGACACCTGAGTCT
1 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGTTGGCGACACCTGAGTCT
* * * * * * * *
414224 AAGCTCGA-ATGAGTTGGTGGTACCCTAGTCAAAGCCTGCATAAGCTAGCGGCACCTGAGTCT
1 AAGC-CCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGTTGGCGACACCTGAGTCT
** *
414286 AAGCCCGTACGAGTTGGTGGCA-CCTAAGTCAAAGCCCACACAAGTTGGC-AGCACCTGAGTCT
1 AAGCCCACACGAGTTGGTGGCACCCT-AGTCAAAGCCCGCACAAGTTGGCGA-CACCTGAGTCT
* * * *
414348 AAGCCCACACGAGTTGGCGGCA-CTTGAGTCAAAGCTCGCATAAGTTGGCG
1 AAGCCCACACGAGTTGGTGGCACCCT-AGTCAAAGCCCGCACAAGTTGGCG
414398 GTACTTTCTA
Statistics
Matches: 192, Mismatches: 39, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
61 4 0.02
62 187 0.97
63 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.19
Consensus pattern (62 bp):
AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGTTGGCGACACCTGAGTCT
Found at i:414398 original size:31 final size:31
Alignment explanation
Indices: 414096--414398 Score: 198
Period size: 31 Copynumber: 9.8 Consensus size: 31
414086 GCCTTAGAAT
* ** *
414096 GTCAAAGCCCACATGAGTTGGTGGCACCCT-A
1 GTCAAAGCCCGCACAAGTTGGCGGCA-CCTGA
* * * *
414127 ATCAAAGCCCGAACAAGTTGGCGACACTTGA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* * * **
414158 GTCTAAGCCTGCACGAGTTGTTGGCACCAT-A
1 GTCAAAGCCCGCACAAGTTGGCGGCACC-TGA
* * *
414189 GTCGAAGCCCGCACAAGCTGGCGACACCTGA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* * * ** * *
414220 GTCTAAGCTCGAATGAGTTGGTGGTACCCT-A
1 GTCAAAGCCCGCACAAGTTGGCGGCA-CCTGA
* * * *
414251 GTCAAAGCCTGCATAAGCTAGCGGCACCTGA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* * * * *
414282 GTCTAAGCCCGTACGAGTTGGTGGCACCTAA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* *
414313 GTCAAAGCCCACACAAGTTGGCAGCACCTGA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* * * *
414344 GTCTAAGCCCACACGAGTTGGCGGCACTTGA
1 GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
* *
414375 GTCAAAGCTCGCATAAGTTGGCGG
1 GTCAAAGCCCGCACAAGTTGGCGG
414399 TACTTTCTAG
Statistics
Matches: 200, Mismatches: 67, Indels: 10
0.72 0.24 0.04
Matches are distributed among these distances:
30 6 0.03
31 190 0.95
32 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.19
Consensus pattern (31 bp):
GTCAAAGCCCGCACAAGTTGGCGGCACCTGA
Found at i:414577 original size:63 final size:60
Alignment explanation
Indices: 414401--414657 Score: 279
Period size: 59 Copynumber: 4.2 Consensus size: 60
414391 GTTGGCGGTA
* **
414401 CTTTCTAGTCCTCAAAGAGCATGACACTTTCTTTTCAAAGCCCACACAAGTTAATGGCAC
1 CTTTCTAGTCCTCAAAGAGCAGGACACTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
414461 C-TTCTAGTCCTTAAAGAGTAGGATACTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
1 CTTTCTAGTCCTCAAAGAGCAGGACACTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
414520 CTTTC-AGTCCTCAAAGAGCTAGAGGACACTTTTCTTTTCAAAGCCCACACAAATTGGTAGCAT
1 CTTTCTAGTCCTCAAAGAGC---AGGACAC-TTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
*
414583 CTTT-TAGTCCTTAAAGAGCAGGACACTTTCTTTTTTTCTTTGAAAGCCCACACAAGTTGGTGGC
1 CTTTCTAGTCCTCAAAGAGCAGGACACTTTC---TTTTC----AAAGCCCACACAAGTTGGTGGC
414647 AC
59 AC
*
414649 ATTT-TAGTC
1 CTTTCTAGTC
414658 TTTATAGGGC
Statistics
Matches: 165, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
59 68 0.41
60 11 0.07
62 11 0.07
63 46 0.28
66 29 0.18
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (60 bp):
CTTTCTAGTCCTCAAAGAGCAGGACACTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:414592 original size:122 final size:119
Alignment explanation
Indices: 414401--414657 Score: 300
Period size: 122 Copynumber: 2.1 Consensus size: 119
414391 GTTGGCGGTA
* * *
414401 CTTTCTAGTCCTCAAAGAGCATGACACTTTCTTTTCAAAGCCCACACAAGTTAATGGCACCTTCT
1 CTTTC-AGTCCTCAAAGAGCAGGACACTTTCTTTTCAAAGCCCACACAAATTAATAGCACCTTCT
* *
414466 AGTCCTTAAAGAGTAGGATACTTTC-CTTTCAAAGCCCACACAAGTTGGTGGCAC
65 AGTCCTTAAAGAGCAGGACACTTTCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
** *
414520 CTTTCAGTCCTCAAAGAGCTAGAGGACACTTTTCTTTTCAAAGCCCACACAAATTGGTAGCATCT
1 CTTTCAGTCCTCAAAGAGC---AGGACAC-TTTCTTTTCAAAGCCCACACAAATTAATAGCACCT
* *
414585 TTTAGTCCTTAAAGAGCAGGACACTTTCTTTTTTTCTTTGAAAGCCCACACAAGTTGGTGGCAC
62 TCTAGTCCTTAAAGAGCAGGACACTTTC------TCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
414649 ATTTTAGTC
1 CTTTCAGTC
414658 TTTATAGGGC
Statistics
Matches: 115, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
118 14 0.12
119 5 0.04
121 6 0.05
122 55 0.48
129 35 0.30
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (119 bp):
CTTTCAGTCCTCAAAGAGCAGGACACTTTCTTTTCAAAGCCCACACAAATTAATAGCACCTTCTA
GTCCTTAAAGAGCAGGACACTTTCTCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:414926 original size:13 final size:13
Alignment explanation
Indices: 414908--414933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
414898 TACAAATAGT
414908 AAATGTATCGATA
1 AAATGTATCGATA
414921 AAATGTATCGATA
1 AAATGTATCGATA
414934 CAAAGCCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAATGTATCGATA
Found at i:418176 original size:13 final size:13
Alignment explanation
Indices: 418158--418183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
418148 CATTTTTTGG
418158 TGTATCGATACAT
1 TGTATCGATACAT
418171 TGTATCGATACAT
1 TGTATCGATACAT
418184 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:418195 original size:19 final size:19
Alignment explanation
Indices: 418138--418201 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
418128 TACAAGCTAA
*
418138 TGTATCGATACATTTTTTGG
1 TGTATCGATACATATTTT-G
418158 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
418171 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
418190 TGTATCGATACA
1 TGTATCGATACA
418202 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:418198 original size:32 final size:33
Alignment explanation
Indices: 418138--418201 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
418128 TACAAGCTAA
*
418138 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATATTTTGGTGTATCGATACAT
418171 TGTATCGATACATATTTT-GTGTATCGATACA
1 TGTATCGATACATATTTTGGTGTATCGATACA
418202 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATATTTTGGTGTATCGATACAT
Found at i:418278 original size:20 final size:20
Alignment explanation
Indices: 418232--418305 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
418222 ATCCCAATGA
***
418232 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
418253 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
418273 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
418293 TATGTATCGATAC
1 CATGTATCGATAC
418306 TTTAAGGGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:426917 original size:19 final size:20
Alignment explanation
Indices: 426874--426924 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
426864 TACAAGCTAA
**
426874 TGTATCGATACATTTTTTGG
1 TGTATCGATACATACTTTGG
426894 TGTATCGATACATACTTT-G
1 TGTATCGATACATACTTTGG
426913 TGTATCGATACA
1 TGTATCGATACA
426925 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATACTTTGG
Found at i:428086 original size:6 final size:6
Alignment explanation
Indices: 428075--428138 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
428065 TTTAAAATTG
428075 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
428123 TTATAT TTATAT TTAT
1 TTATAT TTATAT TTAT
428139 GCATGGAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:429692 original size:20 final size:20
Alignment explanation
Indices: 429661--429715 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
429651 CTGTCAGTTT
* *
429661 CATGTATTGATACAATTTAA
1 CATGTATCGATACAATTGAA
** *
429681 GGTGTATCGATACTA-TGAA
1 CATGTATCGATACAATTGAA
429700 CATGTATCGATACAAT
1 CATGTATCGATACAAT
429716 GTATCAATAC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:429743 original size:33 final size:32
Alignment explanation
Indices: 429683--429746 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
429673 CAATTTAAGG
* *
429683 TGTATCGATACTATGAACATGTATCGATACAA
1 TGTATCAATACTAAGAACATGTATCGATACAA
*
429715 TGTATCAATACTAAGCAATATGTATCGATACA
1 TGTATCAATACTAAG-AACATGTATCGATACA
429747 TCTGGGCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (32 bp):
TGTATCAATACTAAGAACATGTATCGATACAA
Found at i:429877 original size:22 final size:22
Alignment explanation
Indices: 429845--429925 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
429835 ACTTTGAATT
429845 ATTT-TTGCTTGAAAACATTTG
1 ATTTATTGCTTGAAAACATTTG
*
429866 ATTTATTGCTTGAAAAAAATTT-
1 ATTTATTGCTTG-AAAACATTTG
* *
429888 A--TACTTAACTTTAAAACATTTG
1 ATTTA-TT-GCTTGAAAACATTTG
*
429910 ATTTATTGCTTAAAAA
1 ATTTATTGCTTGAAAA
429926 ATATTTATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 19 0.40
23 10 0.21
24 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
ATTTATTGCTTGAAAACATTTG
Found at i:429887 original size:23 final size:21
Alignment explanation
Indices: 429845--429927 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
429835 ACTTTGAATT
*
429845 ATTTTTGCTTGAAAACATTTG
1 ATTTTTGCTTGAAAAAATTTG
429866 ATTTATTGCTTGAAAAAAATTT-
1 ATTT-TTGCTTG-AAAAAATTTG
* ** * *
429888 ATACTTAACTTTAAAACATTTG
1 AT-TTTTGCTTGAAAAAATTTG
429910 ATTTATTGCTT-AAAAAAT
1 ATTT-TTGCTTGAAAAAAT
429928 ATTTATACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
21 19 0.40
22 19 0.40
23 9 0.19
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (21 bp):
ATTTTTGCTTGAAAAAATTTG
Found at i:429908 original size:21 final size:21
Alignment explanation
Indices: 429879--429952 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 21
429869 TATTGCTTGA
*
429879 AAAAAATTTATACTTAACTTT
1 AAAACATTTATACTTAACTTT
* *
429900 AAAACATTTGAT--TTATTGCTTAA
1 AAAACATTT-ATACTTA--ACTT-T
* *
429923 AAAATATTTATACTTAACTCT
1 AAAACATTTATACTTAACTTT
429944 AAAACATTT
1 AAAACATTT
429953 TTGATATTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
20 3 0.08
21 16 0.41
22 9 0.23
23 8 0.21
24 3 0.08
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAACATTTATACTTAACTTT
Found at i:429919 original size:44 final size:44
Alignment explanation
Indices: 429856--429952 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
429846 TTTTTGCTTG
*
429856 AAAACATTTGATTTATTGCTTGAAAAAA-ATTTATACTTAACTTT
1 AAAACATTTGATTTATTGCTT-AAAAAATATTTATACTTAACTCT
429900 AAAACATTTGATTTATTGCTTAAAAAATATTTATACTTAACTCT
1 AAAACATTTGATTTATTGCTTAAAAAATATTTATACTTAACTCT
429944 AAAACATTT
1 AAAACATTT
429953 TTGATATTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 6 0.12
44 45 0.88
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (44 bp):
AAAACATTTGATTTATTGCTTAAAAAATATTTATACTTAACTCT
Found at i:430573 original size:43 final size:43
Alignment explanation
Indices: 430525--430653 Score: 190
Period size: 43 Copynumber: 3.0 Consensus size: 43
430515 AATAAAACTC
*
430525 ATATACTTCTCCCTTTTAATAAATTCTCCTATTTTTAAAGCTT
1 ATATACTTCTCCCTTTTAATAAATTCTCCCATTTTTAAAGCTT
* *
430568 ATATACTTCTTCCCTTTT-ATAAATTCTCCCCTTTTTAAAGCTC
1 ATATACTTC-TCCCTTTTAATAAATTCTCCCATTTTTAAAGCTT
*
430611 ATATACTTTTTCCC-TTTAATAAATTCTCCCATTTTTAAAGCTT
1 ATATAC-TTCTCCCTTTTAATAAATTCTCCCATTTTTAAAGCTT
430654 TAAAACAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
42 3 0.04
43 64 0.83
44 10 0.13
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.48
Consensus pattern (43 bp):
ATATACTTCTCCCTTTTAATAAATTCTCCCATTTTTAAAGCTT
Found at i:440814 original size:20 final size:19
Alignment explanation
Indices: 440788--440842 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
440778 ACTGCCAGTT
440788 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
*
440807 TCCATGTATCGATAGAATGA
1 T-CATGTATCGATACAATGA
*
440827 TCATATATCGATACAA
1 TCATGTATCGATACAA
440843 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:447479 original size:18 final size:19
Alignment explanation
Indices: 447456--447496 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
447446 TTTCAATATT
* *
447456 TTTTAA-TTTATTTTTTTC
1 TTTTAATTTTATTATTGTC
447474 TTTTAATTTTATTATTGTC
1 TTTTAATTTTATTATTGTC
447493 TTTT
1 TTTT
447497 TATGCTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTAATTTTATTATTGTC
Found at i:449535 original size:13 final size:13
Alignment explanation
Indices: 449517--449542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
449507 ACAATTCATC
449517 ATGTATCGATACA
1 ATGTATCGATACA
449530 ATGTATCGATACA
1 ATGTATCGATACA
449543 TTTGTCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:449617 original size:20 final size:20
Alignment explanation
Indices: 449591--449646 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
449581 ACTGCTAGTT
*
449591 TCATGTATCGATACAATTG-
1 TCATGTATTGATACAATTGA
*
449610 TCCATGTATTGATA-AAATGA
1 T-CATGTATTGATACAATTGA
449630 TCATGTATTGATACAAT
1 TCATGTATTGATACAAT
449647 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
TCATGTATTGATACAATTGA
Found at i:451322 original size:19 final size:19
Alignment explanation
Indices: 451278--451333 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
451268 CTGCCATTCT
**
451278 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
451298 CATGTATCGATGCAATGAA
1 CATGTATCGATACAATGAA
451317 CATGTATCGATACAATG
1 CATGTATCGATACAATG
451334 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:451336 original size:13 final size:13
Alignment explanation
Indices: 451318--451344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
451308 TGCAATGAAC
451318 ATGTATCGATACA
1 ATGTATCGATACA
451331 ATGTATCGATACA
1 ATGTATCGATACA
451344 A
1 A
451345 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:451914 original size:22 final size:21
Alignment explanation
Indices: 451887--451932 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
451877 AGTTTTCATT
*
451887 TTTCTCCCCTTTAATCAAAGAA
1 TTTCTCCCCCTTAATCAAA-AA
451909 TTTCTCCCCCTTAATCAAAAA
1 TTTCTCCCCCTTAATCAAAAA
451930 TTT
1 TTT
451933 ATTTATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTCTCCCCCTTAATCAAAAA
Found at i:455972 original size:21 final size:21
Alignment explanation
Indices: 455946--456000 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
455936 GAAACTGGTA
*
455946 ATGTATCGATACAATT-TCATC
1 ATGTATCGATACAATTAT-ACC
455967 ATGTATCGATAC-ATTATACC
1 ATGTATCGATACAATTATACC
455987 ATGTATCGATACAA
1 ATGTATCGATACAA
456001 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTATACC
Found at i:456073 original size:19 final size:20
Alignment explanation
Indices: 456029--456081 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
456019 TTGCCAATCT
**
456029 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
456049 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
456068 CATGTATCGATACA
1 CATGTATCGATACA
456082 TTCAAAGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:456110 original size:13 final size:13
Alignment explanation
Indices: 456092--456119 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
456082 TTCAAAGCAT
456092 AATGTATCGATAC
1 AATGTATCGATAC
456105 AATGTATCGATAC
1 AATGTATCGATAC
456118 AA
1 AA
456120 AGCATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:461500 original size:28 final size:28
Alignment explanation
Indices: 461444--461515 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
461434 GAAATAAAGC
** **
461444 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
461472 CGGGGTTGGAGTATCCCCAATGAAATAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
461500 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
461516 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCAAGGAAATAA
Found at i:461613 original size:52 final size:51
Alignment explanation
Indices: 461503--461890 Score: 213
Period size: 52 Copynumber: 7.4 Consensus size: 51
461493 GAAATAACGA
* ** * **
461503 GGTTGGAGTATCCTCGATT-GTGAAAAATTGGTGTTTTTGGAAATAAAATCAA
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGGAAATAAAA-CCG
* * * *
461555 AGTTGGAGTATCCTCGATTAAAGGAAAATTAGTGTTTTAGAAATAAAACCG
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAACCG
* * *** * * * *
461606 GGTTTGGAGTATCCCCAATT--ATGAGAAATCAATATTTTGGAAACAAAGTCGG
1 GG-TTGGAGTATCCCCGATTAAAGGA-AAATTGGTGTTTTGGAAATAAA-ACCG
* * * *
461658 GGTTGGAGTATCCCCTCGGAGGTAACAGG---GTTGGAGTATCCTCGATGAAAT--AA-CG
1 GGTTGGAGTAT-CCC-C-GA-TTAA-AGGAAAATTGGTGT-T--TTG--GAAATAAAACCG
* * *
461713 AGGTTGGAGTATCCTCGATTGTGAA--AAAATTGGTGTTTTTGGAAATAAAATCAG
1 -GGTTGGAGTATCCCCGA-T-TAAAGGAAAATTGGTG-TTTTGGAAATAAAA-CCG
* * * *
461767 AGTTGGAGTATCCCCGATAAAAGGAAAATTGGTGTTTTGAAAATAAAACTGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAAC-CG
*
461819 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAACC-G
*
461871 GGTTGGAGTTTCCCCGATTA
1 GGTTGGAGTATCCCCGATTA
461891 TGAACAATTG
Statistics
Matches: 256, Mismatches: 50, Indels: 60
0.70 0.14 0.16
Matches are distributed among these distances:
50 8 0.03
51 31 0.12
52 139 0.54
53 39 0.15
54 13 0.05
55 6 0.02
56 11 0.04
57 3 0.01
58 2 0.01
59 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAACCG
Found at i:461647 original size:211 final size:210
Alignment explanation
Indices: 461386--461838 Score: 732
Period size: 211 Copynumber: 2.2 Consensus size: 210
461376 CGATGATTAG
* *
461386 GAAATAAAATCGGGATTGGAGTATCCCC--TATGAGAAATCAATATTTTGGAAATAAAGCCGGGG
1 GAAATAAAACCGGGATTGGAGTATCCCCATTATGAGAAATCAATATTTTGGAAACAAAGCCGGGG
*
461449 TTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
66 TTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
* *
461514 CCTCGATTGTG-AAAAATTGGTGTTTTTGGAAATAAAATCAAAGTTGGAGTATCCTCGATTAAAG
131 CCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAAAGTTGGAGTATCCCCGATAAAAG
461578 GAAAATTAGTGTTTT
196 GAAAATTAGTGTTTT
* *
461593 AGAAATAAAACCGGGTTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAACAAAGTCGG
1 -GAAATAAAACCGGGATTGGAGTATCCCC-ATTATGAGAAATCAATATTTTGGAAACAAAGCCGG
* *
461658 GGTTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCTCGATGAAATAACGAGGTTGGAGT
64 GGTTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGT
*
461723 ATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATAAA
129 ATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAAAGTTGGAGTATCCCCGATAAA
*
461788 AGGAAAATTGGTGTTTT
194 AGGAAAATTAGTGTTTT
* *
461805 GAAAATAAAACTGGGGTTGGAGTATCCCCGATTA
1 G-AAATAAAACCGGGATTGGAGTATCCCC-ATTA
461839 AAGGAAAATT
Statistics
Matches: 226, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
208 26 0.12
211 107 0.47
212 93 0.41
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (210 bp):
GAAATAAAACCGGGATTGGAGTATCCCCATTATGAGAAATCAATATTTTGGAAACAAAGCCGGGG
TTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCCCAATGAAATAACGAGGTTGGAGTAT
CCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCAAAGTTGGAGTATCCCCGATAAAAG
GAAAATTAGTGTTTT
Found at i:461795 original size:53 final size:51
Alignment explanation
Indices: 461738--461888 Score: 221
Period size: 52 Copynumber: 2.9 Consensus size: 51
461728 CGATTGTGAA
* * *
461738 AAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATAAAAGG
1 AAAATTGGTG-TTTTGAAAATAAAA-CGGGGTTGGAGTATCCCCGATAAAAGG
*
461791 AAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTGTTTTGAAAATAAAAC-GGGGTTGGAGTATCCCCGATAAAAGG
*
461843 AAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTTTCCCCGAT
1 AAAATTGGTGTTTTGAAAATAAAA-CGGGGTTGGAGTATCCCCGAT
461889 TATGAACAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
51 1 0.01
52 79 0.87
53 11 0.12
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
AAAATTGGTGTTTTGAAAATAAAACGGGGTTGGAGTATCCCCGATAAAAGG
Found at i:464271 original size:13 final size:13
Alignment explanation
Indices: 464253--464278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464243 ACAAAGATCG
464253 ATGTATCGATACA
1 ATGTATCGATACA
464266 ATGTATCGATACA
1 ATGTATCGATACA
464279 TTCTACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:464463 original size:21 final size:21
Alignment explanation
Indices: 464422--464463 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
464412 GTTGGGACCT
*
464422 TGTATCGATACATTTATACAA
1 TGTATCGATACATTTAGACAA
*
464443 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTAGACAA
464464 AAATGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTAGACAA
Found at i:465837 original size:24 final size:25
Alignment explanation
Indices: 465785--465841 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
465775 TTAATTACAC
* *
465785 AAATAATAATAACAATAATAAATCT
1 AAATAAAAATAACAATAACAAATCT
465810 -AATAAAAATAACAAT-ACAAA-CT
1 AAATAAAAATAACAATAACAAATCT
465832 AAAATAAAAA
1 -AAATAAAAA
465842 AACTATTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 22 0.79
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (25 bp):
AAATAAAAATAACAATAACAAATCT
Found at i:465894 original size:16 final size:17
Alignment explanation
Indices: 465868--465903 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
465858 TAAATATAAA
465868 AATATAAATTAATACAT
1 AATATAAATTAATACAT
*
465885 AATA-AAATTAATACTT
1 AATATAAATTAATACAT
465901 AAT
1 AAT
465904 TATAGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATAAATTAATACAT
Done.