Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 312 of 362
Found at i:104237920 original size:50 final size:50
Alignment explanation
Indices: 104237820--104237946 Score: 175
Period size: 50 Copynumber: 2.5 Consensus size: 50
104237810 CACTGATCAG
* * *
104237820 GTAGCCGGAGCTACCACTTTTCACTTTTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCAC-TTTCATTTGTCATTGATCAGATAAGT
* *
104237871 GTAGCCGAAGCTATCACTTATCACTTTCACTTT-TCCTTGATCGGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCA-TTTGTCATTGATCAGATAAGT
*
104237921 GTAGCCGAAGTTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
104237947 GTTGCCATGG
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 45 0.65
51 24 0.35
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCATTGATCAGATAAGT
Found at i:104243732 original size:17 final size:18
Alignment explanation
Indices: 104243712--104243751 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
104243702 AACAAACAAG
104243712 TTATTTTAAAA-TCTTAA
1 TTATTTTAAAATTCTTAA
*
104243729 TTATTTTAAAATTTTTAA
1 TTATTTTAAAATTCTTAA
104243747 TTATT
1 TTATT
104243752 AAATTCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTTTAAAATTCTTAA
Found at i:104244262 original size:45 final size:46
Alignment explanation
Indices: 104244204--104244304 Score: 125
Period size: 45 Copynumber: 2.2 Consensus size: 46
104244194 TATTTCTAAT
*
104244204 AATTATTTGAAATATT-TCACATATAAAAATAATA-ATATTTGAAAC
1 AATTATTTAAAATATTAT-ACATATAAAAATAATAGATATTTGAAAC
* * *
104244249 AATTTTTTAAAATATTATATATATAAAAATAATAGTGATATTTGAAAT
1 AATTATTTAAAATATTATACATATAAAAATAATA--GATATTTGAAAC
104244297 AATTATTT
1 AATTATTT
104244305 GATTTTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 29 0.62
46 1 0.02
48 17 0.36
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (46 bp):
AATTATTTAAAATATTATACATATAAAAATAATAGATATTTGAAAC
Found at i:104252665 original size:20 final size:21
Alignment explanation
Indices: 104252642--104252686 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
104252632 TTATTTTGTG
104252642 TAAAAAAAATTTT-ATCAATA
1 TAAAAAAAATTTTAATCAATA
* *
104252662 TAAATAATATTTTAAATCAATA
1 TAAAAAAAATTTT-AATCAATA
104252684 TAA
1 TAA
104252687 TATAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAAAAATTTTAATCAATA
Found at i:104256753 original size:25 final size:23
Alignment explanation
Indices: 104256725--104256778 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
104256715 ATCAAATAGA
104256725 CTAAAAACATTAAAATAAATGTTTC
1 CTAAAAA-ATTAAAA-AAATGTTTC
* *
104256750 CTAACAAATTAAAAATATGTTT-
1 CTAAAAAATTAAAAAAATGTTTC
104256772 -TAAAAAA
1 CTAAAAAA
104256779 ATCTTTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.23
23 7 0.27
24 7 0.27
25 6 0.23
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (23 bp):
CTAAAAAATTAAAAAAATGTTTC
Found at i:104258868 original size:12 final size:12
Alignment explanation
Indices: 104258846--104258876 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
104258836 TAGGGTAGGA
104258846 AAAAGAAGAAAAT
1 AAAA-AAGAAAAT
104258859 AAAAAAGAAAAT
1 AAAAAAGAAAAT
104258871 AAAAAA
1 AAAAAA
104258877 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAAAGAAAAT
Found at i:104262501 original size:16 final size:16
Alignment explanation
Indices: 104262480--104262537 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
104262470 TTTTTTTAAA
104262480 AAAATTATAATTTTTT
1 AAAATTATAATTTTTT
104262496 AAAATTATAATTTTTAT
1 AAAATTATAATTTTT-T
* *
104262513 AAATATTTTGAA-TTTTA
1 AAA-ATTAT-AATTTTTT
104262530 AAAATTAT
1 AAAATTAT
104262538 TTTGAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 19 0.53
17 7 0.19
18 8 0.22
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AAAATTATAATTTTTT
Found at i:104262528 original size:19 final size:19
Alignment explanation
Indices: 104262488--104262549 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
104262478 AAAAAATTAT
*
104262488 AATTTTT-TAAA-ATTAT-
1 AATTTTTATAAATATTTTG
104262504 AATTTTTATAAATATTTTG
1 AATTTTTATAAATATTTTG
*
104262523 AA-TTTTAAAAATTATTTTG
1 AATTTTTATAAA-TATTTTG
104262542 AAATTTTT
1 -AATTTTT
104262550 GTTGAGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.18
17 4 0.11
18 12 0.32
19 9 0.24
20 2 0.05
21 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTTTATAAATATTTTG
Found at i:104262534 original size:18 final size:20
Alignment explanation
Indices: 104262507--104262548 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
104262497 AAATTATAAT
*
104262507 TTTTATAAA-TATTTTG-AA
1 TTTTAAAAATTATTTTGAAA
104262525 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTGAAA
104262545 TTTT
1 TTTT
104262549 TGTTGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAA
Found at i:104262778 original size:3 final size:3
Alignment explanation
Indices: 104262770--104262803 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
104262760 TTGCTAACCC
*
104262770 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
104262804 GATACTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:104265265 original size:17 final size:17
Alignment explanation
Indices: 104265243--104265275 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104265233 TGATTACCTC
*
104265243 CTTTTTTTTTTCTTTTT
1 CTTTTTTTTATCTTTTT
104265260 CTTTTTTTTATCTTTT
1 CTTTTTTTTATCTTTT
104265276 GGGTATGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTTTTATCTTTTT
Found at i:104266838 original size:30 final size:32
Alignment explanation
Indices: 104266788--104266861 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
104266778 TAATAATTTT
* *
104266788 TATTTTTATGATTTTAAAAAAATTAAAT-TAA
1 TATTATTATTATTTTAAAAAAATTAAATATAA
* *
104266819 -ATTATTATTATTTTTAAAAATTTAAATATAA
1 TATTATTATTATTTTAAAAAAATTAAATATAA
*
104266850 TTTTATTATTAT
1 TATTATTATTAT
104266862 CAATTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 23 0.64
31 3 0.08
32 10 0.28
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (32 bp):
TATTATTATTATTTTAAAAAAATTAAATATAA
Found at i:104267844 original size:11 final size:11
Alignment explanation
Indices: 104267828--104267853 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
104267818 GTCGCCTCTT
104267828 CCTTCGTTCTA
1 CCTTCGTTCTA
104267839 CCTTCGTTCTA
1 CCTTCGTTCTA
104267850 CCTT
1 CCTT
104267854 TGCCTCCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:104270885 original size:16 final size:16
Alignment explanation
Indices: 104270864--104270905 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
104270854 TTATTAAATT
*
104270864 ATATATTTTAATTATA
1 ATATATTTTAATAATA
104270880 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
104270895 AT-TATGTTTAA
1 ATATAT-TTTAA
104270906 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:104270890 original size:15 final size:15
Alignment explanation
Indices: 104270855--104270896 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
104270845 TTAAGAATTT
*
104270855 TATTAAATTAT-ATA
1 TATTTAATTATAATA
104270869 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
104270883 TATTTAATAATAAT
1 TATTTAATTATAAT
104270897 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:104271030 original size:18 final size:17
Alignment explanation
Indices: 104271002--104271036 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
104270992 ATTATTAAGA
*
104271002 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
104271019 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
104271037 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:104271116 original size:151 final size:154
Alignment explanation
Indices: 104270839--104271149 Score: 511
Period size: 151 Copynumber: 2.0 Consensus size: 154
104270829 ATAAGAATAT
* *
104270839 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
*
104270904 AAATATGATTAAAATATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAAT-AAT-
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
*
104270967 A-ATTTACCAAAACAAATTTCTGC
131 ACATTTACCAAAACAAATTTATGC
*
104270990 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATTTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
* *
104271055 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAATAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAAT-A-AA
104271120 TAATCATTTACCAAAACAAATTTATGC
129 TAA-CATTTACCAAAACAAATTTATGC
104271147 TAA
1 TAA
104271150 GGGTATTCTA
Statistics
Matches: 147, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
151 119 0.81
154 3 0.02
155 1 0.01
157 24 0.16
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAAATA
ACATTTACCAAAACAAATTTATGC
Found at i:104274702 original size:10 final size:10
Alignment explanation
Indices: 104274687--104274711 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
104274677 TCAAATAATA
104274687 AAAAAAAAGT
1 AAAAAAAAGT
104274697 AAAAAAAAGT
1 AAAAAAAAGT
104274707 AAAAA
1 AAAAA
104274712 TAATAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAAAGT
Found at i:104277990 original size:97 final size:98
Alignment explanation
Indices: 104277805--104278002 Score: 256
Period size: 97 Copynumber: 2.0 Consensus size: 98
104277795 TTTTTCTCTA
* * * *
104277805 CCAACATTGCTATCTCTAATTTTTCTATTCTGAGTATAGTGCTAATTTTTCCATTGCTTAGTATT
1 CCAACATTGCTATCTCTAATTTTTCTATTCAGAGTACAATACTAATTTTTCCATTGCTTAGTATT
* **
104277870 CTATTGTCCTGAACTCCCTTTGTGTCATTA-TG
66 CTATTGGCAAGAACTCCCTTTGTGTCATTATTG
** * *
104277902 CCAACATTTTTATCTCTGATTTTTCTATTCAGAGTACAATACTGATTTTTCCATTGCTTA-TATT
1 CCAACATTGCTATCTCTAATTTTTCTATTCAGAGTACAATACTAATTTTTCCATTGCTTAGTATT
* *
104277966 CTATTGGCAAGAACTCCTTGTTGTGTCTTTATTG
66 CTATTGGCAAGAACTCCCT-TTGTGTCATTATTG
104278000 CCA
1 CCA
104278003 TATATACTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 19 0.22
97 62 0.72
98 5 0.06
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (98 bp):
CCAACATTGCTATCTCTAATTTTTCTATTCAGAGTACAATACTAATTTTTCCATTGCTTAGTATT
CTATTGGCAAGAACTCCCTTTGTGTCATTATTG
Found at i:104282846 original size:14 final size:15
Alignment explanation
Indices: 104282829--104282858 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
104282819 TTAGTGTATT
104282829 ATATTTTTAAA-AAA
1 ATATTTTTAAATAAA
104282843 ATATTTTTAAATAAA
1 ATATTTTTAAATAAA
104282858 A
1 A
104282859 AGTAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTTAAATAAA
Found at i:104283819 original size:14 final size:14
Alignment explanation
Indices: 104283800--104283829 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
104283790 CATTAATATT
104283800 TTAAAAAAATAAAA
1 TTAAAAAAATAAAA
*
104283814 TTAAAATAATAAAA
1 TTAAAAAAATAAAA
104283828 TT
1 TT
104283830 TATAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TTAAAAAAATAAAA
Found at i:104285347 original size:9 final size:9
Alignment explanation
Indices: 104285335--104285374 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
104285325 TATTTTCCTT
104285335 TTTTTATAA
1 TTTTTATAA
*
104285344 TTTTTCTAA
1 TTTTTATAA
* *
104285353 ATTTTATTA
1 TTTTTATAA
104285362 TTTTTATAA
1 TTTTTATAA
104285371 TTTT
1 TTTT
104285375 AGAATGAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTATAA
Found at i:104288769 original size:51 final size:51
Alignment explanation
Indices: 104288687--104288806 Score: 197
Period size: 51 Copynumber: 2.4 Consensus size: 51
104288677 ACTTTTGATC
*
104288687 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
104288738 AGTGATAAGTGATAAGTGGTAGCTTCT-GCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTT-TAGCTACACTTATCTGATCAGTGACA
*
104288789 AGTGACAAGTGACAAGTG
1 AGTGACAAGTGATAAGTG
104288807 ATAAATGTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 63 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:104288794 original size:7 final size:7
Alignment explanation
Indices: 104288782--104288807 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
104288772 TTATCTGATC
104288782 AGTGACA
1 AGTGACA
104288789 AGTGACA
1 AGTGACA
104288796 AGTGACA
1 AGTGACA
104288803 AGTGA
1 AGTGA
104288808 TAAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:104295039 original size:37 final size:35
Alignment explanation
Indices: 104294998--104295083 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 35
104294988 AATGAGTAAA
* *
104294998 TTTTAAATTTTTATTATAATTTTAT-TAATTTTTCTAT
1 TTTTAAATTTTTAATA-AATTTTGTAT-ATTTTTC-AT
*
104295035 TTTTAATATTTGTAATAAATTTTGTATATTTTTCAT
1 TTTTAA-ATTTTTAATAAATTTTGTATATTTTTCAT
104295071 TTTTAAAGTTTTT
1 TTTTAAA-TTTTT
104295084 TTAAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
35 1 0.02
36 12 0.29
37 20 0.48
38 9 0.21
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (35 bp):
TTTTAAATTTTTAATAAATTTTGTATATTTTTCAT
Found at i:104295612 original size:23 final size:22
Alignment explanation
Indices: 104295596--104295642 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
104295586 ATTTTTCAAT
104295596 AAAAATACATAAAATTTTATAA
1 AAAAATACATAAAATTTTATAA
* *
104295618 ATAAATACATACAATTTTATAA
1 AAAAATACATAAAATTTTATAA
104295640 AAA
1 AAA
104295643 TATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAATACATAAAATTTTATAA
Found at i:104305176 original size:11 final size:11
Alignment explanation
Indices: 104305160--104305189 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
104305150 TGTGATAATG
*
104305160 TTCCAACCGAC
1 TTCCAACCAAC
104305171 TTCCAACCAAC
1 TTCCAACCAAC
104305182 TTCCAACC
1 TTCCAACC
104305190 TTTATGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.47, G:0.03, T:0.20
Consensus pattern (11 bp):
TTCCAACCAAC
Found at i:104305360 original size:39 final size:39
Alignment explanation
Indices: 104305316--104305402 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
104305306 ATGCAAAATG
*
104305316 CATCAAATAAGTTTGGATAATAGCCTAAACACCCAACTT
1 CATCAAACAAGTTTGGATAATAGCCTAAACACCCAACTT
*
104305355 CATCAAACAAGTTTGGCTAATAGCCTAAACACCCAACTT
1 CATCAAACAAGTTTGGATAATAGCCTAAACACCCAACTT
104305394 CATCAAACA
1 CATCAAACA
104305403 TGTTAGTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (39 bp):
CATCAAACAAGTTTGGATAATAGCCTAAACACCCAACTT
Found at i:104307396 original size:29 final size:28
Alignment explanation
Indices: 104307364--104307444 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
104307354 TATTTTCTAT
*
104307364 TTTTATTTTAAAAAGTTTATTTTTTATAA
1 TTTTATTTTAAAAACTTTATTTTTTA-AA
104307393 TTTTATTTCTAAAAACTTGT-TTTTTTAAA
1 TTTTATTT-TAAAAACTT-TATTTTTTAAA
* * *
104307422 TGTTATTTTTAAAATTTTATTTT
1 TTTTATTTTAAAAACTTTATTTT
104307445 ATTTTTACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 11 0.24
29 17 0.38
30 15 0.33
31 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATTTTAAAAACTTTATTTTTTAAA
Found at i:104308335 original size:16 final size:19
Alignment explanation
Indices: 104308304--104308343 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
104308294 CTAAAATTTT
104308304 AAAAATTATATATTTAA-A
1 AAAAATTATATATTTAATA
104308322 AAAAATTAT-T-TTTAATA
1 AAAAATTATATATTTAATA
104308339 AAAAA
1 AAAAA
104308344 GTTGGTCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATATATTTAATA
Found at i:104313744 original size:18 final size:19
Alignment explanation
Indices: 104313710--104313745 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
104313700 TAGCCGATTA
104313710 TATTTTCAAAAAAAAAAAG
1 TATTTTCAAAAAAAAAAAG
*
104313729 TATTTT-AAAAATAAAAA
1 TATTTTCAAAAAAAAAAA
104313746 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
TATTTTCAAAAAAAAAAAG
Found at i:104313801 original size:24 final size:26
Alignment explanation
Indices: 104313740--104313803 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
104313730 ATTTTAAAAA
104313740 TAAAAATTATAAAA-AATAAACTATT
1 TAAAAATTATAAAATAATAAACTATT
** *
104313765 TAAATTTTTTAAAATAA-AAA-TATT
1 TAAAAATTATAAAATAATAAACTATT
*
104313789 TAAAAATTCTAAAAT
1 TAAAAATTATAAAAT
104313804 TTCGACACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 16 0.50
25 14 0.44
26 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAAAATTATAAAATAATAAACTATT
Found at i:104321644 original size:21 final size:21
Alignment explanation
Indices: 104321618--104321661 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
104321608 TGGGGTGATT
104321618 TTGGATTGTTGTAAAAAGAAG
1 TTGGATTGTTGTAAAAAGAAG
104321639 TTGGATTGTTGTAAAAAGAAG
1 TTGGATTGTTGTAAAAAGAAG
104321660 TT
1 TT
104321662 TGTTGTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (21 bp):
TTGGATTGTTGTAAAAAGAAG
Found at i:104324267 original size:13 final size:14
Alignment explanation
Indices: 104324251--104324286 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
104324241 CAATCTCATA
104324251 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
104324264 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
104324277 TCTC-ATTTCA
1 TCTCAATTTCA
104324287 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:104324276 original size:18 final size:19
Alignment explanation
Indices: 104324238--104324278 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
104324228 TGGTTCATGT
104324238 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
104324257 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
104324275 TTTC
1 TTTC
104324279 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:104324468 original size:39 final size:38
Alignment explanation
Indices: 104324401--104324535 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
104324391 ACCAATATGG
* * *
104324401 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTA-TCCGAAGAAATATTTGA
* * * *
104324440 CACCCAGTGTCTCATCGGCCTATCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTATCCGAAGAAATATTTGA
* * * * *
104324478 TACCCAGTACCTCATCGAATCTATCCAAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTATCCGAAGAAATAT-TTGA
*
104324519 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
104324536 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 36 0.49
40 3 0.04
41 16 0.22
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTATCCGAAGAAATATTTGA
Found at i:104324801 original size:18 final size:19
Alignment explanation
Indices: 104324775--104324813 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
104324765 TTTCAATTCA
104324775 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
104324794 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
104324812 AT
1 AT
104324814 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:104326132 original size:5 final size:5
Alignment explanation
Indices: 104326122--104326178 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
104326112 TTACTTATTT
* *
104326122 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
104326170 ATAT- ATATA
1 ATATA ATATA
104326179 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:104326138 original size:12 final size:12
Alignment explanation
Indices: 104326121--104326176 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
104326111 TTTACTTATT
104326121 TATATAATATAA
1 TATATAATATAA
104326133 TATATAATATAATA
1 TATATAATAT-A-A
104326147 TACTATAATATAA
1 TA-TATAATATAA
*
104326160 TA-ATAATTTAA
1 TATATAATATAA
104326171 TATATA
1 TATATA
104326177 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:104326191 original size:26 final size:26
Alignment explanation
Indices: 104326123--104326178 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
104326113 TACTTATTTA
*
104326123 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
104326150 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
104326175 TATA
1 TATA
104326179 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:104331006 original size:17 final size:18
Alignment explanation
Indices: 104330984--104331017 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
104330974 TCTATTGAGT
104330984 CGTGTGGG-CCACATGGA
1 CGTGTGGGCCCACATGGA
104331001 CGTGTGGGCCCACATGG
1 CGTGTGGGCCCACATGG
104331018 GTCAACCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (18 bp):
CGTGTGGGCCCACATGGA
Found at i:104334259 original size:22 final size:21
Alignment explanation
Indices: 104334234--104334287 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
104334224 GTTCATGTAA
104334234 TTAAATTGTATATTTATATGTT
1 TTAAATTGTATA-TTATATGTT
*
104334256 TTAAATTG-A-ATTATTTGTT
1 TTAAATTGTATATTATATGTT
*
104334275 TCTGAATTGTATA
1 T-TAAATTGTATA
104334288 ATTTCCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 2 0.07
22 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (21 bp):
TTAAATTGTATATTATATGTT
Found at i:104342183 original size:23 final size:22
Alignment explanation
Indices: 104342135--104342197 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
104342125 CTTCATGCGC
* * *
104342135 GCAAGTGACAATAGCAGTCTCGT
1 GCAAGTGACAGTGGCA-CCTCGT
104342158 GCAAGTGACAGTGGCACCTCGAT
1 GCAAGTGACAGTGGCACCTCG-T
*
104342181 GCAAGTGATAGTGGCAC
1 GCAAGTGACAGTGGCAC
104342198 TTTGGTGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 4 0.11
23 31 0.89
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (22 bp):
GCAAGTGACAGTGGCACCTCGT
Found at i:104344232 original size:12 final size:12
Alignment explanation
Indices: 104344211--104344239 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
104344201 AAATGAGGTT
104344211 AAAG-GAATACA
1 AAAGTGAATACA
104344222 AAAGTGAATACA
1 AAAGTGAATACA
104344234 AAAGTG
1 AAAGTG
104344240 CTAAAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAGTGAATACA
Found at i:104355520 original size:17 final size:17
Alignment explanation
Indices: 104355498--104355534 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
104355488 AATAGGGAGT
*
104355498 AAGGAATTACTCCAATG
1 AAGGAATTACTCCAAGG
*
104355515 AAGGAATTTCTCCAAGG
1 AAGGAATTACTCCAAGG
104355532 AAG
1 AAG
104355535 CCAATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (17 bp):
AAGGAATTACTCCAAGG
Found at i:104361903 original size:12 final size:12
Alignment explanation
Indices: 104361886--104361920 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
104361876 AACAGAAAAT
104361886 AGTCCTCCGCTA
1 AGTCCTCCGCTA
104361898 AGTCCTCCGCTA
1 AGTCCTCCGCTA
104361910 AGTCCTCCGCT
1 AGTCCTCCGCT
104361921 GCACCGACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.43, G:0.17, T:0.26
Consensus pattern (12 bp):
AGTCCTCCGCTA
Found at i:104367044 original size:19 final size:20
Alignment explanation
Indices: 104367013--104367057 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
104367003 CGGAAAATAA
104367013 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
104367033 TTTCTG-AAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
104367052 TTTCTG
1 TTTCTG
104367058 GTGTTTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:104367160 original size:18 final size:18
Alignment explanation
Indices: 104367134--104367176 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
104367124 AAAAGTTATT
*
104367134 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
104367152 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
104367170 TTTATAT
1 TTTATAT
104367177 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:104374453 original size:24 final size:24
Alignment explanation
Indices: 104374424--104374474 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
104374414 ATTCAAATTG
* *
104374424 CTACTAACAAGCTAACAACTCCTC
1 CTACTAACAAGCTAACAAATCCCC
104374448 CTACTAACAAGCTAACAAATCCCC
1 CTACTAACAAGCTAACAAATCCCC
104374472 CTA
1 CTA
104374475 AGACTTAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.37, G:0.04, T:0.20
Consensus pattern (24 bp):
CTACTAACAAGCTAACAAATCCCC
Found at i:104374517 original size:26 final size:26
Alignment explanation
Indices: 104374481--104374534 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
104374471 CCTAAGACTT
*
104374481 AGTCTTATTATTTTAAAAATAGTTGC
1 AGTCTTATTATTTTAAAAATAGCTGC
104374507 AGTCTTATTATTTTAAAAATAGCTGC
1 AGTCTTATTATTTTAAAAATAGCTGC
104374533 AG
1 AG
104374535 CCTTGAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (26 bp):
AGTCTTATTATTTTAAAAATAGCTGC
Found at i:104376985 original size:26 final size:26
Alignment explanation
Indices: 104376949--104377002 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
104376939 CCAAAGACTT
104376949 AGTCTTATTATTTTAAAAATAGCCGC
1 AGTCTTATTATTTTAAAAATAGCCGC
*
104376975 AGTCTTATTATTTTAAAAATAGCTGC
1 AGTCTTATTATTTTAAAAATAGCCGC
104377001 AG
1 AG
104377003 CCTTGAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
AGTCTTATTATTTTAAAAATAGCCGC
Found at i:104393860 original size:18 final size:18
Alignment explanation
Indices: 104393819--104393861 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
104393809 ATAATTGTAT
*
104393819 AATTATAATTTATAAAAA
1 AATTATAATCTATAAAAA
*
104393837 AA--ATAATCTCTAAAAA
1 AATTATAATCTATAAAAA
104393853 AATTATAAT
1 AATTATAAT
104393862 TCTTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 14 0.67
18 7 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTATAATCTATAAAAA
Found at i:104397951 original size:21 final size:21
Alignment explanation
Indices: 104397917--104397960 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
104397907 AAATCTCTAC
*
104397917 AATTTCTCCCTAAAGCTCTCA
1 AATTTCTCACTAAAGCTCTCA
* **
104397938 AATTTCTCATTAAATTTCTCA
1 AATTTCTCACTAAAGCTCTCA
104397959 AA
1 AA
104397961 GCTCATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTCTCACTAAAGCTCTCA
Found at i:104398233 original size:53 final size:53
Alignment explanation
Indices: 104398117--104398226 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
104398107 ATAACGGTTT
* * *
104398117 ATTTTAAATTTTGAATATTATTTAATATTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTCTTTCATTTATATAATTTTAATTA
104398170 ATTTTAATTTTTGAATATTATTTAATATTCTTTCATTTATATAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTCTTTCATTTATATAATTTTAATTA
104398223 ATTT
1 ATTT
104398227 GTATTTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (53 bp):
ATTTTAATTTTTGAATATTATTTAATATTCTTTCATTTATATAATTTTAATTA
Found at i:104403557 original size:126 final size:126
Alignment explanation
Indices: 104403222--104403718 Score: 533
Period size: 126 Copynumber: 4.0 Consensus size: 126
104403212 GGTCAATTAT
* * * * *** * *
104403222 GAACTACTGTAGAAAAAAAGCGTCTACGTGGGAGCTTTTTTCAAAAATTTTGCTGACATTGCATC
1 GAACTACTATAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCTGTAATTTTGCTAACAGTGCATC
* * *
104403287 CTGCTTGAAGCATCTTTGACACTGTTTGTTCAGAAACATCTTCTCAAAATTA--TTTT-AG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * *
104403345 GAACTACTATTGAAAAAGAACGTTCACGTAGGAGC-TTTTTCTATAAATTTGCTAACAGTGCATC
1 GAACTACTATAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCTGTAATTTTGCTAACAGTGCATC
* ** * *
104403409 CTGCTTAAATTGTTTTTGACACTATTTTTTCAGAAACATCTTCTCAAAATTATTTTTTCAT
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * * * * *
104403470 GAACTACTATCGAAAAAGAGCATCCATGT-GGTAACTTTTTTCCGTAATTTTACTTACAGTGAAT
1 GAACTACTATAGAAAAAGAGCGTCCACGTAGG-AGCTTTTTTCTGTAATTTTGCTAACAGTGCAT
** * *
104403534 TTTGCTTGAAGCGTTTTTGACACTAATTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * *
104403596 GAACTACTGTAGAAAAAGAGTGCCCACGTAGGAGCTTTTTT-TGTATTTTTGCTGACAGTGCATC
1 GAACTACTATAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCTGTAATTTTGCTAACAGTGCATC
* * * *
104403660 CTGTTTGAAGTGTTTTT-ATACTATTTGTTCAAAAACGA-CTTCTCAAAATTATTTTTTCA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAC-ATCTTCTCAAAATTATTTTTTCA
104403719 AGGTAAAAAT
Statistics
Matches: 306, Mismatches: 61, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
122 69 0.23
123 28 0.09
124 43 0.14
125 58 0.19
126 106 0.35
127 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (126 bp):
GAACTACTATAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCTGTAATTTTGCTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
Found at i:104403813 original size:28 final size:30
Alignment explanation
Indices: 104403781--104403853 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
104403771 AAAAACTAAG
*
104403781 CCCTAATTTAATTAAATTT-AACCTTA-AA
1 CCCTAATTTAATTAAATTTAAACCCTAGAA
*
104403809 CCCTAATTTAATT-TATTTAAAACCCTAGAA
1 CCCTAATTTAATTAAATTT-AAACCCTAGAA
*
104403839 CCCTAATTTACTTAA
1 CCCTAATTTAATTAA
104403854 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 4 0.11
28 13 0.35
29 6 0.16
30 14 0.38
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (30 bp):
CCCTAATTTAATTAAATTTAAACCCTAGAA
Found at i:104403843 original size:30 final size:28
Alignment explanation
Indices: 104403776--104403853 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
104403766 TTAAAAAAAA
*
104403776 CTAAGCCCTAATTTAATTAAATTTAACC
1 CTAAACCCTAATTTAATTAAATTTAACC
* *
104403804 TTAAACCCTAATTTAATT-TATTTAAAACC
1 CTAAACCCTAATTTAATTAAATTT--AACC
*
104403833 CTAGAACCCTAATTTACTTAA
1 CTA-AACCCTAATTTAATTAA
104403854 TTTTTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.10
28 16 0.40
29 6 0.15
30 14 0.35
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.37
Consensus pattern (28 bp):
CTAAACCCTAATTTAATTAAATTTAACC
Found at i:104403914 original size:18 final size:18
Alignment explanation
Indices: 104403884--104403928 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
104403874 CATAAACCCT
104403884 AAACCCT-AATTTATTTA
1 AAACCCTAAATTTATTTA
104403901 AAACCCTAAATTTATTTA
1 AAACCCTAAATTTATTTA
*
104403919 AAATCCTAAA
1 AAACCCTAAA
104403929 AACCCTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (18 bp):
AAACCCTAAATTTATTTA
Found at i:104403955 original size:27 final size:28
Alignment explanation
Indices: 104403890--104403964 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
104403880 CCCTAAACCC
*
104403890 TAATTTATTT-AAAACCCTAAATTTATT
1 TAATTTATTTAAAAACCCTAAATTTACT
* *
104403917 TAA--AATCCTAAAAACCCT-AATTTACT
1 TAATTTAT-TTAAAAACCCTAAATTTACT
*
104403943 TAATTTATTTAAAAACCATAAA
1 TAATTTATTTAAAAACCCTAAA
104403965 CCCTAATGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
25 2 0.05
26 11 0.30
27 20 0.54
28 4 0.11
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (28 bp):
TAATTTATTTAAAAACCCTAAATTTACT
Found at i:104404799 original size:12 final size:12
Alignment explanation
Indices: 104404782--104404807 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104404772 GTAAAAAGGA
104404782 AACAAATAGATG
1 AACAAATAGATG
104404794 AACAAATAGATG
1 AACAAATAGATG
104404806 AA
1 AA
104404808 TAAGCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (12 bp):
AACAAATAGATG
Found at i:104405143 original size:16 final size:16
Alignment explanation
Indices: 104405122--104405152 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104405112 ATATATATAT
104405122 AAAATGAATAAAATAA
1 AAAATGAATAAAATAA
*
104405138 AAAATGAATAGAATA
1 AAAATGAATAAAATA
104405153 CATAATAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAAATGAATAAAATAA
Found at i:104405277 original size:13 final size:12
Alignment explanation
Indices: 104405259--104405316 Score: 73
Period size: 13 Copynumber: 4.7 Consensus size: 12
104405249 AAAAATGATA
104405259 AAATAAATCAAAC
1 AAATAAAT-AAAC
104405272 AAATAACATAAA-
1 AAATAA-ATAAAC
*
104405284 AAATAAACAAAC
1 AAATAAATAAAC
104405296 AAATAAATAAGAC
1 AAATAAATAA-AC
104405309 AAATAAAT
1 AAATAAAT
104405317 GATTCTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 4 0.10
12 15 0.38
13 19 0.47
14 2 0.05
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:104405285 original size:24 final size:23
Alignment explanation
Indices: 104405258--104405315 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 23
104405248 AAAAAATGAT
104405258 AAAATAAATCAAACAAATAACATAA
1 AAAATAAA-CAAACAAATAA-ATAA
104405283 AAAATAAACAAACAAATAAATAA
1 AAAATAAACAAACAAATAAATAA
104405306 GACAAATAAA
1 -A-AAATAAA
104405316 TGATTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.13
24 12 0.39
25 15 0.48
ACGTcount: A:0.74, C:0.10, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAATAAACAAACAAATAAATAA
Found at i:104406678 original size:22 final size:21
Alignment explanation
Indices: 104406625--104406680 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
104406615 GCCTTTTCTG
*
104406625 TATTTGGGTTAAGGTTGGGTT
1 TATTTGGGTCAAGGTTGGGTT
* * *
104406646 AATTTTAGGTCAGGGTTTGGGTT
1 TA-TTTGGGTCAAGG-TTGGGTT
104406669 TATTTGGGTCAA
1 TATTTGGGTCAA
104406681 AGTTTGTTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
21 1 0.04
22 17 0.65
23 8 0.31
ACGTcount: A:0.18, C:0.04, G:0.34, T:0.45
Consensus pattern (21 bp):
TATTTGGGTCAAGGTTGGGTT
Found at i:104407708 original size:23 final size:24
Alignment explanation
Indices: 104407680--104407724 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
104407670 TTTATTGAAA
*
104407680 TTAATTAATTGATT-ATTTTATAT
1 TTAATTAATTAATTAATTTTATAT
104407703 TTAATTAATTAATTAATTTTAT
1 TTAATTAATTAATTAATTTTAT
104407725 TGAGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTAATTAATTAATTAATTTTATAT
Found at i:104415798 original size:3 final size:3
Alignment explanation
Indices: 104415792--104415837 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
104415782 GCTTCAATTT
104415792 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
104415838 GTTCTTTCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:104417331 original size:25 final size:25
Alignment explanation
Indices: 104417303--104417358 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
104417293 AATAACATAA
* * *
104417303 ATAATAGTATTTAAATCTCAAACTT
1 ATAAAAGTAATTAAATATCAAACTT
104417328 ATAAAAGTAATTAAATATCAAACTT
1 ATAAAAGTAATTAAATATCAAACTT
*
104417353 AAAAAA
1 ATAAAA
104417359 TATTAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (25 bp):
ATAAAAGTAATTAAATATCAAACTT
Found at i:104417370 original size:25 final size:25
Alignment explanation
Indices: 104417313--104417364 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
104417303 ATAATAGTAT
* *
104417313 TTAAATCTCAAACTTATAAAAGTAA
1 TTAAATATCAAACTTATAAAAATAA
104417338 TTAAATATCAAACTTA-AAAAAT-A
1 TTAAATATCAAACTTATAAAAATAA
104417361 TTAA
1 TTAA
104417365 TTATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 5 0.20
25 15 0.60
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAAATATCAAACTTATAAAAATAA
Found at i:104420649 original size:23 final size:23
Alignment explanation
Indices: 104420622--104420665 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
104420612 ACTAGTAATC
* *
104420622 AAAATTACTCAAATAATTTCATA
1 AAAATTAATCAAATAAATTCATA
104420645 AAAATTAATCAAATAAATTCA
1 AAAATTAATCAAATAAATTCA
104420666 AGTGCATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATTAATCAAATAAATTCATA
Found at i:104421782 original size:20 final size:20
Alignment explanation
Indices: 104421757--104421796 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
104421747 CATTAAAAGG
*
104421757 TCAGTGCTTGTGCTTCCATC
1 TCAGTGCTAGTGCTTCCATC
104421777 TCAGTGCTAGTGCTTCCATC
1 TCAGTGCTAGTGCTTCCATC
104421797 ATTCACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.30, G:0.20, T:0.38
Consensus pattern (20 bp):
TCAGTGCTAGTGCTTCCATC
Found at i:104429604 original size:2 final size:2
Alignment explanation
Indices: 104429597--104429621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104429587 CCTATGGCAA
104429597 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
104429622 GTTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104431982 original size:29 final size:30
Alignment explanation
Indices: 104431920--104431986 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
104431910 CATATCTAAC
*
104431920 TTTAATTTAATATGTAATTATATACATCAAT
1 TTTAATTTAATATATAATTATATACAT-AAT
*
104431951 TTTAATTTAATATATAATTATATATAT-AT
1 TTTAATTTAATATATAATTATATACATAAT
104431980 TTTAATT
1 TTTAATT
104431987 GTGATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 9 0.26
31 25 0.74
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTAATTTAATATATAATTATATACATAAT
Found at i:104433104 original size:3 final size:3
Alignment explanation
Indices: 104433096--104433135 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
104433086 GCTTACTTGT
*
104433096 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
104433136 CTTCTTGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:104443483 original size:28 final size:27
Alignment explanation
Indices: 104443430--104443515 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
104443420 TGCACTTAAC
*
104443430 ATTAAA-TTTTTTATTTATTAGAAAATG
1 ATTAAATTTTTTTATTT-TTAAAAAATG
* *
104443457 TTTAAATTTTTATTATTTTTAAAAAATC
1 ATTAAATTTTT-TTATTTTTAAAAAATG
*
104443485 ATTAAATAATTTTT-TTTTTAAAAAATG
1 ATTAAAT-TTTTTTATTTTTAAAAAATG
104443512 ATTA
1 ATTA
104443516 TTAAAATGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 21 0.42
28 20 0.40
29 9 0.18
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTAAATTTTTTTATTTTTAAAAAATG
Found at i:104444548 original size:14 final size:14
Alignment explanation
Indices: 104444525--104444554 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
104444515 ACCTAAAAGT
*
104444525 TTTCTTTCACTTAG
1 TTTCTCTCACTTAG
104444539 TTTCTCTCACTTAG
1 TTTCTCTCACTTAG
104444553 TT
1 TT
104444555 GCACCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTCTCTCACTTAG
Found at i:104445067 original size:12 final size:12
Alignment explanation
Indices: 104445045--104445072 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
104445035 AAAAAAAAAC
104445045 AAAAACAAAAGG
1 AAAAACAAAAGG
104445057 AAAAACAAAAGG
1 AAAAACAAAAGG
104445069 AAAA
1 AAAA
104445073 GAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAGG
Found at i:104445072 original size:18 final size:17
Alignment explanation
Indices: 104445028--104445077 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
104445018 CATAAACTTG
*
104445028 CAAAAA-AAAAAAAAAA
1 CAAAAACAAAAGAAAAA
104445044 CAAAAACAAAAGGAAAAA
1 CAAAAACAAAA-GAAAAA
**
104445062 CAAAAGGAAAAGAAAA
1 CAAAAACAAAAGAAAA
104445078 GAAAAGCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 14 0.48
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (17 bp):
CAAAAACAAAAGAAAAA
Found at i:104447346 original size:6 final size:6
Alignment explanation
Indices: 104447335--104447359 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
104447325 ATAAATTTAG
104447335 ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A
104447360 GAAAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:104447624 original size:14 final size:14
Alignment explanation
Indices: 104447588--104447642 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
104447578 TCGGCGGTCC
*
104447588 AAGGTTTCAAGATAT
1 AAGGTTT-AAGATTT
**
104447603 AAAATTTAAGATTT
1 AAGGTTTAAGATTT
*
104447617 AAGGTTTAAGGTTT
1 AAGGTTTAAGATTT
104447631 AAGGTTTAAGAT
1 AAGGTTTAAGAT
104447643 CTGGAGTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 28 0.85
15 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (14 bp):
AAGGTTTAAGATTT
Found at i:104456229 original size:18 final size:18
Alignment explanation
Indices: 104456208--104456243 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
104456198 TTGTTGGTTT
*
104456208 TGATGATGTTGTTGATGA
1 TGATGATGGTGTTGATGA
104456226 TGATGATGGTGTTGATGA
1 TGATGATGGTGTTGATGA
104456244 AACTGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (18 bp):
TGATGATGGTGTTGATGA
Found at i:104461515 original size:29 final size:29
Alignment explanation
Indices: 104461479--104461537 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
104461469 ACTCGTATTT
104461479 ATATTTGATAAAAGTGATTATTTTATTAA
1 ATATTTGATAAAAGTGATTATTTTATTAA
104461508 ATATTTGATAAAAGTGATTATTTTATTAA
1 ATATTTGATAAAAGTGATTATTTTATTAA
104461537 A
1 A
104461538 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (29 bp):
ATATTTGATAAAAGTGATTATTTTATTAA
Found at i:104463192 original size:25 final size:21
Alignment explanation
Indices: 104463123--104463187 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
104463113 CCTGATCAGT
** * *
104463123 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
104463144 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
104463165 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
104463186 AT
1 AT
104463188 CGATAAAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:104470919 original size:21 final size:21
Alignment explanation
Indices: 104470893--104470975 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
104470883 TGATCAGTAT
*
104470893 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
104470914 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* * *
104470935 ACGACACACGAGGTGCTTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
104470957 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
104470976 GATCGATAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 33 0.69
22 1 0.02
23 14 0.29
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:104470943 original size:23 final size:22
Alignment explanation
Indices: 104470891--104470965 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
104470881 CCTGATCAGT
** *
104470891 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
104470912 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
*
104470933 ATACGACACACGAGGTGCTTGAA
1 ATACGACACACGAGGTGCCTG-A
104470956 ATACGACACA
1 ATACGACACA
104470966 TAAAGTGCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 35 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:104473324 original size:20 final size:20
Alignment explanation
Indices: 104473292--104473329 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104473282 AAATTAATTT
104473292 AAACTAAAGGTATCGATAGC
1 AAACTAAAGGTATCGATAGC
104473312 AAACTTAAA-GTATCGATA
1 AAAC-TAAAGGTATCGATA
104473330 CTTCTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (20 bp):
AAACTAAAGGTATCGATAGC
Found at i:104474050 original size:22 final size:20
Alignment explanation
Indices: 104474025--104474065 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
104474015 GGGACTTAAT
104474025 CGAAAATTCAGAGAATTTTTCA
1 CGAAAATTCA-A-AATTTTTCA
*
104474047 CGAAATTTCAAAATTTTTC
1 CGAAAATTCAAAATTTTTC
104474066 CAATGTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (20 bp):
CGAAAATTCAAAATTTTTCA
Found at i:104475863 original size:12 final size:12
Alignment explanation
Indices: 104475848--104475888 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
104475838 TGATAATATA
*
104475848 AATAACAACGAT
1 AATAACAACAAT
*
104475860 AATAACAATAAT
1 AATAACAACAAT
*
104475872 AATAACAATAAT
1 AATAACAACAAT
104475884 AATAA
1 AATAA
104475889 TAATGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (12 bp):
AATAACAACAAT
Found at i:104475872 original size:3 final size:3
Alignment explanation
Indices: 104475858--104475900 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
104475848 AATAACAACG
* *
104475858 ATA ATA ACA ATA ATA ATA ACA ATA ATA ATA ATA ATGA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
104475901 TAAAATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:104475903 original size:18 final size:18
Alignment explanation
Indices: 104475824--104475900 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
104475814 TACATAATAG
104475824 AATAATAATGAA-AATGAT
1 AATAATAAT-AATAATGAT
* *
104475842 AAT-ATAAATAACAACGAT
1 AATAAT-AATAATAATGAT
* * *
104475860 AATAACAATAATAATAAC
1 AATAATAATAATAATGAT
104475878 AATAATAATAATAATGAAT
1 AATAATAATAATAATG-AT
104475897 AATA
1 AATA
104475901 TAAAATTTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 4 0.09
18 36 0.78
19 6 0.13
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AATAATAATAATAATGAT
Found at i:104475937 original size:4 final size:4
Alignment explanation
Indices: 104475923--104475978 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
104475913 ATTATAAAAA
* * * *
104475923 AAAT AAGT AAAT AAAT AAAT -AAT GAAAT AAAA ATAAT AAGT AAAT AAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A-AAT AAAT AAAT AAAT
104475972 AAAT AAA
1 AAAT AAA
104475979 AACTAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
3 3 0.07
4 32 0.78
5 6 0.15
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:104475960 original size:25 final size:26
Alignment explanation
Indices: 104475932--104475988 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
104475922 AAAATAAGTA
**
104475932 AATAAATAAATAATGAAATAAAAA-T
1 AATAAATAAATAAACAAATAAAAACT
*
104475957 AATAAGTAAATAAACAAATAAAAACT
1 AATAAATAAATAAACAAATAAAAACT
104475983 AATAAA
1 AATAAA
104475989 GGTTTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (26 bp):
AATAAATAAATAAACAAATAAAAACT
Found at i:104476087 original size:3 final size:3
Alignment explanation
Indices: 104476081--104476148 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
104476071 AAGAATAAGA
104476081 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
104476129 ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG AT
104476149 AGTTGAAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:104478457 original size:10 final size:10
Alignment explanation
Indices: 104478444--104478528 Score: 55
Period size: 10 Copynumber: 7.9 Consensus size: 10
104478434 CTAATTTCCC
104478444 CTTTCTTTTT
1 CTTTCTTTTT
104478454 CTTTCTTTTTT
1 CTTTC-TTTTT
*
104478465 CTTTCTCTCTT
1 CTTTCT-TTTT
104478476 -TTTCGTTTCACTT
1 CTTTC-TTT---TT
* *
104478489 CTCTATTCTTT
1 CTTTCTT-TTT
104478500 CTTTCTTTTT
1 CTTTCTTTTT
* *
104478510 ATTTCTTTTA
1 CTTTCTTTTT
104478520 CTTTCTTTT
1 CTTTCTTTT
104478529 ATTTACTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
10 30 0.52
11 21 0.36
13 4 0.07
14 3 0.05
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.72
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:104478523 original size:20 final size:20
Alignment explanation
Indices: 104478500--104478537 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104478490 TCTATTCTTT
104478500 CTTTCTTTTTATTT-CTTTTA
1 CTTTC-TTTTATTTACTTTTA
104478520 CTTTCTTTTATTTACTTT
1 CTTTCTTTTATTTACTTT
104478538 ATGTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (20 bp):
CTTTCTTTTATTTACTTTTA
Found at i:104487420 original size:14 final size:14
Alignment explanation
Indices: 104487401--104487430 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
104487391 GTTGCTTACG
104487401 TAGTTGTTCTCCTC
1 TAGTTGTTCTCCTC
104487415 TAGTTGTTCTCCTC
1 TAGTTGTTCTCCTC
104487429 TA
1 TA
104487431 TTTTGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.27, G:0.13, T:0.50
Consensus pattern (14 bp):
TAGTTGTTCTCCTC
Found at i:104490241 original size:49 final size:50
Alignment explanation
Indices: 104490072--104490261 Score: 220
Period size: 50 Copynumber: 3.8 Consensus size: 50
104490062 TGTGAGAGCA
* * *** * *
104490072 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG--TTAGGTCG
* * *
104490124 CGTATGTAGTACTAAGTGCAGGTTACTACGTGTACCAGATAGTTAGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
* * *
104490174 CATGTGTAGTACTAAGTGCAGGCTATTACGTGTACTAGATTGTT-GGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
* *
104490223 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
104490262 CAGCTTCAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
49 40 0.34
50 45 0.38
52 33 0.28
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCG
Found at i:104490483 original size:16 final size:15
Alignment explanation
Indices: 104490462--104490491 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
104490452 AAATAGAGTA
104490462 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
104490478 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
104490492 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:104493054 original size:14 final size:14
Alignment explanation
Indices: 104493035--104493064 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
104493025 TATTTTCAAG
104493035 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
104493049 ATAGATTCACGCAT
1 ATAGATTAACGCAT
104493063 AT
1 AT
104493065 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:104496051 original size:32 final size:32
Alignment explanation
Indices: 104496010--104496073 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
104496000 AGCTCCTTTG
*
104496010 TCTCCTGTGTCAATATCTTGATCGGTTCTTCA
1 TCTCCTGTGTCAATATCTTGACCGGTTCTTCA
104496042 TCTCCTGTGTCAATATCTTGACCGGTTCTTCA
1 TCTCCTGTGTCAATATCTTGACCGGTTCTTCA
104496074 CTATAAGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (32 bp):
TCTCCTGTGTCAATATCTTGACCGGTTCTTCA
Found at i:104496758 original size:9 final size:9
Alignment explanation
Indices: 104496744--104496775 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
104496734 TTTATACAAA
104496744 TAATTCGGT
1 TAATTCGGT
*
104496753 TAATTCGGG
1 TAATTCGGT
104496762 TAATTCGGT
1 TAATTCGGT
104496771 TAATT
1 TAATT
104496776 TTATACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:104497568 original size:23 final size:23
Alignment explanation
Indices: 104497534--104497577 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
104497524 TGTACAGACA
104497534 TAGTACCGCTGTGAGCCTCGCGT
1 TAGTACCGCTGTGAGCCTCGCGT
*
104497557 TAGTACCTCTGTGAGCCTCGC
1 TAGTACCGCTGTGAGCCTCGC
104497578 TAGTATCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (23 bp):
TAGTACCGCTGTGAGCCTCGCGT
Found at i:104503926 original size:12 final size:12
Alignment explanation
Indices: 104503909--104503941 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
104503899 TGTTTTTACC
104503909 TAATTCCTTCAA
1 TAATTCCTTCAA
104503921 TAATTCCTTCAA
1 TAATTCCTTCAA
104503933 TAATTCCTT
1 TAATTCCTT
104503942 TTTTTCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTCCTTCAA
Found at i:104512348 original size:13 final size:13
Alignment explanation
Indices: 104512330--104512366 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
104512320 AGATAATTAG
104512330 CAAATCATACATA
1 CAAATCATACATA
104512343 CAAATCATACATA
1 CAAATCATACATA
*
104512356 TAAATTCATAC
1 CAAA-TCATAC
104512367 CAAACTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (13 bp):
CAAATCATACATA
Found at i:104515169 original size:47 final size:47
Alignment explanation
Indices: 104515098--104515595 Score: 843
Period size: 47 Copynumber: 10.5 Consensus size: 47
104515088 ATTCAGCCAA
104515098 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515147 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515194 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515243 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515290 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
104515339 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515386 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
104515433 GAAGGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
104515480 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * ** *
104515527 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACATGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
104515574 GAAAGTGTATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
104515596 TCCCGAAGGG
Statistics
Matches: 430, Mismatches: 15, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
47 329 0.77
49 101 0.23
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:104515205 original size:96 final size:96
Alignment explanation
Indices: 104515098--104515595 Score: 864
Period size: 96 Copynumber: 5.2 Consensus size: 96
104515088 ATTCAGCCAA
104515098 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
104515163 GATAAGGCCTAATGGCCGATGTGATGAATGT
66 GATAAGGCCTAATGGCCGATGTGATGAATGT
104515194 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
104515259 GATAAGGCCTAATGGCCGATGTGATGAATGT
66 GATAAGGCCTAATGGCCGATGTGATGAATGT
104515290 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
*
104515355 GATAAGGCCTAATAGCCGATGTGATGAATGT
66 GATAAGGCCTAATGGCCGATGTGATGAATGT
*
104515386 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
104515449 GATAAGGCCTAATGGCCGATGTGATGAATGT
66 GATAAGGCCTAATGGCCGATGTGATGAATGT
104515480 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
* * * * * ** *
104515543 GACAGGGCCGAGTGGCCAACATGATGGATGT
66 GATAAGGCCTAATGGCCGATGTGATGAATGT
104515574 GAAAGTGTATA-A-ATGTGATAAG
1 GAAAGTGTATATATATGTGATAAG
104515596 TCCCGAAGGG
Statistics
Matches: 388, Mismatches: 12, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
94 187 0.48
95 1 0.00
96 200 0.52
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
GATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:104515852 original size:37 final size:37
Alignment explanation
Indices: 104515714--104515851 Score: 231
Period size: 37 Copynumber: 3.7 Consensus size: 37
104515704 CCGAGCTCTA
104515714 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
104515751 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* *
104515788 AAGACCCGATGACTACGTGTGGAGATTTTGTTCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* * *
104515825 AAGACCTGATAACTTCGTGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
104515852 TCGTCTGAGC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
Found at i:104517736 original size:21 final size:22
Alignment explanation
Indices: 104517690--104517730 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
104517680 TAGTTATCTA
*
104517690 ATCAATTCTAATCAATGATTCT
1 ATCAATTCTAATCAATAATTCT
*
104517712 ATCAATT-TAATCCATAATT
1 ATCAATTCTAATCAATAATT
104517731 TCATCATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (22 bp):
ATCAATTCTAATCAATAATTCT
Found at i:104517995 original size:16 final size:16
Alignment explanation
Indices: 104517974--104518004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104517964 TTTCTTTTGT
*
104517974 TTCTTTATTTTATTTA
1 TTCTTTATTTCATTTA
104517990 TTCTTTATTTCATTT
1 TTCTTTATTTCATTT
104518005 TATTTACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTATTTCATTTA
Found at i:104526215 original size:12 final size:12
Alignment explanation
Indices: 104526198--104526224 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
104526188 AATGATTGTT
104526198 CAACTCTAAAAA
1 CAACTCTAAAAA
104526210 CAACTCTAAAAA
1 CAACTCTAAAAA
104526222 CAA
1 CAA
104526225 AAAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAACTCTAAAAA
Found at i:104527947 original size:2 final size:2
Alignment explanation
Indices: 104527940--104527979 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
104527930 ATATGAAATG
104527940 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
104527980 AGATTAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:104531208 original size:58 final size:58
Alignment explanation
Indices: 104531118--104531230 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
104531108 TATTAAGGCC
* *
104531118 TGAAATTTTTTTGTCTAAGTTAGGTTCTGAACTTGACAATTATTCTCACATTGGGGTT
1 TGAAATTTTTTTGTCTAAATTAGGTTCTGAACTTGACAAATATTCTCACATTGGGGTT
* * * *
104531176 TGAAATTTTTTTTTCTAAATTAGG-TCTTGAACTTGGCAAATGTTTTCACATTGGG
1 TGAAATTTTTTTGTCTAAATTAGGTTC-TGAACTTGACAAATATTCTCACATTGGG
104531231 ACTTCAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 2 0.04
58 46 0.96
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (58 bp):
TGAAATTTTTTTGTCTAAATTAGGTTCTGAACTTGACAAATATTCTCACATTGGGGTT
Found at i:104531243 original size:58 final size:58
Alignment explanation
Indices: 104531120--104531246 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 58
104531110 TTAAGGCCTG
* * * ** *
104531120 AAATTTTTTTGTCTAAGTTAGGTTCTGAACTTGACAATTATTCTCACATTGGGGTTTG
1 AAATTTTTTTTTCTAAATTAGGTTCTGAACTTGACAAATATTCTCACATTGGGACTTC
* * *
104531178 AAATTTTTTTTTCTAAATTAGG-TCTTGAACTTGGCAAATGTTTTCACATTGGGACTTC
1 AAATTTTTTTTTCTAAATTAGGTTC-TGAACTTGACAAATATTCTCACATTGGGACTTC
104531236 -AATTTTTTTTT
1 AAATTTTTTTTT
104531247 ATCCAAGTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 13 0.22
58 46 0.78
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (58 bp):
AAATTTTTTTTTCTAAATTAGGTTCTGAACTTGACAAATATTCTCACATTGGGACTTC
Found at i:104532411 original size:24 final size:24
Alignment explanation
Indices: 104532362--104532413 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
104532352 GTTTATATTA
* *
104532362 AATATCTCATATTTAATTTAATTT
1 AATATCTCATATTTAATGTAAATT
*
104532386 AATATTTCATA-TTAATAGTAAATT
1 AATATCTCATATTTAAT-GTAAATT
104532410 AATA
1 AATA
104532414 AAATACTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (24 bp):
AATATCTCATATTTAATGTAAATT
Found at i:104532441 original size:31 final size:30
Alignment explanation
Indices: 104532399--104532503 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 30
104532389 ATTTCATATT
*
104532399 AATAGTAAATTAATAAAATACTATATAGATA
1 AATATTAAATTAATAAAATA-TATATAGATA
** * * *
104532430 AATATTAAATTAAATTCAATAT-TTTATATT
1 AATATTAAATT-AATAAAATATATATAGATA
*
104532460 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATA-TATATAGATA
104532491 AATATTAAATTAA
1 AATATTAAATTAA
104532504 ATTCAATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.12
30 17 0.28
31 29 0.48
32 7 0.12
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (30 bp):
AATATTAAATTAATAAAATATATATAGATA
Found at i:104532459 original size:61 final size:61
Alignment explanation
Indices: 104532370--104532521 Score: 232
Period size: 61 Copynumber: 2.5 Consensus size: 61
104532360 TAAATATCTC
* * *
104532370 ATATTTAATTTAATTTAATATTTCATATTAATAGTAAATTAATAAAATACTATATAGATAA
1 ATATTAAATTAAATTCAATATTTCATATTAATAGTAAATTAATAAAATACTATATAGATAA
* * * *
104532431 ATATTAAATTAAATTCAATATTTTATATTAATATTAAATTAATAAAATATTATCTAGATAA
1 ATATTAAATTAAATTCAATATTTCATATTAATAGTAAATTAATAAAATACTATATAGATAA
*
104532492 ATATTAAATTAAATTCAATATATCATATTA
1 ATATTAAATTAAATTCAATATTTCATATTA
104532522 GTACCTAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 82 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (61 bp):
ATATTAAATTAAATTCAATATTTCATATTAATAGTAAATTAATAAAATACTATATAGATAA
Found at i:104532481 original size:16 final size:15
Alignment explanation
Indices: 104532399--104532503 Score: 51
Period size: 16 Copynumber: 6.9 Consensus size: 15
104532389 ATTTCATATT
*
104532399 AATAGTAAATTAATAA
1 AATATTAAATTAAT-A
* *
104532415 AATACTATA-TAGATA
1 AATATTAAATTA-ATA
*
104532430 AATATTAAATTAAATTC
1 AATATTAAATT-AA-TA
*
104532447 AATATT---TTATATT
1 AATATTAAATTA-ATA
104532460 AATATTAAATTAATAA
1 AATATTAAATTAAT-A
104532476 AATATT--ATCTAGATA
1 AATATTAAAT-TA-ATA
104532491 AATATTAAATTAA
1 AATATTAAATTAA
104532504 ATTCAATATA
Statistics
Matches: 69, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
13 8 0.12
14 5 0.07
15 22 0.32
16 24 0.35
17 10 0.14
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
AATATTAAATTAATA
Found at i:104534815 original size:19 final size:19
Alignment explanation
Indices: 104534765--104534815 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
104534755 TTTTGTATTT
* *
104534765 TATTTTTGGGAATTTTATA
1 TATTTTTGAGATTTTTATA
**
104534784 TATTTTTCTGATTTTTA-A
1 TATTTTTGAGATTTTTATA
104534802 TAATTTTTGAGATT
1 T-ATTTTTGAGATT
104534816 CTTTGAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (19 bp):
TATTTTTGAGATTTTTATA
Found at i:104539525 original size:24 final size:24
Alignment explanation
Indices: 104539493--104539538 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
104539483 TCTTCTTTTT
* *
104539493 TATTTTTTAATATTATATATAATA
1 TATTTTTTAATAATATAAATAATA
104539517 TATTTTTTAATAATATAAATAA
1 TATTTTTTAATAATATAAATAA
104539539 ATCATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTTTTAATAATATAAATAATA
Found at i:104540117 original size:14 final size:14
Alignment explanation
Indices: 104540098--104540131 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
104540088 TTTAATTATG
104540098 TAAAATTAT-AAAAT
1 TAAAATT-TGAAAAT
104540112 TAAAATTTGAAAAT
1 TAAAATTTGAAAAT
104540126 TAAAAT
1 TAAAAT
104540132 AAAGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
TAAAATTTGAAAAT
Found at i:104540475 original size:9 final size:9
Alignment explanation
Indices: 104540461--104540498 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
104540451 AATTGAAAAG
104540461 TTAATTATA
1 TTAATTATA
104540470 TTAATTAT-
1 TTAATTATA
104540478 TTGAATTA-A
1 TT-AATTATA
104540487 TTAATTATA
1 TTAATTATA
104540496 TTA
1 TTA
104540499 TAAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
TTAATTATA
Done.