Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 130 of 170
Found at i:39562810 original size:23 final size:23
Alignment explanation
Indices: 39562746--39563048 Score: 265
Period size: 23 Copynumber: 13.0 Consensus size: 23
39562736 CATATATATA
39562746 TATATACAAAATTGGACAGCATT
1 TATATACAAAATTGGACAGCATT
* *
39562769 TATACACCAAAATTTGACAGCATT
1 TATATA-CAAAATTGGACAGCATT
39562793 TATATACAAAATTGGACAGCATT
1 TATATACAAAATTGGACAGCATT
* *
39562816 TAT-TCACCAAAATTGGGCAGCATA
1 TATAT-A-CAAAATTGGACAGCATT
* * *
39562840 TATATACCAATTTGGACAGCACT
1 TATATACAAAATTGGACAGCATT
* * * *
39562863 TATACACAAAATTTGATAGCATG
1 TATATACAAAATTGGACAGCATT
39562886 TATATACAAAATTGGACAGCATT
1 TATATACAAAATTGGACAGCATT
* *
39562909 TAT-TCACCAAAATTGGGCAGCATA
1 TATAT-A-CAAAATTGGACAGCATT
* * *
39562933 TATATACCAATTTGGACAGCACT
1 TATATACAAAATTGGACAGCATT
* * *
39562956 TATACACAAAATTTGACA-CATG
1 TATATACAAAATTGGACAGCATT
* *
39562978 TATATACAAAATTGGGCAACATT
1 TATATACAAAATTGGACAGCATT
* * *
39563001 TAT-TCACCAAAATTGGGCAACATA
1 TATAT-A-CAAAATTGGACAGCATT
* *
39563025 TATATAC-CAATTTGAGCAGCATT
1 TATATACAAAATTGGA-CAGCATT
39563048 T
1 T
39563049 TAGCATAAAA
Statistics
Matches: 223, Mismatches: 45, Indels: 24
0.76 0.15 0.08
Matches are distributed among these distances:
22 25 0.11
23 116 0.52
24 79 0.35
25 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (23 bp):
TATATACAAAATTGGACAGCATT
Found at i:39562815 original size:47 final size:47
Alignment explanation
Indices: 39562743--39563048 Score: 359
Period size: 47 Copynumber: 6.6 Consensus size: 47
39562733 CAGCATATAT
39562743 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* * * *
39562790 ATTTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* * * *
39562837 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGATAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* * * *
39562883 ATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* * *
39562930 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACA-C
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* * * * * * *
39562975 ATGTATATACAAAATTGGGCAACATTTATTCACCAAAATTGGGCAAC
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
* *
39563022 ATATATATAC-CAATTTGAGCAGCATTT
1 ATATATATACAAAATTGGA-CAGCATTT
39563049 TAGCATAAAA
Statistics
Matches: 214, Mismatches: 41, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
45 26 0.12
46 63 0.29
47 125 0.58
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (47 bp):
ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
Found at i:39563061 original size:93 final size:93
Alignment explanation
Indices: 39562743--39563038 Score: 504
Period size: 93 Copynumber: 3.2 Consensus size: 93
39562733 CAGCATATAT
* * * *
39562743 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATTTATATACAAAATTGG
1 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAAATTGG
39562808 ACAGCATTTATTCACCAAAATTGGGCAGC
65 ACAGCATTTATTCACCAAAATTGGGCAGC
*
39562837 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGATAGCATGTATATACAAAATTGGA
1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
39562902 CAGCATTTATTCACCAAAATTGGGCAGC
66 CAGCATTTATTCACCAAAATTGGGCAGC
*
39562930 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACA-CATGTATATACAAAATTGGG
1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
* *
39562994 CAACATTTATTCACCAAAATTGGGCAAC
66 CAGCATTTATTCACCAAAATTGGGCAGC
39563022 ATATATATACCAATTTG
1 ATATATATACCAATTTG
39563039 AGCAGCATTT
Statistics
Matches: 193, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
92 62 0.32
93 102 0.53
94 29 0.15
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (93 bp):
ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
CAGCATTTATTCACCAAAATTGGGCAGC
Found at i:39564014 original size:30 final size:31
Alignment explanation
Indices: 39563980--39564065 Score: 122
Period size: 30 Copynumber: 2.7 Consensus size: 31
39563970 TAAATATATA
39563980 TTTTTTATTTTTAAAAATATTTTAAAATAC-
1 TTTTTTATTTTTAAAAATATTTTAAAATACT
39564010 TTTTTTATTTTT-AAAATATTTTTAAAATACT
1 TTTTTTATTTTTAAAAATA-TTTTAAAATACT
*
39564041 TTTTTTAATTTTCTAAAAAAATTTT
1 TTTTTT-ATTTT-TAAAAATATTTT
39564066 TGGTGTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
29 6 0.12
30 23 0.46
31 6 0.12
32 5 0.10
33 5 0.10
34 5 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTATTTTTAAAAATATTTTAAAATACT
Found at i:39568937 original size:20 final size:21
Alignment explanation
Indices: 39568910--39568964 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
39568900 AACAGCGGTG
**
39568910 GCGGTGAGATTAGTTACT-TA
1 GCGGTGAGATTAGACACTATA
* *
39568930 GTGGTGAGATTGGACACTATA
1 GCGGTGAGATTAGACACTATA
39568951 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
39568965 AATAATGGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.27, C:0.09, G:0.35, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGACACTATA
Found at i:39569297 original size:12 final size:12
Alignment explanation
Indices: 39569282--39569308 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39569272 TTAAATTTTC
39569282 TATTAATATACA
1 TATTAATATACA
39569294 TATTAATATACA
1 TATTAATATACA
39569306 TAT
1 TAT
39569309 ATGATTTATT
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTAATATACA
Found at i:39593485 original size:27 final size:28
Alignment explanation
Indices: 39593453--39593520 Score: 102
Period size: 27 Copynumber: 2.4 Consensus size: 28
39593443 TATGGTTTCT
39593453 TTTCTTGTTTTAATCTTCCTTTCT-TCC
1 TTTCTTGTTTTAATCTTCCTTTCTCTCC
*
39593480 TTTCTTGTTTCAATCTTCCTTTCTCTCC
1 TTTCTTGTTTTAATCTTCCTTTCTCTCC
*
39593508 TTGTCTTATTTTA
1 TT-TCTTGTTTTA
39593521 CTCTCATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.64
28 5 0.14
29 8 0.22
ACGTcount: A:0.09, C:0.25, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTCTTGTTTTAATCTTCCTTTCTCTCC
Found at i:39599118 original size:29 final size:29
Alignment explanation
Indices: 39599085--39599166 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
39599075 AGATGCACCA
*
39599085 AAGTGCAATAAC-TAAACAGAATGACATTG
1 AAGTGCAATAACAT-AACAGAATGACACTG
* *
39599114 AAGTGCAATATCATAATAGAATGACACTG
1 AAGTGCAATAACATAACAGAATGACACTG
*** *
39599143 AAGTGTTTTAGCATAACAGAATGA
1 AAGTGCAATAACATAACAGAATGA
39599167 TACCAAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 43 0.98
30 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (29 bp):
AAGTGCAATAACATAACAGAATGACACTG
Found at i:39601730 original size:19 final size:19
Alignment explanation
Indices: 39601651--39601730 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 19
39601641 CTATTTTTTT
*
39601651 TTTTATATAAATTTTTGAGTA
1 TTTTATATGAATTTTTGA--A
* *
39601672 TTTTATAT-AGTTTTATAAA
1 TTTTATATGAATTTT-TGAA
*
39601691 TTTTA-AT-AATTTTTTAA
1 TTTTATATGAATTTTTGAA
*
39601708 -TTTATATGTATTTTTGAA
1 TTTTATATGAATTTTTGAA
39601726 TTTTA
1 TTTTA
39601731 ATTTAGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 15 0.31
19 10 0.20
20 5 0.10
21 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTATATGAATTTTTGAA
Found at i:39602824 original size:11 final size:11
Alignment explanation
Indices: 39602808--39602865 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
39602798 GTGGTGCCGG
39602808 AAAAAGAAAAA
1 AAAAAGAAAAA
* *
39602819 AAAAAGAGAGA
1 AAAAAGAAAAA
*
39602830 AAAGAGAAAGAA
1 AAAAAGAAA-AA
*
39602842 AGAGAAGAAAAA
1 A-AAAAGAAAAA
*
39602854 AAATAGAAAAA
1 AAAAAGAAAAA
39602865 A
1 A
39602866 TAAGGTATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
11 25 0.69
12 5 0.14
13 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:39602832 original size:15 final size:14
Alignment explanation
Indices: 39602808--39602865 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
39602798 GTGGTGCCGG
39602808 AAAAAGA-AAAAAA
1 AAAAAGAGAAAAAA
*
39602821 AAAGAGAGAAAAGAGA
1 AAAAAGAGAAAA-A-A
*
39602837 AAGAAAGAGAAGAAA
1 AA-AAAGAGAAAAAA
*
39602852 AAAAATAGAAAAAA
1 AAAAAGAGAAAAAA
39602866 TAAGGTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 6 0.17
14 14 0.39
15 4 0.11
16 4 0.11
17 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAGAGAAAAAA
Found at i:39603208 original size:34 final size:35
Alignment explanation
Indices: 39603162--39603242 Score: 94
Period size: 37 Copynumber: 2.3 Consensus size: 35
39603152 TTTTACATTA
* * **
39603162 TATTATTGTTAG-T-TATTATTTTTAGTAAAACCC
1 TATTATTATTAGTTATATTATTTTGAGTAAAAAAC
39603195 TAATTATTATTAGTTAGTATTATTTTGAGTAAAAAAC
1 T-ATTATTATTAGTTA-TATTATTTTGAGTAAAAAAC
39603232 TATTATTATTA
1 TATTATTATTA
39603243 TTGTGTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.03
34 10 0.25
35 1 0.03
36 10 0.25
37 18 0.45
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.51
Consensus pattern (35 bp):
TATTATTATTAGTTATATTATTTTGAGTAAAAAAC
Found at i:39603242 original size:76 final size:77
Alignment explanation
Indices: 39603040--39603265 Score: 237
Period size: 76 Copynumber: 2.9 Consensus size: 77
39603030 TAGTTATTAA
* * * *
39603040 TAATTATTGTTACTTAGTATTATTGTTAGTCAAAAACTAATATTATTATTATGGTTAGTTATTAG
1 TAATTATTATTAGTTAGTATTATTGTTAGT-AAAAA--ACTATTATTATTATTGTTAGTTATTAG
39603105 GATTAGTAAAAACCC
63 GATTAGTAAAAACCC
* **** **
39603120 TAATTATTATTTTAGTTAGTATGATTGTTAGT-TTTTAC-ATTA-TATTATTGTTAGTTATTATT
1 TAATTATTA--TTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATTGTTAGTTATTAGG
*
39603182 TTTAGT-AAAACCC
64 ATTAGTAAAAACCC
39603195 TAATTATTATTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTATTGTGTTAGTTATTAG
1 TAATTATTATTAGTTAGTATTATTGTT-AGTAAAAAACTATTATTATTA-T-TGTTAGTTATTAG
39603259 GATTAGT
63 GATTAGT
39603266 GGTTAAACGT
Statistics
Matches: 118, Mismatches: 20, Indels: 18
0.76 0.13 0.12
Matches are distributed among these distances:
72 2 0.02
73 17 0.14
74 2 0.02
75 20 0.17
76 27 0.23
77 5 0.04
78 18 0.15
80 8 0.07
82 19 0.16
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (77 bp):
TAATTATTATTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTATTGTTAGTTATTAGGAT
TAGTAAAAACCC
Found at i:39608709 original size:153 final size:153
Alignment explanation
Indices: 39608430--39608965 Score: 757
Period size: 153 Copynumber: 3.5 Consensus size: 153
39608420 CAAAACAAAG
* * *
39608430 TTAGTAAAAAACCCTTATTTCGACCCTTTGTTCATATTTTTTCCCCAGATTTTATTACTTTCAAA
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTT-CTCAGATTTTATTACTTTCAAA
*
39608495 AAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
65 AAATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
* * * *
39608560 ATTAATTTTATTTTTTAAATAAAT
130 ATTTAGTGTGTTTTTTAAATAAAT
39608584 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
* *
39608649 AATATACTATTTTCTAATTTTCTAATTTTATATTATTTTAGTACATTATGTTTGAAATGTATTAA
66 AATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
39608714 TTTAGTGTGTTTTTTAAATAAAT
131 TTTAGTGTGTTTTTTAAATAAAT
*
39608737 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTC-CCGTATTTTATTACTTTC--A
1 TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAG-ATTTTATTACTTTCAAA
*
39608799 AAA-A-AC-A-TAT-T-ATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
65 AAATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTA
*
39608858 ATTTAGTGTGTTTTTTATATAAAT
130 ATTTAGTGTGTTTTTTAAATAAAT
* * * *
39608882 TTAGTAAAAAAAACCTTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACT
1 TTAGT--AAAAAACCCTTATTTCGGCCCTTTGTTCGTA---TT-TT-TTCTCAGATTTTATTACT
**
39608947 TTCAATGAATATACTATTT
59 TTCAAAAAATATACTATTT
39608966 CCATTTTTTT
Statistics
Matches: 344, Mismatches: 23, Indels: 26
0.88 0.06 0.07
Matches are distributed among these distances:
145 74 0.22
146 1 0.00
147 30 0.09
148 1 0.00
149 2 0.01
150 3 0.01
151 6 0.02
152 18 0.05
153 162 0.47
154 42 0.12
155 1 0.00
156 2 0.01
157 1 0.00
158 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (153 bp):
TTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCAGATTTTATTACTTTCAAAA
AATATACTATTTTCTAATTTTCTTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
TTTAGTGTGTTTTTTAAATAAAT
Found at i:39609280 original size:10 final size:10
Alignment explanation
Indices: 39609265--39609330 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
39609255 TTCCTTATTT
39609265 TTTTTCTTTC
1 TTTTTCTTTC
*
39609275 TTTTTCCTTC
1 TTTTTCTTTC
** **
39609285 CCTCCCTCTTC
1 TTTTTCT-TTC
39609296 TTCTTCTCTTTTC
1 TT-TT-TCT-TTC
39609309 TTTTTCTTTC
1 TTTTTCTTTC
39609319 TTTTTCTTTC
1 TTTTTCTTTC
39609329 TT
1 TT
39609331 CTCCTTCTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 26 0.62
11 6 0.14
12 3 0.07
13 7 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:39609315 original size:13 final size:14
Alignment explanation
Indices: 39609296--39609349 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
39609286 CTCCCTCTTC
39609296 TTCTTCTCTTTTCT
1 TTCTTCTCTTTTCT
39609310 TT-TTCTTTCTTTTTCT
1 TTCTTC--TC-TTTTCT
*
39609326 TTCTTCTC-CTTCT
1 TTCTTCTCTTTTCT
39609339 TTCTTCTCTTT
1 TTCTTCTCTTT
39609350 CAGCCGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 15 0.45
14 3 0.09
15 4 0.12
16 8 0.24
17 3 0.09
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTCTCTTTTCT
Found at i:39609319 original size:17 final size:17
Alignment explanation
Indices: 39609293--39609332 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
39609283 TCCCTCCCTC
39609293 TTCTTC-TTCTCTTTTCT
1 TTCTTCTTTCT-TTTTCT
39609310 TT-TTCTTTCTTTTTCT
1 TTCTTCTTTCTTTTTCT
39609326 TTCTTCT
1 TTCTTCT
39609333 CCTTCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTCTTTTTCT
Found at i:39609429 original size:27 final size:27
Alignment explanation
Indices: 39609380--39609450 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
39609370 ATATAAGAGG
* *
39609380 CTGGTGTCGCCTGTGGCCGTGGCACCT
1 CTGGTGTCGCCTCTGGCCCTGGCACCT
*
39609407 TTGGTGTCGCCTCT-GCCACTGGCACCT
1 CTGGTGTCGCCTCTGGCC-CTGGCACCT
* *
39609434 CTGGTGCCGCCTTTGGC
1 CTGGTGTCGCCTCTGGC
39609451 AGGCCCTCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 3 0.08
27 31 0.86
28 2 0.06
ACGTcount: A:0.04, C:0.35, G:0.32, T:0.28
Consensus pattern (27 bp):
CTGGTGTCGCCTCTGGCCCTGGCACCT
Found at i:39609986 original size:22 final size:20
Alignment explanation
Indices: 39609950--39610008 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
39609940 GGCCCGACCC
39609950 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
39609972 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
39609993 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
39610009 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:39610034 original size:29 final size:29
Alignment explanation
Indices: 39609975--39610065 Score: 130
Period size: 29 Copynumber: 3.1 Consensus size: 29
39609965 ACCAAAAATT
*
39609975 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAA--ATTTAAAAAA
*
39610007 TATTTTAAAATTAAAAAAAATTTAAAAAG
1 TATTTTAAAATTAAAAAAAATTTAAAAAA
39610036 TATTTTAAAATT-AAAAAAATTTAAAAAA
1 TATTTTAAAATTAAAAAAAATTTAAAAAA
39610064 TA
1 TA
39610066 AATATATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 17 0.30
29 20 0.36
31 13 0.23
32 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAA
Found at i:39611514 original size:22 final size:22
Alignment explanation
Indices: 39611465--39611514 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
39611455 TAAGTATTTA
*
39611465 ATTTTTTTTCATTATTAAAAAT
1 ATTTTTTTTCATTACTAAAAAT
* *
39611487 AATTTTTTTCATTACCT-AACAT
1 ATTTTTTTTCATTA-CTAAAAAT
39611509 ATTTTT
1 ATTTTT
39611515 CAATTTTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTTTTCATTACTAAAAAT
Found at i:39611557 original size:30 final size:32
Alignment explanation
Indices: 39611523--39611583 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
39611513 TTCAATTTTC
* *
39611523 AAAAACAAT-AAAAA-ATATTTTTAAAAATGA
1 AAAAAAAATGAAAAATATATTTTCAAAAATGA
39611553 AAAAAAAATGAAAAATATATTTTCAAAAATG
1 AAAAAAAATGAAAAATATATTTTCAAAAATG
39611584 GGGAGCCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 5 0.19
32 14 0.52
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (32 bp):
AAAAAAAATGAAAAATATATTTTCAAAAATGA
Found at i:39613102 original size:125 final size:122
Alignment explanation
Indices: 39612879--39613129 Score: 385
Period size: 125 Copynumber: 2.0 Consensus size: 122
39612869 AACCCCCAAT
* *
39612879 AGTAAAGACGTACCTTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
1 AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
* * *
39612944 CAATGACTCCATCTCTAGTTCTTCCAAGCTGTAAGAAAATATCAGTAGTACATTGTA
66 CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
* * *
39613001 AGTAAAGACATACCCTGTGAGAGATCTTATTTTATCAAGGTCTCTAACAAAATCAGAATCAACAT
1 AGTAAAGACATACCCTGTGAGAGATC---TTTTATCAAGGTCTCCAAAAAAATCAAAATCAACAT
* *
39613066 ACTCAATGACTCCATCTCTAGTTCTTCCAAATTGTAAGAAAATATCAATAGTATATCGTA
63 ACTCAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
39613126 AGTA
1 AGTA
39613130 TCTGAAAATC
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
122 24 0.21
125 92 0.79
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (122 bp):
AGTAAAGACATACCCTGTGAGAGATCTTTTATCAAGGTCTCCAAAAAAATCAAAATCAACATACT
CAATGACTCCATCTCTAGTTCTTCCAAACTGTAAGAAAATATCAATAGTACATCGTA
Found at i:39628741 original size:13 final size:14
Alignment explanation
Indices: 39628703--39628741 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
39628693 TTTATTTAGT
*
39628703 AAATATGTATTTTTA
1 AAATATATA-TTTTA
39628718 AAATATATATTTTA
1 AAATATATATTTTA
39628732 AAAT-TATATT
1 AAATATATATT
39628742 ATTTATGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AAATATATATTTTA
Found at i:39629240 original size:16 final size:16
Alignment explanation
Indices: 39629219--39629254 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39629209 TGTTTAAGAA
*
39629219 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
39629235 ATTATTATAATATTAT
1 ATTATTATAATATTAC
39629251 ATTA
1 ATTA
39629255 ACTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:39629997 original size:3 final size:3
Alignment explanation
Indices: 39629989--39630029 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
39629979 GTGAGGTAAG
39629989 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39630030 AGATGAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39631519 original size:20 final size:20
Alignment explanation
Indices: 39631481--39631519 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39631471 TATTACTCAC
*
39631481 TTTATCATTTTAAATATTTT
1 TTTATCATTTTAAAGATTTT
39631501 TTTATCA-TTTATAAGATTT
1 TTTATCATTTTA-AAGATTT
39631520 ATCACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATCATTTTAAAGATTTT
Found at i:39631685 original size:20 final size:19
Alignment explanation
Indices: 39631660--39631712 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
39631650 AAAAATTCAA
*
39631660 ATTTTATATTAAAATATTT
1 ATTTTATATTAAAATAATT
*
39631679 ATATTTATATTTAAATAATT
1 AT-TTTATATTAAAATAATT
39631699 ATTTT-TCATTAAAA
1 ATTTTAT-ATTAAAA
39631713 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 17 0.59
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTATATTAAAATAATT
Found at i:39633708 original size:4 final size:4
Alignment explanation
Indices: 39633699--39633729 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
39633689 ATATACTGTT
39633699 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
39633730 AAAAATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:39634055 original size:5 final size:5
Alignment explanation
Indices: 39634047--39634072 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39634037 ACACATTACA
39634047 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
39634073 ACTTTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:39636609 original size:18 final size:18
Alignment explanation
Indices: 39636588--39636625 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39636578 TAGAAACAGC
39636588 AAAAA-AGCACGATAGCAA
1 AAAAATAGCA-GATAGCAA
*
39636606 AAAAATAGTAGATAGCAA
1 AAAAATAGCAGATAGCAA
39636624 AA
1 AA
39636626 GCAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAATAGCAGATAGCAA
Found at i:39637865 original size:6 final size:6
Alignment explanation
Indices: 39637847--39637878 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
39637837 ATGATATGAT
*
39637847 TATTAA TACTAA TATTAA TATTAA TATTAA TA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TA
39637879 ATATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
TATTAA
Found at i:39637886 original size:12 final size:12
Alignment explanation
Indices: 39637847--39637887 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
39637837 ATGATATGAT
*
39637847 TATTAATACTAA
1 TATTAATAATAA
*
39637859 TATTAATATTAA
1 TATTAATAATAA
*
39637871 TATTAATAATAT
1 TATTAATAATAA
39637883 TATTA
1 TATTA
39637888 TTACATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TATTAATAATAA
Found at i:39637886 original size:18 final size:18
Alignment explanation
Indices: 39637845--39637887 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39637835 TTATGATATG
*
39637845 ATTATTAATACTAATATT
1 ATTATTAATACTAATAAT
* *
39637863 AATATTAATATTAATAAT
1 ATTATTAATACTAATAAT
39637881 ATTATTA
1 ATTATTA
39637888 TTACATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTAATACTAATAAT
Found at i:39647294 original size:30 final size:30
Alignment explanation
Indices: 39647233--39647294 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
39647223 GGAGTGGAGG
* ** **
39647233 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
*
39647263 GGAGTAAAAGTTTTGAGTAAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
39647293 GG
1 GG
39647295 TTTGGGAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGAAAAAGTAAAAA
Found at i:39648593 original size:124 final size:123
Alignment explanation
Indices: 39648379--39648647 Score: 400
Period size: 124 Copynumber: 2.2 Consensus size: 123
39648369 TTTTTTCGAA
* * ** *
39648379 TTGACGTATCTG-GTCAAATAGT-TGGAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
1 TTGACGTTTCTGAG-CAAATAGTAT-AAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTG
* * *
39648442 TGAAATCGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGTAAGAAATAATTTTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAA-TTTTT
39648502 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
*
39648567 GAAATCGCGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAGGAAATAATTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTT
39648626 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
39648648 GTCAAATCAC
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 22 0.17
124 92 0.69
125 19 0.14
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTT
Found at i:39649022 original size:23 final size:23
Alignment explanation
Indices: 39648994--39649532 Score: 385
Period size: 23 Copynumber: 20.9 Consensus size: 23
39648984 CTGTTAATTA
39648994 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
* *
39649017 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
39649040 AATTAAAATAGGTTAGGGTTAGGGTTTTT
1 AATT--AA-A--TTA-GGTTAGGGTTTTT
* *
39649069 AACTAAATTAGGTTAGGGATTTT
1 AATTAAATTAGGTTAGGGTTTTT
39649092 AATTAAATTAGGTTAGGGATTTTAATT
1 AATTAAATTAGGTTAGGG--TTT--TT
*
39649119 AAATTAAATTAGTTTAGGGATTTTAATT
1 -AATTAAATTAGGTTAGGG--TTT--TT
39649147 AAATTAAATTAGGTTAGGGATTTTAATT
1 -AATTAAATTAGGTTAGGG--TTT--TT
39649175 AAATTAAATTAGGTTAGGGTTTTTAATT
1 -AATTAAATTAGGTTAGGG--TTT--TT
39649203 AAATTAAATTAGGTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
* *
39649227 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
*
39649250 AATTAAATTAGGTTAGTGTTAGGGTTTT
1 AATTAAATTAGGTTA--G---GGTTTTT
*
39649278 CATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AAT-T-AA--A--TTA-GGTTAGGGTTTTT
* *
39649308 AACTAAATTAGGTTAGGATTTTTAATT
1 AATTAAATTAGGTTAGG--GTTT--TT
*
39649335 AAATTAAATTAGGCTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
*
39649359 AATTATATTAGGTTAGGGTTTTTAATT
1 AATTAAATTAGGTTAGGG--TTT--TT
*
39649386 AAATTAAATTAAGTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTT
* *
39649410 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
39649433 AATTAAATTAGGTTAGGGTAAGGGTTTTT
1 AATTAAATTAGG-T----T-AGGGTTTTT
39649462 AATTAAATTAAGTTAGGTTAGGGTTTTT
1 AATT--A--AA-TTAGGTTAGGGTTTTT
* *
39649490 AATTAAGTTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
39649513 AATTAAATTAGGTTAGGGTT
1 AATTAAATTAGGTTAGGGTT
39649533 AGGGTTTTTA
Statistics
Matches: 437, Mismatches: 35, Indels: 88
0.78 0.06 0.16
Matches are distributed among these distances:
23 176 0.40
24 14 0.03
25 11 0.03
26 12 0.03
27 8 0.02
28 157 0.36
29 31 0.07
30 9 0.02
31 1 0.00
32 1 0.00
33 4 0.01
34 8 0.02
35 5 0.01
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:39649027 original size:28 final size:28
Alignment explanation
Indices: 39648987--39649549 Score: 515
Period size: 28 Copynumber: 21.4 Consensus size: 28
39648977 AGTTCTTCTG
39648987 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649015 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* **
39649038 TTAATTAAAATAGGTTAGGGTTAGGG--T
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* *
39649065 TT--TT-AACTAAATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649090 TTAATT--A---AATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* *
39649113 TTAATTAAATTAAATTAGTTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649141 TTAATTAAATTAAATTAGGTTAGGGATT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39649169 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39649197 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649225 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
39649248 TTAATTAAATTAGGTTAGTGTTAGGG-TT
1 TTAATTAAATTAAATTAG-GTTAGGGTTT
* * **
39649276 TTCATGTAAAATAGGTTAGGGTTAGGG--T
1 TTAAT-TAAATTAAATTA-GGTTAGGGTTT
* *
39649304 TT--TT-AACTAAATTAGGTTAGGATTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649329 TTAATTAAATTAAATTAGGCTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
39649357 TTAATT--A-T--ATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649380 TTAATTAAATTAAATTAAGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649408 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
** *
39649431 TTAATTAAATTAGGTTAGGGTAAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
39649460 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
39649488 TTAATTAAGTT--A--A-GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
39649511 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
39649540 TTAATCAAAT
1 TTAATTAAAT
39649550 AATGTCAAAA
Statistics
Matches: 455, Mismatches: 35, Indels: 89
0.79 0.06 0.15
Matches are distributed among these distances:
23 136 0.30
24 18 0.04
25 12 0.03
26 7 0.02
27 11 0.02
28 194 0.43
29 76 0.17
30 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
TTAATTAAATTAAATTAGGTTAGGGTTT
Found at i:39649144 original size:51 final size:51
Alignment explanation
Indices: 39648994--39649532 Score: 493
Period size: 51 Copynumber: 10.4 Consensus size: 51
39648984 CTGTTAATTA
*
39648994 AATTAAATTAGGTTAGGGTTTTTAATTAAGTT--A--A-GTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * *
39649040 AATTAAAATAGGTTAGGGTTAGGGTTT--TT-AACTAAATTAGGTTAGGGATTTT
1 AATTAAATTAGGTTAGGGTT----TTTAATTAAATTAAATTAGGTTAGGGTTTTT
* *
39649092 AATTAAATTAGGTTAGGGATTTTAATTAAATTAAATTAGTTTAGGGATTTTAATT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT
*
39649147 AAATTAAATTAGGTTAGGGATTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT
*
39649203 AAATTAAATTAGGTTAGGGTTTTTAATTAAGTT--A--A-GTTAGGGTTTTT
1 -AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * * **
39649250 AATTAAATTAGGTTAGTGTTAGGGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTA--G---GGTTTTTAAT-TAAATTAAATTA-GGTTAGGGTTTTT
* * *
39649308 AACTAAATTAGGTTAGGATTTTTAATTAAATTAAATTAGGCTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* *
39649359 AATTATATTAGGTTAGGGTTTTTAATTAAATTAAATTAAGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
* * ** *
39649410 AATTAAGTTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTT
*
39649462 AATTAAATTAAGTTAGGTTAGGGTTTTTAATTAAGTT--A--A-GTTAGGGTTTTT
1 AATT--A--AA-TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
39649513 AATTAAATTAGGTTAGGGTT
1 AATTAAATTAGGTTAGGGTT
39649533 AGGGTTTTTA
Statistics
Matches: 415, Mismatches: 43, Indels: 70
0.79 0.08 0.13
Matches are distributed among these distances:
46 47 0.11
47 6 0.01
48 6 0.01
49 5 0.01
50 5 0.01
51 138 0.33
52 58 0.14
53 10 0.02
54 2 0.00
55 2 0.00
56 87 0.21
57 23 0.06
58 26 0.06
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (51 bp):
AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT
Found at i:39650856 original size:34 final size:34
Alignment explanation
Indices: 39650809--39650877 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
39650799 GCCAGTAAAA
*
39650809 TATTTTACGTAAAATGATTT-CGGGAAAATGTTT
1 TATTTTACGTAAAATGATTTACGGGAAAATATTT
* *
39650842 TATTTTTCTGTAAAATGATTTACTGGAAAATATTT
1 TATTTTAC-GTAAAATGATTTACGGGAAAATATTT
39650877 T
1 T
39650878 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 7 0.23
34 12 0.39
35 12 0.39
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (34 bp):
TATTTTACGTAAAATGATTTACGGGAAAATATTT
Found at i:39652335 original size:23 final size:25
Alignment explanation
Indices: 39652299--39652345 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
39652289 ATAACAAAAA
39652299 ATAAATTAATAAATATCTAAAATAC
1 ATAAATTAATAAATATCTAAAATAC
*
39652324 ATAAA-TAA-AAATATCTTAAATA
1 ATAAATTAATAAATATCTAAAATA
39652346 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAATTAATAAATATCTAAAATAC
Found at i:39652575 original size:22 final size:22
Alignment explanation
Indices: 39652545--39652586 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39652535 ATTTGGAGAT
*
39652545 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
39652567 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
39652587 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:39652594 original size:30 final size:30
Alignment explanation
Indices: 39652558--39652616 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
39652548 TTGAAGGAAA
*
39652558 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAATTTGAGAGT
39652588 TTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGGAATTTGAGAG
39652617 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAATTTGAGAGT
Found at i:39652607 original size:52 final size:51
Alignment explanation
Indices: 39652536--39652638 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
39652526 TTAATATGGA
* * *
39652536 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAA-TTGAGAG
* *
39652587 TTTGAGAGAATTTTGGAAGGAATTTGAGAGAATTTTTGAACGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
39652639 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.34
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
Found at i:39652612 original size:22 final size:22
Alignment explanation
Indices: 39652587--39652657 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
39652577 AATTTGAGAG
*
39652587 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
39652609 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
39652632 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
39652653 ATTGA
1 TTTGA
39652658 TATTGAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 4 0.09
22 38 0.83
23 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:39653872 original size:13 final size:13
Alignment explanation
Indices: 39653854--39653879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39653844 TTTTGATATA
39653854 TTTTATAATTTTT
1 TTTTATAATTTTT
39653867 TTTTATAATTTTT
1 TTTTATAATTTTT
39653880 ACAAATTTTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATAATTTTT
Found at i:39653926 original size:19 final size:20
Alignment explanation
Indices: 39653898--39653948 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
39653888 TTCAGAAAAT
*
39653898 TTTAAT-ATTTTTTTTAA-G
1 TTTAATAATTTTTTATAACG
*
39653916 TTTAATAATTTTTTATAACT
1 TTTAATAATTTTTTATAACG
*
39653936 TTTATTAATTTTT
1 TTTAATAATTTTT
39653949 ATCTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 12 0.43
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATAATTTTTTATAACG
Found at i:39670593 original size:7 final size:7
Alignment explanation
Indices: 39670577--39670607 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39670567 AAGAGGAAGA
39670577 AATAAAG
1 AATAAAG
*
39670584 AATAAGG
1 AATAAAG
39670591 AATAAAG
1 AATAAAG
39670598 AATAAAG
1 AATAAAG
39670605 AAT
1 AAT
39670608 TTGAGAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
AATAAAG
Found at i:39671601 original size:510 final size:511
Alignment explanation
Indices: 39670635--39671659 Score: 1712
Period size: 510 Copynumber: 2.0 Consensus size: 511
39670625 TCCATCCAAA
*
39670635 GATAATAGAAGGCTGGTAGAGAGGAATGAAGGGATAGATAAATGCTTTATGCTCTTAGAGAAAGC
1 GATAATAGAAGGCTGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGC
* * *
39670700 CAATGATCAATTGCATAATGAGCTTTCTATGCTTCGAGCTGAAAAACTTGGCCTTTAGGAAAGTA
66 CAATGATCAATTGCATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTA
*
39670765 TGGAAACCATGGGTGAGAAGCACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCC
131 TGGAAACCATGGGTGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCC
*
39670830 CTACGAAGTACTAAGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAAC
196 CTACGAAGTACCAAGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAAC
* * *
39670895 ATTTTGTTGCACACCTAAGTTGTTGGGGGGCCTTTTGATGCTTGGAGGGTAAACCTCGATGCCTT
261 ATTTTGTTGCACACCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTT
* * *
39670960 GAGTCATCTTAAAGATTCTCAACTTGGTTTTGACATCCACTTCCCTTCGGGACCTGCTTGGGAAG
326 AAGTCATCTCAAAGATACTCAACTTGGTTTTGACATCCACTTCCCTTCGGGACCTGCTTGGGAAG
*
39671025 AGTTCACTAAAGAGTGGAAGAACTCAAATAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGT
391 AGTTCACTAAAGAGTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGT
* * *
39671090 GTTGCTCCCTTCGTAGATTCTAAGAAAGGT-GAGCGAAAATACAATGGAAGATGTT
456 GTTGCTCCATTCGCAGATTCTAAGAAAGGTAGAGCGAAAATACAAGGGAAGATGTT
* *
39671145 GATAATAGGAGGTTGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGC
1 GATAATAGAAGGCTGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGC
*
39671210 CAATGATCAATTGCATAAAGAGATTTCTATGCTTCAAGTTGAAAAACTTGGCCTTTAGGAAAGTA
66 CAATGATCAATTGCATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTA
39671275 TGGAAACCATGGGTGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCC
131 TGGAAACCATGGGTGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCC
39671340 CTACGAAGTACCAAGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAAC
196 CTACGAAGTACCAAGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAAC
* * *
39671405 ATTTTGTTGCACACCTAAGTTGTTGGTAGGCCTTTTGACGCTCGGAGGGTGAACCTTGATGCCTT
261 ATTTTGTTGCACACCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTT
*** *
39671470 AAGTCATCTCAAAGATACTCAACTTGGTTTTGACATTTGCTTTCCTTCGGGACCTGCTTGGGAAG
326 AAGTCATCTCAAAGATACTCAACTTGGTTTTGACATCCACTTCCCTTCGGGACCTGCTTGGGAAG
* * * * *
39671535 AGTTC-CTTGAAGAGTGGAAGAACTCAAACGAACTTTTTGTGGCTGATAAACCTGTTGAGGATAG
391 AGTTCAC-TAAAGAGTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAG
* * *
39671599 TGTTGCTCCATTCGCAGATTTTGAGAAAGGTGAGAGCGAAGATACAAGGGAAGATGTT
455 TGTTGCTCCATTCGCAGATTCTAAGAAAGGT-AGAGCGAAAATACAAGGGAAGATGTT
39671657 GAT
1 GAT
39671660 GATTCAAATG
Statistics
Matches: 478, Mismatches: 34, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
509 1 0.00
510 451 0.94
512 26 0.05
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (511 bp):
GATAATAGAAGGCTGGTAGAGAGGAATGAAGGGATAGATAAATGCCTTATGCTCTTAGAGAAAGC
CAATGATCAATTGCATAAAGAGATTTCTATGCTTCAAGCTGAAAAACTTGGCCTTTAGGAAAGTA
TGGAAACCATGGGTGAGAAGAACAAAATTGATACGGCTAACTTTGAAAAGTGCCATGAGGAAGCC
CTACGAAGTACCAAGCAGAGACGATGCACAAGTTTCAGGACTATATGCCAGACTTGAAGTCAAAC
ATTTTGTTGCACACCTAAGTTGTTGGGAGGCCTTTTGACGCTCGGAGGGTAAACCTCGATGCCTT
AAGTCATCTCAAAGATACTCAACTTGGTTTTGACATCCACTTCCCTTCGGGACCTGCTTGGGAAG
AGTTCACTAAAGAGTGGAAGAACTCAAACAAACTTTTTATGGCTGATAAACCTGTTAAGCATAGT
GTTGCTCCATTCGCAGATTCTAAGAAAGGTAGAGCGAAAATACAAGGGAAGATGTT
Found at i:39672146 original size:134 final size:134
Alignment explanation
Indices: 39671906--39672219 Score: 421
Period size: 134 Copynumber: 2.3 Consensus size: 134
39671896 AACTGTTCAT
* * *
39671906 GATCGTAAATCAACAAGTTTTAATAATATCAGTCGTGATCATAATTCAGCAAACTGTTTGAATGA
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCATAAATCAGCAAACTGTTTGAATAA
* * * * * * *
39671971 AGTTGTGGTCGTAAATCAGTGAACTCAAAATAAATTGTTCATGATTGTAAATCAATGAACTTAAG
66 AGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
39672036 TTGC
131 TTGC
* * * *
39672040 GATCGTAAATCAGCAAGCTTTAATAATACCAGTCGTGATCATAAATCAGCGAACTTTTTGAATAA
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCATAAATCAGCAAACTGTTTGAATAA
* * * * *
39672105 AGTTGCGATTGTAAATTAGAGAACTTAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAA
66 AGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
*
39672170 TTGT
131 TTGC
* * *
39672174 GATCATAAATCAACAAGTTTTAATAATACCAGTTGTGATCGTAAAT
1 GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCATAAAT
39672220 TGACAAACAA
Statistics
Matches: 155, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
134 155 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (134 bp):
GATCGTAAATCAACAAGTTTTAATAATACCAGTCGTGATCATAAATCAGCAAACTGTTTGAATAA
AGTTGCGATCGTAAATCAGAGAACTCAAAATAAACTGTTCATAATCGTAAATCAATGAACTTAAA
TTGC
Found at i:39672292 original size:233 final size:232
Alignment explanation
Indices: 39671997--39672436 Score: 619
Period size: 233 Copynumber: 1.9 Consensus size: 232
39671987 CAGTGAACTC
** * *
39671997 AAAATAAATTGTTCATGATTGTAAATCAATGAACTTAAGTTGCGATCGTAAATCAGCAAGCTTTA
1 AAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAGCTTTA
* ** *
39672062 ATAATACCAGTCGTGATCATAAATCAGCGAACTTTTTGAATAAAGTTGCGATTGTAAATTAGAGA
66 ATAATACCAGTCGTGATCATAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATCAGAGA
* * * * *
39672127 ACTTAAAATGAACTGTTCATAATCGTAAATCAGTGAACTTAAATTGTGATCATAAATCAACAAGT
131 ACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTT-AAGTGTGATCATAAATCAACAAGC
39672192 TTTAATAATACCAGTTGTGATCGTAAATTGACAAACAA
195 TTTAATAATACCAGTTGTGATCGTAAATTGACAAACAA
* *
39672230 AAAATAAATTGTTCGTGATCATAAATCAATGAACTTAAGTTGTGATCATAAATCAACAAGCTTTA
1 AAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAGCTTTA
** * ** * *
39672295 ATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATCAGTGA
66 ATAATACCAGTCGTGATCATAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATCAGAGA
* * * * * *
39672360 ACTCAAAATGAATTATTCATGATCGTAAATCAATTAACTTAAGTGTGATCTTAAATTAACATGCT
131 ACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATCATAAATCAACAAGCT
39672425 TTAATAATACCA
196 TTAATAATACCA
39672437 TTCATAATCA
Statistics
Matches: 179, Mismatches: 28, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
232 32 0.18
233 147 0.82
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (232 bp):
AAAATAAATTGTTCATGATCATAAATCAATGAACTTAAGTTGCGATCATAAATCAACAAGCTTTA
ATAATACCAGTCGTGATCATAAATCAGCGAACTGTTTGAATAAAGTTGCGACCGTAAATCAGAGA
ACTCAAAATGAACTATTCATAATCGTAAATCAATGAACTTAAGTGTGATCATAAATCAACAAGCT
TTAATAATACCAGTTGTGATCGTAAATTGACAAACAA
Found at i:39672383 original size:134 final size:134
Alignment explanation
Indices: 39672230--39672853 Score: 696
Period size: 134 Copynumber: 4.7 Consensus size: 134
39672220 TGACAAACAA
* * * * * * *
39672230 AAAATAAATTGTTCGTGATCATAAATCAATGAACTTAAGTTGTGATCATAAATCAACAAGCTTTA
1 AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCATAAATCAGCAAGCTTTA
* * ** * *
39672295 ATAATACCAGTCGTGATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATCAGTGA
66 ATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAATCAGCGA
39672360 ACTC
131 ACTC
* * * * * * *
39672364 AAAATGAATTATTCATGATCGTAAATCAATTAACTTAAG-TGTGATCTTAAATTAACATGCTTTA
1 AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCATAAATCAGCAAGCTTTA
* * * * * *
39672428 ATAATACCATTCATAATCATAAATCAGCGAACTGTTTGAATGGAGTTGCAATTGTAAATCAAC-A
66 ATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAATCAGCGA
39672492 AGCTC
131 A-CTC
* * * *
39672497 AAAATTAACTGTTCATGATCGTAAATCAATAAACTTAAGTTGTGATCGTAAATCAGTAAGCTTTA
1 AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCATAAATCAGCAAGCTTTA
* * * * * * **
39672562 ATAATACTAGTTGTGATCGTAAATCAGTGAACTTTTTGAATGGACTTGCGATCGTAAATTGGCGA
66 ATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAATCAGCGA
39672627 ACTC
131 ACTC
* * * * *
39672631 AAAATGAACTGTTTATGATCATAAATTAATAAACCTAAGCTGTGAT-AGTAAATCAGTAAGCTTT
1 AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCA-TAAATCAGCAAGCTTT
* * * * * * * *
39672695 AATAATTCTAGTCGTGATTGTAAATCAGCGAATTGTTTGAATGGAGTTACAATCATGAATGAGCG
65 AATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAATCAGCG
39672760 AACTC
130 AACTC
* * * **
39672765 ATAATGAACTGGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAGCAAGCTTTA
1 AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCATAAATCAGCAAGCTTTA
*
39672830 ATAATACCAGTTGTGATCGTAAAT
66 ATAATACCAGTCGTGATCGTAAAT
39672854 ACCCGAACTC
Statistics
Matches: 409, Mismatches: 76, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
132 2 0.00
133 111 0.27
134 294 0.72
135 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (134 bp):
AAAATGAACTGTTCATGATCGTAAATCAATAAACTTAAGCTGTGATCATAAATCAGCAAGCTTTA
ATAATACCAGTCGTGATCGTAAATCAGCGAACTGTTTGAATGGAGTTGCAATCGTAAATCAGCGA
ACTC
Found at i:39672818 original size:268 final size:267
Alignment explanation
Indices: 39672245--39672853 Score: 770
Period size: 268 Copynumber: 2.3 Consensus size: 267
39672235 AAATTGTTCG
* * * *
39672245 TGATCATAAATCAATGAACTTAAGTTGTGATCATAAATCAACAAGCTTTAATAATACCAGTCGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
* * * * *
39672310 ATTGTAAATCAGTGAACTGTTTGAATGGAGTTGTGACCGTAAATCAGTGAACTCAAAATGAATTA
66 ATCGTAAATCAGTGAACTGTTTGAATGGACTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
* * * ** * * *
39672375 TTCATGATCGTAAATCAATTAACTTAAGTGTGATCTTAAATTAACATGCTTTAATAATACCATTC
131 TTCATGATCATAAATCAATAAACCTAAGTGTGATAGTAAATCAACAAGCTTTAATAATACCAGTC
* ** *
39672440 ATAATCATAAATCAGCGAACTGTTTGAATGGAGTTGCAATTGTAAATCAACAAGCTCAAAATTAA
196 ATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCATAAATCAACAAGCTCAAAATGAA
*
39672505 CTGTTCA
261 CTGGTCA
* * *
39672512 TGATCGTAAATCAATAAACTTAAGTTGTGATCGTAAATCAGTAAGCTTTAATAATACTAGTTGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
* * ** *
39672577 ATCGTAAATCAGTGAACTTTTTGAATGGACTTGCGATCGTAAATTGGCGAACTCAAAATGAACTG
66 ATCGTAAATCAGTGAACTGTTTGAATGGACTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
* * ** * *
39672642 TTTATGATCATAAATTAATAAACCTAAGCTGTGATAGTAAATCAGTAAGCTTTAATAATTCTAGT
131 TTCATGATCATAAATCAATAAACCTAAG-TGTGATAGTAAATCAACAAGCTTTAATAATACCAGT
* * ** * * * * *
39672707 CGTGATTGTAAATCAGCGAATTGTTTGAATGGAGTTACAATCATGAATGAGCGAA-CTCATAATG
195 CATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCATAAATCAAC-AAGCTCAAAATG
39672771 AACTGGTCA
259 AACTGGTCA
* *
39672780 TGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
1 TGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
39672845 ATCGTAAAT
66 ATCGTAAAT
39672854 ACCCGAACTC
Statistics
Matches: 290, Mismatches: 50, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
267 136 0.47
268 152 0.52
269 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (267 bp):
TGATCGTAAATCAATGAACTTAAGTTGTGATCGTAAATCAGCAAGCTTTAATAATACCAGTTGTG
ATCGTAAATCAGTGAACTGTTTGAATGGACTTGCGACCGTAAATCAGCGAACTCAAAATGAACTA
TTCATGATCATAAATCAATAAACCTAAGTGTGATAGTAAATCAACAAGCTTTAATAATACCAGTC
ATAATCATAAATCAGCGAACTGTTTGAATGGAGTTACAATCATAAATCAACAAGCTCAAAATGAA
CTGGTCA
Found at i:39672919 original size:71 final size:71
Alignment explanation
Indices: 39672838--39672969 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
39672828 TAATAATACC
* * *
39672838 AGTTGTGATCGTAAAT-ACCCGAACTCAAAATGAACTGTTCATGATCGTAAATCAACGAACTGTT
1 AGTTGCGATCGTAAATCA-CCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACTGTT
39672902 TGAATAG
65 TGAATAG
* * * *
39672909 AGTTGCGATCGTAAATCAGCAAACTCAAAATGAACTATTTATGATCGTTAATCAATGAACT
1 AGTTGCGATCGTAAATCACCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACT
39672970 TAAGTTGTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
71 52 0.98
72 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (71 bp):
AGTTGCGATCGTAAATCACCAAACTCAAAATGAACTATTCATGATCGTAAATCAACGAACTGTTT
GAATAG
Found at i:39672955 original size:170 final size:170
Alignment explanation
Indices: 39672709--39673023 Score: 450
Period size: 170 Copynumber: 1.9 Consensus size: 170
39672699 ATTCTAGTCG
* * * * * * * *
39672709 TGATTGTAAATCAGCGAATTGTTTGAATGGAGTTACAATCATGAATGAGCGAACTCATAATGAAC
1 TGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATGAAC
* *
39672774 TGGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAGCAAGCTTTAATAATACCA
66 TAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATACCA
* *
39672839 GTTGTGATCGTAAATACCCGAACTCAAAATGAACTGTTCA
131 GTCGTGATCATAAATACCCGAACTCAAAATGAACTGTTCA
* * *
39672879 TGATCGTAAATCAACGAACTGTTTGAATAGAGTTGCGATCGTAAATCAGCAAACTCAAAATGAAC
1 TGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATGAAC
* * * * *
39672944 TATTTATGATCGTTAATCAATGAACTTAAGTTGTGATTGTAAATCAACAAGCTTTAATAATTCCA
66 TAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATACCA
39673009 GTCGTGATCATAAAT
131 GTCGTGATCATAAAT
39673024 CAGCGATCTG
Statistics
Matches: 125, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
170 125 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (170 bp):
TGATCGTAAATCAACGAACTGTTTGAATAGAGTTACAATCATAAATCAGCAAACTCAAAATGAAC
TAGTCATGATCGTAAATCAATGAACTTAAGCTGTGATTGTAAATCAACAAGCTTTAATAATACCA
GTCGTGATCATAAATACCCGAACTCAAAATGAACTGTTCA
Found at i:39677043 original size:55 final size:55
Alignment explanation
Indices: 39676957--39677069 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 55
39676947 GGATAAAGTG
* * *
39676957 TAAGCCTTTGTATTTTTTGCCTTGGATAATTGTTGAACTTCTGCCTACAGTTCTC
1 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
* *
39677012 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGGACTTCCGCTTACAGTTCGC
1 TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
39677067 TAA
1 TAA
39677070 CTATGGCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (55 bp):
TAAGCCTTTGTATTTTTTGCCTTGGACAATTGTTGAACTTCCGCCTACAGTTCGC
Found at i:39689618 original size:15 final size:15
Alignment explanation
Indices: 39689582--39689611 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39689572 TCAAAATAAA
*
39689582 AAATTAATTAAAATT
1 AAATTAACTAAAATT
39689597 AAATTAACTAAAATT
1 AAATTAACTAAAATT
39689612 GAGTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAACTAAAATT
Found at i:39691594 original size:84 final size:84
Alignment explanation
Indices: 39691449--39691754 Score: 308
Period size: 84 Copynumber: 3.6 Consensus size: 84
39691439 TCATTGTAAC
* * * * * * * * * *
39691449 AGGCTTAGTAGTGGTAGGAAGCAGACTGGTTGCAAGAATCTGAGTGGTTGCATGCTAGTTTAGGG
1 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTGCTGGTTTAGGG
* *
39691514 CCCTAATTATTGATGCATG
66 CCCTAATTGTTGATGCAAG
* * * * * *
39691533 AGGCTTAGTAGTGGCAGGAGACAAATTGGTTGTAGGAGTTTGGGTGGTTACTTGCTGGTTTAAGG
1 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
39691598 CCTTAGTGGTTGATGCAAG
66 CCCTAATTGTTGATGCAAG
* * ** *
39691617 AAGCTTAATGGTGGTAGGAGGCCGATTGGTTGTAGGAGTTTGAGTGATTGCTTGCTGGTTTAGGG
1 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTGCTGGTTTAGGG
* * *
39691682 -CCTCAATTGTTGCTACACG
66 CCCT-AATTGTTGATGCAAG
* * *
39691701 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGCAAGAATTTGAGTGGTTGCTTG
1 AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTG
39691755 TCGGCTTGTT
Statistics
Matches: 177, Mismatches: 44, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
83 2 0.01
84 175 0.99
ACGTcount: A:0.22, C:0.11, G:0.35, T:0.32
Consensus pattern (84 bp):
AGGCTTAGTGGTGGTAGGAGGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTGCTGGTTTAGGG
CCCTAATTGTTGATGCAAG
Found at i:39692277 original size:13 final size:13
Alignment explanation
Indices: 39692259--39692283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39692249 ATTTAATGGA
39692259 ATATATATATTTC
1 ATATATATATTTC
39692272 ATATATATATTT
1 ATATATATATTT
39692284 GAAGACGAAT
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATATATTTC
Found at i:39694192 original size:37 final size:37
Alignment explanation
Indices: 39694103--39694202 Score: 128
Period size: 37 Copynumber: 2.7 Consensus size: 37
39694093 TTACAAAACT
* * * * *
39694103 TTTGCAGAGAATCTTCACTTTTAATCTCCGTCTTTTC
1 TTTGCAGAGAATCTTTACTATTGATTTCCATCTTTTC
*
39694140 TTTGCAGATAATCTTTACTATTGATTTCCATCTTTTC
1 TTTGCAGAGAATCTTTACTATTGATTTCCATCTTTTC
* *
39694177 TTTGCAGAGAATCTTTATTGTTGATT
1 TTTGCAGAGAATCTTTACTATTGATT
39694203 AGACCTGTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (37 bp):
TTTGCAGAGAATCTTTACTATTGATTTCCATCTTTTC
Found at i:39699650 original size:13 final size:13
Alignment explanation
Indices: 39699632--39699661 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39699622 GGGGTCACAC
39699632 GGCCGTGTAGCCA
1 GGCCGTGTAGCCA
*
39699645 GGCCGTGTAGCGA
1 GGCCGTGTAGCCA
39699658 GGCC
1 GGCC
39699662 ACACACCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.30, G:0.43, T:0.13
Consensus pattern (13 bp):
GGCCGTGTAGCCA
Found at i:39701017 original size:13 final size:13
Alignment explanation
Indices: 39700994--39701053 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
39700984 TCATACATCT
39700994 ATTTCCATATAACC
1 ATTT-CATATAACC
*
39701008 AATTCATATAACC
1 ATTTCATATAACC
* *
39701021 ATTTCATGTAATC
1 ATTTCATATAACC
*
39701034 ATTTCAAATAACC
1 ATTTCATATAACC
39701047 ATTTCAT
1 ATTTCAT
39701054 TCACACATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
13 35 0.92
14 3 0.08
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:39701024 original size:27 final size:27
Alignment explanation
Indices: 39700979--39701051 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
39700969 ATCCAATGTC
* * *
39700979 CCAATTCATACATCTATTTCCATATAA
1 CCAATTCATATAACCATTTCCATATAA
*
39701006 CCAATTCATATAACCATTT-CATGTAA
1 CCAATTCATATAACCATTTCCATATAA
* * *
39701032 TCATTTCAAATAACCATTTC
1 CCAATTCATATAACCATTTC
39701052 ATTCACACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (27 bp):
CCAATTCATATAACCATTTCCATATAA
Found at i:39714561 original size:32 final size:32
Alignment explanation
Indices: 39714508--39714570 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
39714498 AAATTATAAC
* * *
39714508 TATTCAAGTGATATTACTTGAATAGTTATGTT
1 TATTCAAGAGATATTAATTGAATAATTATGTT
*
39714540 TATTTAAGAGATATTAATTGAATAATTATGT
1 TATTCAAGAGATATTAATTGAATAATTATGT
39714571 CTCTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (32 bp):
TATTCAAGAGATATTAATTGAATAATTATGTT
Found at i:39721654 original size:26 final size:26
Alignment explanation
Indices: 39721623--39721740 Score: 70
Period size: 26 Copynumber: 4.7 Consensus size: 26
39721613 CTTATGAACG
39721623 TCCCGATATATGGCTCTTCGTGAGCT
1 TCCCGATATATGGCTCTTCGTGAGCT
* * *
39721649 TCCCGATTAAAT-GCTTTTTGTGAGCT
1 TCCCGA-TATATGGCTCTTCGTGAGCT
* ** *
39721675 TCCTGAT-TAATGGCTCCCCG-AAGCT
1 TCCCGATAT-ATGGCTCTTCGTGAGCT
* * *
39721700 TCCCG--ATATGGCTC-GCTTGAACT
1 TCCCGATATATGGCTCTTCGTGAGCT
39721723 TCCCGAT-TAATGGCTCTT
1 TCCCGATAT-ATGGCTCTT
39721741 TGGAGCTATC
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
22 1 0.01
23 15 0.22
24 2 0.03
25 18 0.27
26 27 0.40
27 4 0.06
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCCCGATATATGGCTCTTCGTGAGCT
Found at i:39721699 original size:25 final size:26
Alignment explanation
Indices: 39721671--39721738 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
39721661 GCTTTTTGTG
*
39721671 AGCTTCCTGATTAATGGCTC-CCCGA
1 AGCTTCCCGATTAATGGCTCGCCCGA
**
39721696 AGCTTCCCGA-T-ATGGCTCGCTTGA
1 AGCTTCCCGATTAATGGCTCGCCCGA
39721720 A-CTTCCCGATTAATGGCTC
1 AGCTTCCCGATTAATGGCTC
39721739 TTTGGAGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 15 0.41
24 6 0.16
25 16 0.43
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCTTCCCGATTAATGGCTCGCCCGA
Found at i:39721843 original size:25 final size:25
Alignment explanation
Indices: 39721792--39721855 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
39721782 AGCTCTTATG
* ***
39721792 AGCTTCCCGTTATACAGCCCGGGTA
1 AGCTTCCCGTTATACAACCCACATA
*
39721817 AGCTTCCCGTTATACAACTCACATA
1 AGCTTCCCGTTATACAACCCACATA
39721842 AGC-TCCCTGTTATA
1 AGCTTCCC-GTTATA
39721856 TGGCTCGAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (25 bp):
AGCTTCCCGTTATACAACCCACATA
Found at i:39722707 original size:21 final size:20
Alignment explanation
Indices: 39722670--39722709 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
39722660 AAGACTTGGA
39722670 TTTGACTTGGTTTAAATGTC
1 TTTGACTTGGTTTAAATGTC
39722690 TTTGA-TTGGCTTGTAAATGT
1 TTTGACTTGG-TT-TAAATGT
39722710 GATAAAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTGACTTGGTTTAAATGTC
Found at i:39736741 original size:22 final size:22
Alignment explanation
Indices: 39736716--39736811 Score: 67
Period size: 22 Copynumber: 4.4 Consensus size: 22
39736706 ATAAAAAAAC
*
39736716 ATAATAAAATAAAATAAAAGAT
1 ATAATAAAAGAAAATAAAAGAT
**
39736738 ATAA-ATTTAGAAAATAAAAGAT
1 ATAATA-AAAGAAAATAAAAGAT
*
39736760 A-AAT-AAAGAAACTAAAA-AT
1 ATAATAAAAGAAAATAAAAGAT
*
39736779 AT-ATAAATCTAGAAAATAAAAAAT
1 ATAATAAA---AGAAAATAAAAGAT
*
39736803 AAAATAAAA
1 ATAATAAAA
39736812 AATAAAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
19 5 0.09
20 12 0.21
21 3 0.05
22 19 0.33
23 10 0.18
24 3 0.05
25 5 0.09
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (22 bp):
ATAATAAAAGAAAATAAAAGAT
Found at i:39736783 original size:43 final size:42
Alignment explanation
Indices: 39736718--39736821 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
39736708 AAAAAAACAT
* *
39736718 AATAAAAT--AAAAT-AAAAGATATAAATTTAGAAAATAAAA
1 AATAAAATAAAAAATAAAAATATATAAATCTAGAAAATAAAA
*
39736757 GAT-AAATAAAGAAACTAAAAATATATAAATCTAGAAAATAAAA
1 AATAAAATAAA-AAA-TAAAAATATATAAATCTAGAAAATAAAA
39736800 AATAAAATAAAAAATAAAAATA
1 AATAAAATAAAAAATAAAAATA
39736822 GGGCTTGGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 4 0.07
39 2 0.04
40 1 0.02
41 3 0.05
42 9 0.16
43 29 0.53
44 7 0.13
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (42 bp):
AATAAAATAAAAAATAAAAATATATAAATCTAGAAAATAAAA
Found at i:39736792 original size:23 final size:21
Alignment explanation
Indices: 39736726--39736819 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 21
39736716 ATAATAAAAT
* *
39736726 AAAATAAAAGATATAAATTTAG
1 AAAATAAAAAATA-AAATCTAG
* **
39736748 AAAATAAAAGAT-AAATAAAG
1 AAAATAAAAAATAAAATCTAG
*
39736768 AAACTAAAAATATATAAATCTAG
1 AAAATAAAAA-ATA-AAATCTAG
*
39736791 AAAATAAAAAATAAAA--TAA
1 AAAATAAAAAATAAAATCTAG
39736810 AAAATAAAAA
1 AAAATAAAAA
39736820 TAGGGCTTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 12 0.20
20 14 0.23
21 5 0.08
22 15 0.25
23 15 0.25
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAATAAAATCTAG
Found at i:39736808 original size:12 final size:12
Alignment explanation
Indices: 39736791--39736818 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39736781 ATAAATCTAG
39736791 AAAATAAAAAAT
1 AAAATAAAAAAT
39736803 AAAATAAAAAAT
1 AAAATAAAAAAT
39736815 AAAA
1 AAAA
39736819 ATAGGGCTTG
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:39738323 original size:31 final size:31
Alignment explanation
Indices: 39738282--39738343 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39738272 AGGCAAATTA
*
39738282 CAAGAGTAATTGAATCCAAATAAAACTCTTT
1 CAAGAATAATTGAATCCAAATAAAACTCTTT
*
39738313 CAAGAATAATTGAATCCTAATAAAACTCTTT
1 CAAGAATAATTGAATCCAAATAAAACTCTTT
39738344 AAAATTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAGAATAATTGAATCCAAATAAAACTCTTT
Found at i:39743901 original size:8 final size:9
Alignment explanation
Indices: 39743880--39743925 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
39743870 TGCAACTTTT
39743880 TTTTTGCGC
1 TTTTTGCGC
39743889 TTTTTGCGC
1 TTTTTGCGC
39743898 TTTTTG-G-
1 TTTTTGCGC
39743905 TTTTT----
1 TTTTTGCGC
39743910 TTTTTGCGC
1 TTTTTGCGC
39743919 TTTTTGC
1 TTTTTGC
39743926 TTTTTTCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.15
7 5 0.15
8 1 0.03
9 22 0.67
ACGTcount: A:0.00, C:0.15, G:0.20, T:0.65
Consensus pattern (9 bp):
TTTTTGCGC
Found at i:39743913 original size:21 final size:21
Alignment explanation
Indices: 39743889--39743931 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39743879 TTTTTTGCGC
*
39743889 TTTTTGCGCTTTTTGGTTTTT
1 TTTTTGCGCTTTTTGCTTTTT
39743910 TTTTTGCGCTTTTTGCTTTTT
1 TTTTTGCGCTTTTTGCTTTTT
39743931 T
1 T
39743932 CTGTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTGCGCTTTTTGCTTTTT
Found at i:39744514 original size:31 final size:31
Alignment explanation
Indices: 39744476--39744537 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
39744466 AGGCAAATTA
39744476 CAAGAGTAATTGAATCCAAATAAAACTCTTT
1 CAAGAGTAATTGAATCCAAATAAAACTCTTT
*
39744507 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCAAATAAAACTCTTT
39744538 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCAAATAAAACTCTTT
Found at i:39753192 original size:14 final size:13
Alignment explanation
Indices: 39753162--39753207 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
39753152 AAATTATTAA
39753162 TTAAGTTTAATAAT
1 TTAA-TTTAATAAT
*
39753176 TTAATTTAATAGCT
1 TTAATTTAATA-AT
39753190 TTAATTTAA-AAT
1 TTAATTTAATAAT
39753202 TTAATT
1 TTAATT
39753208 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.24
13 8 0.28
14 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (13 bp):
TTAATTTAATAAT
Found at i:39753214 original size:13 final size:12
Alignment explanation
Indices: 39753162--39753214 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 12
39753152 AAATTATTAA
39753162 TTAAGTTTAATAAT
1 TTAA-TTTAA-AAT
*
39753176 TTAATTTAATAGCT
1 TTAATTTAA-A-AT
39753190 TTAATTTAAAAT
1 TTAATTTAAAAT
39753202 TTAATTATAAAAT
1 TTAATT-TAAAAT
39753215 AATCAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 7 0.20
13 14 0.40
14 14 0.40
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (12 bp):
TTAATTTAAAAT
Found at i:39753728 original size:18 final size:17
Alignment explanation
Indices: 39753682--39753729 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
39753672 ATTTTTATAC
*
39753682 AAATAATATAAAAATTAT
1 AAATAA-ATAAAAATAAT
*
39753700 AAATATGATAAAAATAAT
1 AAATA-AATAAAAATAAT
39753718 AAAATAAATAAA
1 -AAATAAATAAA
39753730 TATTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAAATAAAAATAAT
Found at i:39757785 original size:14 final size:15
Alignment explanation
Indices: 39757766--39757798 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39757756 ATTATTTACG
*
39757766 AAAATAATACA-AAA
1 AAAATAAAACAGAAA
39757780 AAAATAAAACAGAAA
1 AAAATAAAACAGAAA
39757795 AAAA
1 AAAA
39757799 AGCTACGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAATAAAACAGAAA
Found at i:39757976 original size:10 final size:10
Alignment explanation
Indices: 39757961--39757997 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
39757951 GGTGCTGCAG
39757961 GAAAAAGAGA
1 GAAAAAGAGA
39757971 GAAAAAGAGA
1 GAAAAAGAGA
*
39757981 GAAAGAGAAGA
1 GAAAAAG-AGA
39757992 GAAAAA
1 GAAAAA
39757998 AAAGGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:39763946 original size:157 final size:158
Alignment explanation
Indices: 39763450--39764002 Score: 544
Period size: 160 Copynumber: 3.5 Consensus size: 158
39763440 ATTTCCCCAA
* * * *
39763450 ATTTTATTACTTTCAATAAAAATAT-ATTATTTTTGTATTTTATTATTTTATATTATTTCAGTAC
1 ATTTTATTACTTT-AATAAAAATATCATAATTTCT-AATTTTATTATTTTACATTATTTCAGTAC
* *
39763514 ATTTTGTTTGAAATATTTGTATTAATTATTTTTGAATTTTTAAAAAATTTAGTAAAAGACTCTTA
64 ATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTTA
* **
39763579 CTTCGGCCCTTTGTTCGTATTTTTCTCTCTAC
129 -TTCGGCCCTTTCTTCGTATTTTT-TCTCCGC
* * *
39763611 ATTTTATTACTTT-A-AAAAATATCATAATTTCTAATTTTATAATTTTGCATTATTTCAGTGCAT
1 ATTTTATTACTTTAATAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACAT
* * * * *
39763674 TATT-TTT--TA-ATTT-TATTAATT-TAGTGTG-TTTTTTAAATTAATTTAGTGTAAAAAAAAC
66 T-TTGTTTGAAATATTTGTATTAATTAT-TTCTGAATTTTTAAA-AAATTTA--GT--AAAAAAC
* * * *
39763732 CCTTATTCTTGCCCTTTGC-TCGTATTATTTT-TTCGA
124 TCTTATTC-GGCCCTTT-CTTCGTATT-TTTTCTCCGC
* * * *
39763768 ATTTTATTACTTTCAATAAAAATAT-ATTACTTT-TGTATTTTATTATTTTATATTATTTCATTA
1 ATTTTATTACTTT-AATAAAAATATCA-TAATTTCT-AATTTTATTATTTTACATTATTTCAGTA
*
39763831 CATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTT
63 CATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTT
* *
39763896 ATTTCGGCCATTTCTTTGTATTTTTTCTCCGC
128 A-TTCGGCCCTTTCTTCGTATTTTTTCTCCGC
* * *
39763928 TTTTTATTACTTT-A-AAAAATATCATAATTTCTAATTTTATTATTTTACATGATTTTAGTACAT
1 ATTTTATTACTTTAATAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACAT
*
39763991 TATGTTTGAAAT
66 TTTGTTTGAAAT
39764003 TTATTAATTT
Statistics
Matches: 317, Mismatches: 47, Indels: 60
0.75 0.11 0.14
Matches are distributed among these distances:
153 9 0.03
154 17 0.05
155 4 0.01
156 3 0.01
157 67 0.21
158 66 0.21
159 23 0.07
160 79 0.25
161 16 0.05
162 3 0.01
163 4 0.01
164 17 0.05
165 9 0.03
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (158 bp):
ATTTTATTACTTTAATAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACAT
TTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAAAACTCTTATT
CGGCCCTTTCTTCGTATTTTTTCTCCGC
Found at i:39764402 original size:36 final size:36
Alignment explanation
Indices: 39764360--39764529 Score: 155
Period size: 36 Copynumber: 4.4 Consensus size: 36
39764350 AAAAATTACC
* *
39764360 TTCTTTTTTTCCT-TCCTTCCCTCTTCTTCTTCTTCT
1 TTCTTTTTTTCCTCTCCTTTCCTTTTCTT-TTCTTCT
* *
39764396 TTCTTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTT
1 TTC--TTTTTTTCCTCTCCTTTCCTTTTCTTTTCTTC--T
* *
39764436 TTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 TTC--T-TTTTTTCCTCTCCTTTCCTTTTCTTTTCTTCT
*
39764475 TTCTTTCTTTCCTCTCCTTTCCTTTTC-TTTCTTTCT
1 TTCTTTTTTTCCTCTCCTTTCCTTTTCTTTTC-TTCT
39764511 TTCTTCTTCTTTCCCTCTC
1 TTCTT-TT-TTT-CCTCTC
39764530 ATTCTCTTCC
Statistics
Matches: 116, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.03
36 33 0.28
37 2 0.02
38 17 0.15
39 23 0.20
40 7 0.06
41 31 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (36 bp):
TTCTTTTTTTCCTCTCCTTTCCTTTTCTTTTCTTCT
Found at i:39764420 original size:5 final size:5
Alignment explanation
Indices: 39764412--39764513 Score: 65
Period size: 5 Copynumber: 21.4 Consensus size: 5
39764402 TTTTTTCTTC
* * * * *
39764412 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT TCTTTT TTCTT CTCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC-CTT TCCTT -TCCTT TCCTT
* * *
39764463 TTCTT TCC-T T-CTT T-CTT T-CTT TCCTC TCCTT TCCTT TTCTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
39764508 T-CTT TC
1 TCCTT TC
39764514 TTCTTCTTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
3 1 0.01
4 23 0.30
5 45 0.59
6 7 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:39764447 original size:41 final size:41
Alignment explanation
Indices: 39764364--39764522 Score: 185
Period size: 41 Copynumber: 4.1 Consensus size: 41
39764354 ATTACCTTCT
* *
39764364 TTTTTTCCT-TCCTTCCCTCTTC-TT-CTTCTTCTTTCTTT-
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTC
*
39764402 TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
*
39764443 TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC--TTTCTTTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
*
39764482 ---TTTCCTCTCCTTTCCTTTTCTTTCTTTCTTTCTTC-TTC
1 TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTT-TTCTTTC
39764520 TTT
1 TTT
39764523 CCCTCTCATT
Statistics
Matches: 106, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
36 26 0.25
38 12 0.11
39 22 0.21
40 9 0.08
41 37 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (41 bp):
TTTTTTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
Found at i:39764459 original size:31 final size:32
Alignment explanation
Indices: 39764383--39764524 Score: 132
Period size: 31 Copynumber: 4.4 Consensus size: 32
39764373 TCCTTCCCTC
* * *
39764383 TTCTTCTTC-TTCTTTCTTTTTTTTTCTTCTCCT
1 TTCTTCTCCTTTCCTTCTTTTTCTTTCTT-T-CT
*
39764416 TTCCTT-TTCTTTCCTTCTTTTTCTTTCTTT-T
1 TT-CTTCTCCTTTCCTTCTTTTTCTTTCTTTCT
*
39764447 TTCTTCTCCTTTCCTT-TTCTTTCCTTCTTTCT
1 TTCTTCTCCTTTCCTTCTT-TTTCTTTCTTTCT
* *
39764479 TTCTT-TCCTCTCCTTTCCTTTTCTTTCTTTCT
1 TTCTTCTCCTTTCC-TTCTTTTTCTTTCTTTCT
*
39764511 TTCTTCTTCTTTCC
1 TTCTTCTCCTTTCC
39764525 CTCTCATTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
30 5 0.05
31 29 0.32
32 25 0.27
33 13 0.14
34 20 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (32 bp):
TTCTTCTCCTTTCCTTCTTTTTCTTTCTTTCT
Found at i:39764614 original size:27 final size:27
Alignment explanation
Indices: 39764576--39764638 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
39764566 TAAATAGGCA
*
39764576 GTGCCGCCTGTGGGAGGGGCACCATCG
1 GTGCCGCCTGTGGGAGGGCCACCATCG
39764603 GTGCCGCCTGTGGGAGGGCCACCATCG
1 GTGCCGCCTGTGGGAGGGCCACCATCG
39764630 GTGCCGCCT
1 GTGCCGCCT
39764639 CTGACAGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.10, C:0.33, G:0.41, T:0.16
Consensus pattern (27 bp):
GTGCCGCCTGTGGGAGGGCCACCATCG
Found at i:39770951 original size:74 final size:72
Alignment explanation
Indices: 39770806--39770978 Score: 229
Period size: 74 Copynumber: 2.4 Consensus size: 72
39770796 AGATCGATCA
* * * *
39770806 TTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCCCAACAACGTCATTTTCCGAGCTTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACATAAGCCCAACAACGCCATTTTACGAGCTTT
39770871 CGGGGAT
66 CGGGGAT
* * * * * *
39770878 TTAGCGGCATTTTTGAGAAAACGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTATGAGCT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC--AAAAAACATAAGCCCAACAACGCCATTTTACGAGCT
*
39770943 TTTGGGGAT
64 TTCGGGGAT
39770952 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
39770979 TAATGCTCAG
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
72 24 0.28
74 62 0.72
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (72 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACATAAGCCCAACAACGCCATTTTACGAGCTTT
CGGGGAT
Found at i:39771041 original size:114 final size:114
Alignment explanation
Indices: 39770877--39771757 Score: 1262
Period size: 114 Copynumber: 7.7 Consensus size: 114
39770867 CTTTCGGGGA
* * * *
39770877 TTTAGCGGCATTTTTGAGAAAACGCCGCAAAAAAAACATAAGCCCAACGACGCCGTTTTATGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
*
39770942 TTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
** * * * * *
39770992 TTTAGCAACGTTTCTGAGAAAGCGCTGCAAAAAAACATAAGCCCAACGACGTCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
39771057 TTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
** * *
39771106 TTTAGCGGCGTTTTTGAGAAAATGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
39771171 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGTTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * *
39771220 TTTATCGGCGTTTTTGAGAAAGCGCTGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
39771285 TTCGGGGATTTAGCAGTGTTTTT-AGTAAAGCACCGCTAATGCTTAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGC
*
39771334 TTTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* *
39771399 TTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *** * ** *
39771448 TTTATCAATGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGTTGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
39771513 TTCGGGGATTTAGCGGCGTTTTT-AGTAAAGCGTCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGC
* *
39771562 TTTAGCGGCGTTTTTGAGAAAGCACCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
39771627 TTCGGGGATTTAGCAGCGTTTTTAAGAAAGTGACGCCAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * * *
39771676 TTTAGCGGCGTTTTTGAGAATGCTCCGCAAAAAAACCTAAGCCCAATGGCGCCGTTTTCTGGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
39771741 TTCGGGGATTTAGCGGC
66 TTCGGGGATTTAGCGGC
39771758 TAAAGATTCT
Statistics
Matches: 686, Mismatches: 76, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
113 4 0.01
114 656 0.96
115 26 0.04
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:39772113 original size:15 final size:15
Alignment explanation
Indices: 39772093--39772123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39772083 CATATTTTAA
39772093 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
39772108 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
39772123 G
1 G
39772124 ATTACGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:39772416 original size:15 final size:16
Alignment explanation
Indices: 39772383--39772429 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
39772373 TTTAAGGCTT
*
39772383 AGGGAGTATGGATTT-
1 AGGGATTATGGATTTA
39772398 AGGGATTATGG-TTTA
1 AGGGATTATGGATTTA
39772413 AGGG-TTA-GGATTTA
1 AGGGATTATGGATTTA
39772427 AGG
1 AGG
39772430 TTTAGGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 13 0.45
15 14 0.48
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (16 bp):
AGGGATTATGGATTTA
Found at i:39772441 original size:7 final size:7
Alignment explanation
Indices: 39772431--39772469 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
39772421 GATTTAAGGT
39772431 TTAGGGG
1 TTAGGGG
39772438 TTAGGGG
1 TTAGGGG
39772445 TTTAGGGG
1 -TTAGGGG
**
39772453 TTAGATG
1 TTAGGGG
39772460 TTAGGGG
1 TTAGGGG
39772467 TTA
1 TTA
39772470 AGAGTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:39772448 original size:15 final size:15
Alignment explanation
Indices: 39772427--39772469 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39772417 TTAGGATTTA
39772427 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
39772442 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
39772457 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
39772470 AGAGTTAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:39772456 original size:22 final size:22
Alignment explanation
Indices: 39772414--39772477 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
39772404 TATGGTTTAA
* *
39772414 GGGTTA-GGATTTAAGGTTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
*
39772435 GGGTTAGGGGTTTAGGGGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
** *
39772457 ATGTTAGGGG-TTAAGAGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
39772478 AGATTTAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGGTTAG
Found at i:39772476 original size:14 final size:14
Alignment explanation
Indices: 39772431--39772477 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
39772421 GATTTAAGGT
* *
39772431 TTAGGGGTTAGGGG
1 TTAGGGGTTAAGAG
39772445 TTTAGGGGTT-AGATG
1 -TTAGGGGTTAAGA-G
39772460 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
39772474 TTAG
1 TTAG
39772478 AGATTTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:39772917 original size:19 final size:19
Alignment explanation
Indices: 39772886--39772922 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39772876 CGACCAAATT
39772886 ATAAGAAAAAAATAAAAAA
1 ATAAGAAAAAAATAAAAAA
39772905 ATAA-AAAAGAAATAAAAA
1 ATAAGAAAA-AAATAAAAA
39772923 TGATATGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
ATAAGAAAAAAATAAAAAA
Found at i:39773362 original size:137 final size:138
Alignment explanation
Indices: 39773093--39773407 Score: 307
Period size: 137 Copynumber: 2.3 Consensus size: 138
39773083 AAATTTTAGC
* *
39773093 ATAGCAAAACGACGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTATGAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGAGTTTTTATGAAAAACGC
*** *** ** ** * * *
39773158 TACAAAAGATAAGCAATAGCGGCGTTTTCTATAAAAACACCGCAAAAAATAAATCAATTTATAAA
66 TACAAAAGATAAGCAATAGAAACGTCCGCTATAAAAACAAAGCAAAAAATAAAAAAAATAAAAAA
39773223 AAA-CAAA
131 AAATCAAA
*
39773230 ATAGCAAAACGGCATCATTTTGTTCAAAATGAAATAATATTTTGCGGAGTTTTTATGAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGAGTTTTTATGAAAAACG-
* * ***
39773295 CT-CAAAAGATAAGCAATAGAAAAACG-CCGC-A-AAAAATAAATCAATTTATAAAAAAAATAAA
65 CTACAAAAGATAAGCAATAG--AAACGTCCGCTATAAAAACAAAGCAAAAAATAAAAAAAATAAA
* **
39773356 ATAAAAATTTTTTAGC
128 A-AAAAA----TCAAA
39773372 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATA
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATA
39773408 GCGGCGTTTT
Statistics
Matches: 144, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
136 19 0.13
137 84 0.58
138 3 0.02
139 2 0.01
142 36 0.25
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (138 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGAGTTTTTATGAAAAACGC
TACAAAAGATAAGCAATAGAAACGTCCGCTATAAAAACAAAGCAAAAAATAAAAAAAATAAAAAA
AAATCAAA
Found at i:39773506 original size:109 final size:110
Alignment explanation
Indices: 39773314--39773527 Score: 367
Period size: 109 Copynumber: 2.0 Consensus size: 110
39773304 TAAGCAATAG
* *
39773314 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAATAAAAATTTTTTAGCATAGCAA
1 AAAAACGCCCCAAAAAATAAATCAATTTATAAAAAAAACAAAATAAAAATTTTTTAGCATAGCAA
* * *
39773379 AACGGCGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTTTAT
66 AACGACGTCATTTTGTTCAAAATAAAATAGCAGCGTTTTTTTTAT
*
39773424 AAAAACGCCCCAAAAAATAAATCAATTTAT-AAAAAAACAAAATAAAAATTTTTTAGCATAGTAA
1 AAAAACGCCCCAAAAAATAAATCAATTTATAAAAAAAACAAAATAAAAATTTTTTAGCATAGCAA
39773488 AACGACGTCATTTTGTTCAAAATAAAATAGCAGCGTTTTT
66 AACGACGTCATTTTGTTCAAAATAAAATAGCAGCGTTTTT
39773528 AAAATAAATC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
109 69 0.70
110 29 0.30
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (110 bp):
AAAAACGCCCCAAAAAATAAATCAATTTATAAAAAAAACAAAATAAAAATTTTTTAGCATAGCAA
AACGACGTCATTTTGTTCAAAATAAAATAGCAGCGTTTTTTTTAT
Found at i:39773549 original size:91 final size:91
Alignment explanation
Indices: 39773437--39773607 Score: 306
Period size: 91 Copynumber: 1.9 Consensus size: 91
39773427 AACGCCCCAA
* * *
39773437 AAAATAAATCAATTTATAAAAAAACAAAATAAAAATTTTTTAGCATAGTAAAACGACGTCATTTT
1 AAAATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGACGTCATTTT
39773502 GTTCAAAATAAAATAGCAGCGTTTTT
66 GTTCAAAATAAAATAGCAGCGTTTTT
39773528 AAAATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGACGTCATTTT
1 AAAATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGACGTCATTTT
*
39773593 GTTCAAAATTAAATA
66 GTTCAAAATAAAATA
39773608 ATTTTATAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (91 bp):
AAAATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGACGTCATTTT
GTTCAAAATAAAATAGCAGCGTTTTT
Found at i:39773703 original size:37 final size:37
Alignment explanation
Indices: 39773653--39773727 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
39773643 TAAAAAATAG
39773653 CGCCCTTTTAGTATAGCATAACAGTGTCGTTTTATTC
1 CGCCCTTTTAGTATAGCATAACAGTGTCGTTTTATTC
39773690 CGCCCTTTTAGTATAGCATAACAGTGTCGTTTTATTC
1 CGCCCTTTTAGTATAGCATAACAGTGTCGTTTTATTC
39773727 C
1 C
39773728 AAATTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (37 bp):
CGCCCTTTTAGTATAGCATAACAGTGTCGTTTTATTC
Found at i:39777086 original size:43 final size:43
Alignment explanation
Indices: 39776998--39777162 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
39776988 TTTTTGCAAG
* * * * *
39776998 AAGCGTCGCTAAAGGT-TTGTTCTATAGAGGCGTTTTTTGATAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGA-AA
* * *
39777041 AAGCGTCGCTAAAGGTCTTGATCTATACCGGCATTTGTAGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGAAA
** * * *
39777084 AAGCGCCATTAAAGGTTTTGATCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGAAA
* * *
39777127 AATCACCGCTAAAGGTCTTGAGCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
39777163 ACAAGACCTT
Statistics
Matches: 101, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 83 0.82
44 18 0.18
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGAAA
Found at i:39777287 original size:43 final size:42
Alignment explanation
Indices: 39777173--39777312 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 42
39777163 ACAAGACCTT
* * * *
39777173 TAGCGGCGTTTGTTGTAAAA-CGCCGCTAAAGATCCTAATCTA
1 TAGCGGCGTTT-ATGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
39777215 TAACGACGTTTATGGAAAAGCACCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTATGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * * *
39777257 TAGCGGTGTTTGTGAGGAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTATG-GAAAAGCGCCGCTAAAGGTCCTGATCTA
39777300 TAGCGGCGTTTAT
1 TAGCGGCGTTTAT
39777313 TTCCAAAAGC
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 6 0.08
42 38 0.48
43 35 0.44
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (42 bp):
TAGCGGCGTTTATGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:39777377 original size:17 final size:17
Alignment explanation
Indices: 39777355--39777389 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39777345 ACGACAACGG
39777355 TATTTTTTGCGGCGCTT
1 TATTTTTTGCGGCGCTT
39777372 TATTTTTTGCGGCGCTT
1 TATTTTTTGCGGCGCTT
39777389 T
1 T
39777390 CAAAAGCGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.23, T:0.54
Consensus pattern (17 bp):
TATTTTTTGCGGCGCTT
Found at i:39779875 original size:25 final size:25
Alignment explanation
Indices: 39779811--39779879 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
39779801 ACATTTGTGC
39779811 GAGAAAGCCTTTT-GATT--CCATCT
1 GAGAAA-CCTTTTCGATTACCCATCT
*
39779834 GA-AAA-GTTCTTCGATTACCCATCT
1 GAGAAACCTT-TTCGATTACCCATCT
39779858 GAGAAACCTTTTCGATTACCCA
1 GAGAAACCTTTTCGATTACCCA
39779880 GCCATCTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 8 0.21
25 15 0.39
26 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (25 bp):
GAGAAACCTTTTCGATTACCCATCT
Found at i:39780434 original size:9 final size:9
Alignment explanation
Indices: 39780420--39780534 Score: 65
Period size: 9 Copynumber: 12.3 Consensus size: 9
39780410 ATCTGTTATG
39780420 TATGTATAT
1 TATGTATAT
*
39780429 TATGTATGT
1 TATGTATAT
39780438 TATGTATAT
1 TATGTATAT
*
39780447 TATTGTTTAT
1 TA-TGTATAT
*
39780457 GTCTGTATAT
1 -TATGTATAT
* *
39780467 TACGTATGT
1 TATGTATAT
39780476 TATGTAGTATAT
1 TA--T-GTATAT
39780488 TACTGT-T-T
1 TA-TGTATAT
*
39780496 T-TGTATTT
1 TATGTATAT
*
39780504 TATGTATGT
1 TATGTATAT
*
39780513 TATGTTATGT
1 TATG-TATAT
*
39780523 TATGTTTAT
1 TATGTATAT
39780532 TAT
1 TAT
39780535 TGTTTATAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
6 3 0.04
7 1 0.01
8 4 0.05
9 43 0.52
10 23 0.28
11 2 0.02
12 7 0.08
ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58
Consensus pattern (9 bp):
TATGTATAT
Found at i:39780458 original size:38 final size:38
Alignment explanation
Indices: 39780415--39780571 Score: 120
Period size: 38 Copynumber: 3.9 Consensus size: 38
39780405 AGTATATCTG
39780415 TTATGTATGTATATTATGTATGTTATGTATATTATTGT
1 TTATGTATGTATATTATGTATGTTATGTATATTATTGT
* * *
39780453 TTATGTCTGTATATTACGTATGTTATGTAGTATATTACTGTTTT
1 TTATGTATGTATATTATGTATGTTA--T-GTATATTA---TTGT
* * *
39780497 TGTATTTTATGTATGTTATGTTATGTTATGTTTATTATTGT
1 T-TA-TGTATGTATATTATG-TATGTTATGTATATTATTGT
* * *
39780538 TTATAATATGTATGTTTAT-CATG-TATGTATATTA
1 TTAT-GTATGTAT-ATTATGTATGTTATGTATATTA
39780572 CAATTTATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
38 33 0.35
39 4 0.04
40 10 0.11
41 16 0.17
44 11 0.12
45 3 0.03
46 11 0.12
47 7 0.07
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (38 bp):
TTATGTATGTATATTATGTATGTTATGTATATTATTGT
Found at i:39783954 original size:14 final size:14
Alignment explanation
Indices: 39783935--39783966 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39783925 CCATGGATAA
*
39783935 TTTGATGGTTTTAT
1 TTTGATGGTTCTAT
39783949 TTTGATGGTTCTAT
1 TTTGATGGTTCTAT
39783963 TTTG
1 TTTG
39783967 TTGGATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.22, T:0.62
Consensus pattern (14 bp):
TTTGATGGTTCTAT
Found at i:39799101 original size:15 final size:15
Alignment explanation
Indices: 39799080--39799122 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
39799070 AGAAGGGAAT
39799080 AAGAAAAGGAAAGAA
1 AAGAAAAGGAAAGAA
* * *
39799095 AATAAAAAGAAAGAG
1 AAGAAAAGGAAAGAA
39799110 AAGAAAAGTGAAA
1 AAGAAAAG-GAAA
39799123 AGGGAGTGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (15 bp):
AAGAAAAGGAAAGAA
Found at i:39810923 original size:12 final size:13
Alignment explanation
Indices: 39810898--39810926 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39810888 GATACAGTGT
39810898 AGAATAAGGGAGG
1 AGAATAAGGGAGG
39810911 AGAATAA-GGAGG
1 AGAATAAGGGAGG
39810923 AGAA
1 AGAA
39810927 ATGGAAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (13 bp):
AGAATAAGGGAGG
Found at i:39813512 original size:9 final size:9
Alignment explanation
Indices: 39813493--39813577 Score: 68
Period size: 9 Copynumber: 9.1 Consensus size: 9
39813483 ATTAAATTTT
39813493 AATTA-AAA
1 AATTATAAA
*
39813501 AATTAGAAA
1 AATTATAAA
39813510 AATTATAAA
1 AATTATAAA
39813519 AATTAT-AA
1 AATTATAAA
39813527 AATCGTA-AAA
1 AAT--TATAAA
39813537 GAATTTATAAA
1 -AA-TTATAAA
*
39813548 TAATTTTAAA
1 -AATTATAAA
*
39813558 ATTTTATAAA
1 A-ATTATAAA
39813568 AATTATAAA
1 AATTATAAA
39813577 A
1 A
39813578 TATATAGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
8 10 0.16
9 26 0.41
10 19 0.30
11 7 0.11
12 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (9 bp):
AATTATAAA
Found at i:39813518 original size:19 final size:19
Alignment explanation
Indices: 39813496--39813587 Score: 53
Period size: 20 Copynumber: 4.7 Consensus size: 19
39813486 AAATTTTAAT
39813496 TAAAAAATTAGAAAAATTA
1 TAAAAAATTAGAAAAATTA
* **
39813515 T-AAAAATTA-TAAAATCG
1 TAAAAAATTAGAAAAATTA
* *
39813532 TAAAAGAATTTATAAATAATTT
1 TAAAA-AA-TTAGAAA-AATTA
** *
39813554 TAAAATTTTATAAAAATTA
1 TAAAAAATTAGAAAAATTA
*
39813573 TAAAATATATAGAAA
1 TAAAAAAT-TAGAAA
39813588 TATAGAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.11
18 11 0.20
19 14 0.25
20 15 0.27
21 2 0.04
22 8 0.14
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAAAAATTAGAAAAATTA
Found at i:39813607 original size:49 final size:49
Alignment explanation
Indices: 39813497--39813616 Score: 120
Period size: 49 Copynumber: 2.5 Consensus size: 49
39813487 AATTTTAATT
* * * * *
39813497 AAAAAATTAGAAAA-ATTATAAAAATTATAAAATCGTAAAAGAATTTAT
1 AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAGAATATAA
* * *
39813545 AAATAATTTTAAAATTTTATAAAAATTATAAAAT-AT-ATAGAAATATAGA
1 AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAG-AATATA-A
*
39813594 AAAAAATTATAAAATTGTATAAA
1 AAAAAATTATAAAATTTTATAAA
39813617 GTCGTAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
47 3 0.05
48 17 0.29
49 38 0.66
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (49 bp):
AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAGAATATAA
Found at i:39814890 original size:21 final size:21
Alignment explanation
Indices: 39814827--39814903 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
39814817 CTTTAAAAAT
39814827 AATTTTAAAAAATTATATTTAA
1 AATTTTAAAAAA-TATATTTAA
*
39814849 AATTTTAAAAAATATTTTTTAA
1 AATTTTAAAAAATA-TATTTAA
* *
39814871 AATTTTAAAATATACATTTAA
1 AATTTTAAAAAATATATTTAA
* *
39814892 AATATTATAAAA
1 AATTTTAAAAAA
39814904 CAAATAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 16 0.34
22 31 0.66
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTTAAAAAATATATTTAA
Found at i:39814993 original size:20 final size:20
Alignment explanation
Indices: 39814968--39815005 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39814958 TATAATATTA
*
39814968 AAAATATATATTTAAAATTT
1 AAAATATACATTTAAAATTT
39814988 AAAATATACATTTAAAAT
1 AAAATATACATTTAAAAT
39815006 AGTATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATATACATTTAAAATTT
Found at i:39815027 original size:11 final size:11
Alignment explanation
Indices: 39815011--39815050 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
39815001 AAAATAGTAT
39815011 AAAACAAATAA
1 AAAACAAATAA
39815022 AAAACAAATAAA
1 AAAACAAAT-AA
39815034 GAAGAACAAATAA
1 -AA-AACAAATAA
39815047 AAAA
1 AAAA
39815051 TTAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.42
12 4 0.15
13 4 0.15
14 7 0.27
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:39815043 original size:14 final size:12
Alignment explanation
Indices: 39815011--39815050 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 12
39815001 AAAATAGTAT
39815011 AAAACAAAT-AA
1 AAAACAAATAAA
39815022 AAAACAAATAAA
1 AAAACAAATAAA
39815034 GAAGAACAAATAAA
1 -AA-AACAAATAAA
39815048 AAA
1 AAA
39815051 TTAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 4 0.15
14 10 0.38
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAACAAATAAA
Found at i:39820645 original size:16 final size:16
Alignment explanation
Indices: 39820626--39820667 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
39820616 GTGTATTAAC
39820626 TTTATTTTTCATTAT-T
1 TTTATTTTT-ATTATAT
*
39820642 TTTATTTTTATTTTAT
1 TTTATTTTTATTATAT
39820658 TTTATTTTTA
1 TTTATTTTTA
39820668 GCTACCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTATTATAT
Found at i:39821942 original size:13 final size:13
Alignment explanation
Indices: 39821924--39821957 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
39821914 ATTTTTTAAA
39821924 TTTTGTTTGTTCT-
1 TTTTGTTTGTT-TG
39821937 TTTTGTTTGTTTG
1 TTTTGTTTGTTTG
39821950 TTTTGTTT
1 TTTTGTTT
39821958 TCCACAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (13 bp):
TTTTGTTTGTTTG
Found at i:39835653 original size:51 final size:49
Alignment explanation
Indices: 39835565--39835660 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 49
39835555 GTTTTTCAAG
* *
39835565 TCATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATT
1 TCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
***
39835614 TCATTTCTCTATTTTCATTTTAGAGAAAACTTTAATCATTTCCAAAT
1 TCATTT-TC-ATTTTCATTTTAGAGAAAACCACAATCATTTCCAAAT
39835661 GTTTCTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 6 0.15
50 2 0.05
51 32 0.80
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (49 bp):
TCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
Found at i:39835681 original size:51 final size:51
Alignment explanation
Indices: 39835565--39835679 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 51
39835555 GTTTTTCAAG
* *
39835565 TCATTT-T-CATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATT
1 TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
* ***
39835614 TCATTTCTCTATTTTCATTTTAGAGAAAACTTTAATCATTTCCAAATGT-TT
1 TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAAT-TATT
*
39835665 CTTATTTCTCCATTT
1 -TCATTTCTCCATTT
39835680 CACCATTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
49 6 0.11
50 1 0.02
51 34 0.63
52 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (51 bp):
TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
Done.