Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 1 of 345
Found at i:6938 original size:28 final size:29
Alignment explanation
Indices: 6907--6962 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
6897 TATTATTATT
*
6907 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
6935 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
6963 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:7729 original size:3 final size:3
Alignment explanation
Indices: 7721--7750 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7711 GTGAGGTAAG
7721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7751 GAGTGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:7933 original size:24 final size:25
Alignment explanation
Indices: 7901--7960 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
7891 CGGATTAATT
7901 ATTG-ATTGAAAG-GTGGAAAAA-TG
1 ATTGAATTGAAAGTGT-GAAAAAGTG
7924 ATTGAATTGAAAGTGTGAAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAA--GTG
7951 ATTGAATTGA
1 ATTGAATTGA
7961 GAATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 2 0.06
27 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAAGTG
Found at i:8163 original size:37 final size:39
Alignment explanation
Indices: 8104--8199 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
8094 CGGATAGATT
* * * *
8104 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
8141 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
8180 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
8200 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:18405 original size:24 final size:26
Alignment explanation
Indices: 18372--18419 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
18362 ATATCGGGCG
18372 AAAATAAAAT-TATTTTT-TGAGACT
1 AAAATAAAATGTATTTTTATGAGACT
*
18396 AAAATTAAATGTATTTTTATGAGA
1 AAAATAAAATGTATTTTTATGAGA
18420 ATTTGAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 7 0.33
26 5 0.24
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (26 bp):
AAAATAAAATGTATTTTTATGAGACT
Found at i:22869 original size:16 final size:17
Alignment explanation
Indices: 22838--22870 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22828 TTTAAAAATT
22838 ATATTATTTTTAATTTA
1 ATATTATTTTTAATTTA
*
22855 ATATT-TTTTTCATTTA
1 ATATTATTTTTAATTTA
22871 TTAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATTTTTAATTTA
Found at i:26050 original size:26 final size:26
Alignment explanation
Indices: 25969--26051 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
25959 TTTAATGTTT
25969 AATTTGGTATGTAAGTATTTTTAATC
1 AATTTGGTATGTAAGTATTTTTAATC
** * ** ** *
25995 AATTTAATATTTAATGT-TTAATGTTT
1 AATTTGGTATGTAA-GTATTTTTAATC
26021 AATTTGGTATGTAAGTATTTTTAATC
1 AATTTGGTATGTAAGTATTTTTAATC
26047 AATTT
1 AATTT
26052 AATATCAAAG
Statistics
Matches: 39, Mismatches: 16, Indels: 4
0.66 0.27 0.07
Matches are distributed among these distances:
25 2 0.05
26 35 0.90
27 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (26 bp):
AATTTGGTATGTAAGTATTTTTAATC
Found at i:50919 original size:24 final size:24
Alignment explanation
Indices: 50887--50935 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
50877 GCCTTCTCAG
50887 TCTCCTCTCAGATCATGGTTAGCT
1 TCTCCTCTCAGATCATGGTTAGCT
50911 TCTCCTCTCAGATCATGGTTAGCT
1 TCTCCTCTCAGATCATGGTTAGCT
50935 T
1 T
50936 ACGATGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (24 bp):
TCTCCTCTCAGATCATGGTTAGCT
Found at i:55013 original size:23 final size:23
Alignment explanation
Indices: 54983--55030 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
54973 TGAGTTGTAG
54983 ATTGCCTGAAACCTCGGGGATAT
1 ATTGCCTGAAACCTCGGGGATAT
55006 ATTGCCTGAAACCTCGGGGATAT
1 ATTGCCTGAAACCTCGGGGATAT
55029 AT
1 AT
55031 ACTCTTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (23 bp):
ATTGCCTGAAACCTCGGGGATAT
Found at i:56355 original size:22 final size:22
Alignment explanation
Indices: 56312--56355 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
56302 TACATTAGAT
*
56312 TTAAAAATTATCTATTTTTACTA
1 TTAAAAATTATC-ATTTATACTA
56335 TTAAAAATTAGTC-TTTATACT
1 TTAAAAATTA-TCATTTATACT
56356 TCAATATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 10 0.53
24 2 0.11
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAAAATTATCATTTATACTA
Found at i:63430 original size:22 final size:22
Alignment explanation
Indices: 63387--63431 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
63377 CACATTGGAG
* *
63387 TCTAAATTTTGTTTTTCTAAGT
1 TCTAAATTTTGTTTATCCAAGT
63409 TCTAAATTTCT-TTTATCCAAGT
1 TCTAAATTT-TGTTTATCCAAGT
63431 T
1 T
63432 ACTTCATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (22 bp):
TCTAAATTTTGTTTATCCAAGT
Found at i:64710 original size:13 final size:13
Alignment explanation
Indices: 64694--64720 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64684 CCTGCAAAAA
64694 TGGCAGGCAATGT
1 TGGCAGGCAATGT
64707 TGGCAGGCAATGT
1 TGGCAGGCAATGT
64720 T
1 T
64721 ATGTTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (13 bp):
TGGCAGGCAATGT
Found at i:71823 original size:21 final size:21
Alignment explanation
Indices: 71797--71837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
71787 AGACGAGCAA
* *
71797 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
71818 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
71838 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:77856 original size:6 final size:6
Alignment explanation
Indices: 77824--77855 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
77814 ATGTGGAAAA
*
77824 CTGCTT CTGCTT CTGCTT CTGCTT CTTCTT CT
1 CTGCTT CTGCTT CTGCTT CTGCTT CTGCTT CT
77856 TTAGAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.12, T:0.53
Consensus pattern (6 bp):
CTGCTT
Found at i:78305 original size:26 final size:26
Alignment explanation
Indices: 78272--78322 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
78262 CCTTTCTTAT
78272 TTTAAGATTTGAGCCTAATTTTGTTA
1 TTTAAGATTTGAGCCTAATTTTGTTA
78298 TTTAAGATTTGAGCCTAATTTTGTT
1 TTTAAGATTTGAGCCTAATTTTGTT
78323 TGAGAAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (26 bp):
TTTAAGATTTGAGCCTAATTTTGTTA
Found at i:79367 original size:3 final size:3
Alignment explanation
Indices: 79359--79390 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
79349 TTTTATGTAT
79359 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
79391 CAGCAAAGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:81687 original size:22 final size:23
Alignment explanation
Indices: 81665--81708 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
81655 TTTAATTTTT
81665 ATATTTTTATTTT-TAAGAATTTA
1 ATATTTTTATTTTCTAA-AATTTA
*
81688 ATTTTTTTATTTTCTAAAATT
1 ATATTTTTATTTTCTAAAATT
81709 AAAAATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
ATATTTTTATTTTCTAAAATTTA
Found at i:82957 original size:13 final size:14
Alignment explanation
Indices: 82939--82967 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
82929 ATTTAACTAA
82939 ATTACTAA-TATTT
1 ATTACTAATTATTT
82952 ATTACTAATTATTT
1 ATTACTAATTATTT
82966 AT
1 AT
82968 ATAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTACTAATTATTT
Found at i:92986 original size:16 final size:17
Alignment explanation
Indices: 92957--92991 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
92947 CTCTTAATCT
*
92957 TTTGAAAAATAGTCAAA
1 TTTGAAAAAGAGTCAAA
92974 TTTG-AAAAGAGTCAAA
1 TTTGAAAAAGAGTCAAA
92990 TT
1 TT
92992 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTGAAAAAGAGTCAAA
Found at i:96582 original size:38 final size:38
Alignment explanation
Indices: 96531--96609 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
96521 TAATGTTAGA
*
96531 AAACTGGCTTCGACGACCCATTAAATGTGTAGGGACCG
1 AAACTGGCTTCGACGACCCATGAAATGTGTAGGGACCG
96569 AAACTGGCTTCGACGACCCATGAAATGTGTAGGGACCG
1 AAACTGGCTTCGACGACCCATGAAATGTGTAGGGACCG
96607 AAA
1 AAA
96610 TCCAAAAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.19
Consensus pattern (38 bp):
AAACTGGCTTCGACGACCCATGAAATGTGTAGGGACCG
Found at i:104521 original size:15 final size:15
Alignment explanation
Indices: 104501--104530 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
104491 ATTTTCGTAA
104501 TCAGTGTTGGCCTGT
1 TCAGTGTTGGCCTGT
104516 TCAGTGTTGGCCTGT
1 TCAGTGTTGGCCTGT
104531 ACATTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.33, T:0.40
Consensus pattern (15 bp):
TCAGTGTTGGCCTGT
Found at i:107903 original size:29 final size:30
Alignment explanation
Indices: 107844--107901 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
107834 TCCGAGCCTT
*
107844 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
107874 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
107902 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:108352 original size:50 final size:50
Alignment explanation
Indices: 108239--108480 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
108229 ATTTGGGTAA
* * *
108239 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
108295 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
108345 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
108395 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
** *
108445 AGAACATCCCATGTAAGACCATGTCTGGGACGTGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
108481 TTTGGCATGT
Statistics
Matches: 163, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 89 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:108427 original size:100 final size:103
Alignment explanation
Indices: 108239--108488 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
108229 ATTTGGGTAA
108239 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
108304 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * * *
108345 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
108407 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* * *
108445 AGAACATCCCATGTAAGACCATGTCTGGGACGTGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
108489 GTTATTATCA
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 37 0.28
105 2 0.02
106 39 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:114932 original size:22 final size:22
Alignment explanation
Indices: 114906--114953 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
114896 AATGATTTTA
*
114906 ATAACAT-AATAACCTTAATAAT
1 ATAACATCAATAA-CTTAAAAAT
*
114928 ATAACATCAATAATTTAAAAAT
1 ATAACATCAATAACTTAAAAAT
114950 ATAA
1 ATAA
114954 TTAGAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAACATCAATAACTTAAAAAT
Found at i:129539 original size:17 final size:17
Alignment explanation
Indices: 129519--129552 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
129509 AAATATAAGA
129519 TTTTATAAATTT-AAAAT
1 TTTTAT-AATTTGAAAAT
129536 TTTTATAATTTGAAAAT
1 TTTTATAATTTGAAAAT
129553 GTTAGTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTATAATTTGAAAAT
Found at i:140560 original size:24 final size:25
Alignment explanation
Indices: 140526--140574 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
140516 TTCAAATTCA
*
140526 TATTTTAAGTTTTAAATTATATTTT
1 TATTTTAAGTTTTAAATAATATTTT
*
140551 TATTTT-AGTTTTAAGTAATATTTT
1 TATTTTAAGTTTTAAATAATATTTT
140575 ATTAGTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (25 bp):
TATTTTAAGTTTTAAATAATATTTT
Found at i:142120 original size:34 final size:34
Alignment explanation
Indices: 142078--142145 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
142068 TATACATCAA
*
142078 CATAAAGTATATTAGAAAAGGCAAAATATAATCT
1 CATAAAGTATATTAGAAAAGACAAAATATAATCT
142112 CATAAAGTATATTAGAAAAGACAAAATATAATCT
1 CATAAAGTATATTAGAAAAGACAAAATATAATCT
142146 AACTCTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.26
Consensus pattern (34 bp):
CATAAAGTATATTAGAAAAGACAAAATATAATCT
Found at i:150098 original size:14 final size:14
Alignment explanation
Indices: 150079--150106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
150069 TTATTACGAG
150079 TTTTATCCTTTTAT
1 TTTTATCCTTTTAT
150093 TTTTATCCTTTTAT
1 TTTTATCCTTTTAT
150107 CTTCAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATCCTTTTAT
Found at i:152176 original size:19 final size:21
Alignment explanation
Indices: 152133--152179 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
152123 TTGTATTTTG
152133 ATTAAAATATTGATGTAACTT
1 ATTAAAATATTGATGTAACTT
152154 -TTAAAA-ATTG-T-TAACATT
1 ATTAAAATATTGATGTAAC-TT
152172 ATTAAAAT
1 ATTAAAAT
152180 TATTTATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.17
18 3 0.13
19 10 0.43
20 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (21 bp):
ATTAAAATATTGATGTAACTT
Found at i:155376 original size:23 final size:23
Alignment explanation
Indices: 155350--155398 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
155340 AAATGGTTAA
* * *
155350 ATAAGTTAATATATGACAAAATT
1 ATAAGTAAATAAATCACAAAATT
*
155373 ATAAGTAAATAAATCATAAAATT
1 ATAAGTAAATAAATCACAAAATT
155396 ATA
1 ATA
155399 TTTTGATCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (23 bp):
ATAAGTAAATAAATCACAAAATT
Found at i:162186 original size:2 final size:2
Alignment explanation
Indices: 162179--162207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
162169 GGATAAAGTT
162179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
162208 TGCGATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:166278 original size:27 final size:27
Alignment explanation
Indices: 166247--166305 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
166237 GTGGCTGAAG
** **
166247 AGGTGGGACCTTTGAAGTTGCCTTCAC
1 AGGTGGGACCTTCAAAGGCGCCTTCAC
166274 AGGTGGGACCTTCAAAGGCGCCTTCAC
1 AGGTGGGACCTTCAAAGGCGCCTTCAC
166301 AGGTG
1 AGGTG
166306 TCTAAACCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (27 bp):
AGGTGGGACCTTCAAAGGCGCCTTCAC
Found at i:170815 original size:21 final size:21
Alignment explanation
Indices: 170789--170834 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
170779 AGCGTAGTGT
170789 ATTTTTGTTTTTTACTCTTGG
1 ATTTTTGTTTTTTACTCTTGG
*
170810 ATTTTTGTTTTTTACTTTTGG
1 ATTTTTGTTTTTTACTCTTGG
170831 ATTT
1 ATTT
170835 AATGTATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.07, G:0.13, T:0.70
Consensus pattern (21 bp):
ATTTTTGTTTTTTACTCTTGG
Found at i:171716 original size:16 final size:16
Alignment explanation
Indices: 171683--171716 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
171673 CATAACTGTT
* *
171683 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
171699 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
171715 AA
1 AA
171717 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:174541 original size:21 final size:21
Alignment explanation
Indices: 174515--174555 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
174505 AGACGAGCAA
* *
174515 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
174536 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
174556 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:176493 original size:16 final size:16
Alignment explanation
Indices: 176460--176493 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
176450 GGAGATTGTT
* *
176460 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
176476 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
176492 AA
1 AA
176494 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:184658 original size:11 final size:11
Alignment explanation
Indices: 184642--184666 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
184632 AATAATTGAG
184642 TAACTATTTTA
1 TAACTATTTTA
184653 TAACTATTTTA
1 TAACTATTTTA
184664 TAA
1 TAA
184667 TTAGGTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TAACTATTTTA
Found at i:199298 original size:18 final size:19
Alignment explanation
Indices: 199252--199298 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
199242 TCATAAACAT
* *
199252 TTAATAATTAATATTTAATT
1 TTAATAA-TAATATTAAATA
*
199272 TTAAAAATAA-ATTAAATA
1 TTAATAATAATATTAAATA
199290 TTAATAATA
1 TTAATAATA
199299 GTGAAAGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.61
19 3 0.13
20 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAATAATATTAAATA
Found at i:199573 original size:17 final size:19
Alignment explanation
Indices: 199541--199579 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
199531 ATGTATTTAG
*
199541 TTTTTATATTTATAAATAT
1 TTTTTATATTTATAAAAAT
199560 TTTTTA-ATTT-TAAAAAT
1 TTTTTATATTTATAAAAAT
199577 TTT
1 TTT
199580 AGTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTATATTTATAAAAAT
Found at i:207185 original size:3 final size:3
Alignment explanation
Indices: 207177--207213 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
207167 AAATCATATA
207177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
207214 GCGAACCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:221646 original size:20 final size:20
Alignment explanation
Indices: 221621--221660 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
221611 CAAATCATCA
*
221621 AGTTCA-AATTATTTCGAGTT
1 AGTTCAGAA-TATATCGAGTT
221641 AGTTCAGAATATATCGAGTT
1 AGTTCAGAATATATCGAGTT
221661 TAAATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
AGTTCAGAATATATCGAGTT
Found at i:229456 original size:16 final size:15
Alignment explanation
Indices: 229437--229467 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
229427 ATAAAATTTT
229437 AAAAATTAAAGTTAAA
1 AAAAATTAAA-TTAAA
229453 AAAAATTAAATTAAA
1 AAAAATTAAATTAAA
229468 TTATAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATTAAA
Found at i:231887 original size:16 final size:16
Alignment explanation
Indices: 231866--231899 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
231856 AATATATATA
*
231866 TATATAGACACACACT
1 TATATACACACACACT
*
231882 TATATACATACACACT
1 TATATACACACACACT
231898 TA
1 TA
231900 ACAGAAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (16 bp):
TATATACACACACACT
Found at i:240548 original size:30 final size:30
Alignment explanation
Indices: 240512--240574 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
240502 TGAAGTGCAA
240512 AGGTGCTAATTGGACTTGCTTGCCAACTTT
1 AGGTGCTAATTGGACTTGCTTGCCAACTTT
240542 AGGTGCTAATTGGACTTGCTTGCCAACTTT
1 AGGTGCTAATTGGACTTGCTTGCCAACTTT
240572 AGG
1 AGG
240575 GGTTAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (30 bp):
AGGTGCTAATTGGACTTGCTTGCCAACTTT
Found at i:242089 original size:2 final size:2
Alignment explanation
Indices: 242082--242106 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
242072 TTGTGTTGTC
242082 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
242107 AAAGGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:253142 original size:51 final size:50
Alignment explanation
Indices: 253072--253215 Score: 137
Period size: 51 Copynumber: 2.8 Consensus size: 50
253062 TTATATATTG
* * * *
253072 TATTAATTTTGACAAAATGTGTAAATATTACAGACTAAATTTATTAAAT-TA
1 TATTAA-TTTGATAGAATGTGTAAAT-TTACAGGCTAAATTTATTAAATCAA
* * * *
253123 TGATTAATTTGATAGAATGTGTAAATGTTTCGGGTTAAATTTTTTAAATCAA
1 T-ATTAATTTGATAGAATGTGTAAAT-TTACAGGCTAAATTTATTAAATCAA
** *
253175 TAACAATTTGATAGAATGTGTAAACTTTAAAGGCTAAATTT
1 TATTAATTTGATAGAATGTGTAAA-TTTACAGGCTAAATTT
253216 GTTATTATAC
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
51 67 0.89
52 8 0.11
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (50 bp):
TATTAATTTGATAGAATGTGTAAATTTACAGGCTAAATTTATTAAATCAA
Found at i:254812 original size:37 final size:37
Alignment explanation
Indices: 254771--254849 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
254761 AACTTCACGC
*
254771 TATCACTTGAACAAAAATAACTAATTGTGGGCTAAAA
1 TATCACTTGAACAAAAATAACTAATTGTGGGCAAAAA
*
254808 TATCACTTGAACAACAATAACTAATTGTGGGCAAAAA
1 TATCACTTGAACAAAAATAACTAATTGTGGGCAAAAA
254845 TATCA
1 TATCA
254850 TGAGACAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (37 bp):
TATCACTTGAACAAAAATAACTAATTGTGGGCAAAAA
Found at i:265079 original size:15 final size:15
Alignment explanation
Indices: 265059--265089 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
265049 GCAATCCAAA
265059 TCCTAATACAAAGGC
1 TCCTAATACAAAGGC
265074 TCCTAATACAAAGGC
1 TCCTAATACAAAGGC
265089 T
1 T
265090 TCCATGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TCCTAATACAAAGGC
Found at i:268440 original size:37 final size:37
Alignment explanation
Indices: 268398--268495 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 37
268388 ATGATATTTG
*
268398 TTAAACTAGTGCTATATTTCATTTTGTTTCATATCCC
1 TTAAACTAGTGCTATATTTCATTTTGTTTCATATACC
* **
268435 TTAAACTAAT-CTATA---C-TTTTGTTTTGTATACC
1 TTAAACTAGTGCTATATTTCATTTTGTTTCATATACC
*
268467 TTAAACTGGTGCTATATTTCATTTTGTTT
1 TTAAACTAGTGCTATATTTCATTTTGTTT
268496 AAGATGATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
32 21 0.42
33 6 0.12
36 6 0.12
37 17 0.34
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.51
Consensus pattern (37 bp):
TTAAACTAGTGCTATATTTCATTTTGTTTCATATACC
Found at i:278497 original size:15 final size:15
Alignment explanation
Indices: 278477--278506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
278467 TTTTTATTTA
278477 ATCACTTACGTTATC
1 ATCACTTACGTTATC
278492 ATCACTTACGTTATC
1 ATCACTTACGTTATC
278507 GTTCTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
ATCACTTACGTTATC
Found at i:280747 original size:15 final size:15
Alignment explanation
Indices: 280724--280778 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
280714 TCGTATATCT
*
280724 TAATGAATTAAATTA
1 TAATAAATTAAATTA
*
280739 TAATAAATTTATATCT-
1 TAATAAA-TTAAAT-TA
*
280755 TAATGAATTAAATTA
1 TAATAAATTAAATTA
280770 TAATAAATT
1 TAATAAATT
280779 TTTTACAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 1 0.03
15 19 0.59
16 11 0.34
17 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (15 bp):
TAATAAATTAAATTA
Found at i:280752 original size:31 final size:31
Alignment explanation
Indices: 280717--280779 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
280707 GTAAAAATCG
280717 TATATCTTAATGAATTAAATTATAATAAATT
1 TATATCTTAATGAATTAAATTATAATAAATT
280748 TATATCTTAATGAATTAAATTATAATAAATT
1 TATATCTTAATGAATTAAATTATAATAAATT
280779 T
1 T
280780 TTTACAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
TATATCTTAATGAATTAAATTATAATAAATT
Found at i:280763 original size:16 final size:16
Alignment explanation
Indices: 280717--280763 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
280707 GTAAAAATCG
280717 TATATCTTAATGAA-T
1 TATATCTTAATGAATT
* *
280732 TAAAT-TATAATAAATT
1 TATATCT-TAATGAATT
280748 TATATCTTAATGAATT
1 TATATCTTAATGAATT
280764 AAATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 13 0.52
17 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
TATATCTTAATGAATT
Found at i:290294 original size:31 final size:31
Alignment explanation
Indices: 290231--290296 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
290221 ATCCACTCTG
* * *
290231 AACTTGGCATTTGTTCCAATATTGGGGGCTA
1 AACTTGGCAATTGTTCCAATATTAGAGGCTA
*
290262 AACTTGGCAATTGTTCCCAA-ATTAGAGTCTA
1 AACTTGGCAATTGTT-CCAATATTAGAGGCTA
290293 AACT
1 AACT
290297 CTAGGTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
AACTTGGCAATTGTTCCAATATTAGAGGCTA
Found at i:290376 original size:58 final size:59
Alignment explanation
Indices: 290305--290427 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
290295 CTCTAGGTCT
* * *
290305 TTCAAGGACTAACTTGGACCAAAAA-A-TTTCAAGCCCCAATGTAGGAACAATTGTCAAG
1 TTCAAGGACTAACTTGAACAAAAAAGAGTTT-AAGCCCCAATGTAGGAACAATTATCAAG
* * *
290363 TTCAAGGTCTAACTTGAATAAAAAAGAGTTTAATCCCCAATGTAGGAACAATTATCAAG
1 TTCAAGGACTAACTTGAACAAAAAAGAGTTTAAGCCCCAATGTAGGAACAATTATCAAG
290422 TT-AAGG
1 TTCAAGG
290428 GCCTTTAGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 25 0.44
59 29 0.51
60 3 0.05
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (59 bp):
TTCAAGGACTAACTTGAACAAAAAAGAGTTTAAGCCCCAATGTAGGAACAATTATCAAG
Found at i:294992 original size:3 final size:3
Alignment explanation
Indices: 294934--294983 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
294924 AGTACTTTTG
* *
294934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
294979 GTA TT
1 TTA TT
294984 GGTATTATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.97
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:295443 original size:20 final size:18
Alignment explanation
Indices: 295420--295458 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
295410 TACACCTATA
295420 TATATATATGTACATATTTT
1 TATATATATG--CATATTTT
295440 TATATATATGCATATTTT
1 TATATATATGCATATTTT
295458 T
1 T
295459 TCTTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
TATATATATGCATATTTT
Found at i:295445 original size:18 final size:18
Alignment explanation
Indices: 295422--295458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
295412 CACCTATATA
*
295422 TATATATGTACATATTTT
1 TATATATATACATATTTT
*
295440 TATATATATGCATATTTT
1 TATATATATACATATTTT
295458 T
1 T
295459 TCTTCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATATATATACATATTTT
Found at i:308027 original size:99 final size:100
Alignment explanation
Indices: 307846--308491 Score: 849
Period size: 99 Copynumber: 6.6 Consensus size: 100
307836 CTACAGCGGG
* *
307846 ATCTTACTTCCCT-AAATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-
** * * *
307909 GCAATGCAGAGGAATAGATTGAAG-CTACAACAACGA
65 GCGTTGCAGTGGAACAGATTGAAGTC-ACAACGACGA
*
307945 ATCTTACTTCCCT-ACATTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
* *
308009 CGTTGCAGTGAAACAGATTGAAGTCACAATGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
*
308044 ATCTTACTTCCCTGACATTGCAATTAAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTA
1 ATCTTACTTCCCTGACATTGCAATT-AAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA
*
308109 GCATTGCAGTGG-ACAGATTGAAGTCACAACGACGA
65 GCGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
*
308144 ATCTTACTTCCCTGACATTGCAATT-AAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
308208 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
308243 ATCTTACTT-CCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
* **
308307 CGTTGCAGTGGAACAGGTCAAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* * * * * **
308342 ATCTCACTTCTCC-GGCATTGCAATGT-AAAAGATTGAAGCCACAACGGCGAATCTTA-TTTCCC
1 ATCTTACTTC-CCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTT
* *
308404 AGGCGTTGCAGTGGAACAGA-TCAATTCACAACGACGA
64 A-GCGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* * * *
308441 ATCTTGCTT--C---CATTGCAATGT-AAAAGATTGAAGCCACAACGGCGAATCTTA
1 ATCTTACTTCCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTA
308492 TTCCCAGGTG
Statistics
Matches: 506, Mismatches: 31, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
94 41 0.08
96 1 0.00
98 64 0.13
99 234 0.46
100 114 0.23
101 52 0.10
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (100 bp):
ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
Found at i:308201 original size:199 final size:199
Alignment explanation
Indices: 307846--308491 Score: 872
Period size: 199 Copynumber: 3.3 Consensus size: 199
307836 CTACAGCGGG
* *
307846 ATCTTACTTCCCT-AAATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-
* * * *
307909 GCAATGCAGAGGAATAGATTGAAG-CTACAACAACGAATCTTACTTCCCT-ACATTGCAATTAAA
65 GCATTGCAGTGGAACAGATTGAAGTC-ACAACGACGAATCTTACTTCCCTGACATTGCAATT-AA
*
307972 AAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGAAACAGATTGAAGTCACA
128 AAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACA
*
308037 ATGACGA
193 ACGACGA
*
308044 ATCTTACTTCCCTGACATTGCAATTAAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTA
1 ATCTTACTTCCCTGACATTGCAATT-AAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA
308109 GCATTGCAGTGG-ACAGATTGAAGTCACAACGACGAATCTTACTTCCCTGACATTGCAATTAAAA
65 GCATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTCCCTGACATTGCAATTAAAA
308173 GATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAAC
130 GATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAAC
308238 GACGA
195 GACGA
308243 ATCTTACTT-CCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
* * ** * *
308307 CGTTGCAGTGGAACAGGTCAAAGTCACAACGACGAATCTCACTTCTCC-GGCATTGCAATGTAAA
66 CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTC-CCTGACATTGCAAT-TAAA
* ** * ** * *
308371 AGATTGAAGCCACAACGGCGAATCTTA-TTTCCCAGGCGTTGCAGTGGAACAGA-TCAATTCACA
129 AGATTGAAGCTACAATAGCGGATCTTACTTTCTTA-GCGTTGCAGTGGAACAGATTGAAGTCACA
308434 ACGACGA
193 ACGACGA
* * * *
308441 ATCTTGCTT--C---CATTGCAATGT-AAAAGATTGAAGCCACAACGGCGAATCTTA
1 ATCTTACTTCCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTA
308492 TTCCCAGGTG
Statistics
Matches: 410, Mismatches: 28, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
194 36 0.09
195 1 0.00
197 50 0.12
198 95 0.23
199 170 0.41
200 57 0.14
201 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (199 bp):
ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTCCCTGACATTGCAATTAAAAG
ATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAACG
ACGA
Found at i:308487 original size:45 final size:46
Alignment explanation
Indices: 307846--308497 Score: 192
Period size: 50 Copynumber: 13.3 Consensus size: 46
307836 CTACAGCGGG
* * *
307846 ATCTTACTTCCCTAAATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGG
1 ATCTTACTTCCC---ATTGCAATGT-AAAAGATTGAAGCCACAACGGCGA
* * * * **
307895 ATCTTACTTTCCAGGCAATGCAGA-GGAATAGATTGAAGCTACAACAACGA
1 ATCTTAC-TTCC---CATTGCA-ATGTAAAAGATTGAAGCCACAACGGCGA
* ** *
307945 ATCTTACTTCCCTACATTGCAAT-TAAAAAGATTGAAGCTACAATAGCGG
1 ATCTTACTT-CC--CATTGCAATGT-AAAAGATTGAAGCCACAACGGCGA
* * * * * *
307994 ATCTTACTTTCTTAGCGTTGCAGTG-AAACAGATTGAAGTCACAATGACGA
1 ATCTTAC-TTC---CCATTGCAATGTAAA-AGATTGAAGCCACAACGGCGA
* ** *
308044 ATCTTACTTCCCTGACATTGCAAT-TAAAAAAGATTGAAGCTACAATAGCGG
1 ATCTTACTT-CC---CATTGCAATGT--AAAAGATTGAAGCCACAACGGCGA
* * * * * *
308095 ATCTTACTTTCTTAGCATTGCAGTG-GACAGATTGAAGTCACAACGACGA
1 ATCTTAC-TTC---CCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
* ** *
308144 ATCTTACTTCCCTGACATTGCAAT-TAAAAGATTGAAGCTACAATAGCGG
1 ATCTTACTT-CC---CATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
* * * * * * *
308193 ATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
1 ATCTTAC-TTC---CCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
* * *
308243 ATCTTACTTCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGG
1 ATCTTACTTCC---CATTGCAATGT-AAAAGATTGAAGCCACAACGGCGA
* * * * * * ** * *
308292 ATCTTACTTTCTTAGCGTTGCAGTGGAACAGGTCAAAGTCACAACGACGA
1 ATCTTAC-TTC---CCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
*
308342 ATCTCACTTCTCCGGCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
1 ATCTTAC-T-TCC--CATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
* * * * * ** *
308392 ATCTTATTTCCCAGGCGTTGCAGTGGAACAGA-TCAATTCACAACGACGA
1 ATCTTACTTCCCA----TTGCAATGTAAAAGATTGAAGCCACAACGGCGA
*
308441 ATCTTGCTT-CCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
1 ATCTTACTTCCCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
308486 ATCTTA-TTCCCA
1 ATCTTACTTCCCA
308498 GGTGATGCAG
Statistics
Matches: 435, Mismatches: 113, Indels: 114
0.66 0.17 0.17
Matches are distributed among these distances:
44 14 0.03
45 21 0.05
46 2 0.00
48 9 0.02
49 167 0.38
50 181 0.42
51 35 0.08
52 5 0.01
53 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (46 bp):
ATCTTACTTCCCATTGCAATGTAAAAGATTGAAGCCACAACGGCGA
Found at i:313203 original size:100 final size:100
Alignment explanation
Indices: 312886--313541 Score: 918
Period size: 100 Copynumber: 6.6 Consensus size: 100
312876 CTAACAGCGG
* *
312886 ATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-
** * * *
312950 GCAATGCAGAGGAATAGATTGAAG-CTACAACAACGA
65 GCGTTGCAGTGGAACAGATTGAAGTC-ACAACGACGA
*
312986 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
*
313051 CG-TGCAGTGAAACAGATTGAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* *
313085 ATCTTACTTCCCTGACATTGAAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
*
313150 CATTGCAGTGGAACAGATTGAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* *
313185 ATCTTACTTTCCTGACATTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
313250 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
313285 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
* **
313350 CGTTGCAGTGGAACAGGTCAAAGTCACAACGACGA
66 CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* * * * * **
313385 ATCTCACTTCTC-GGCATTGCAATGT-AAAAGATTGAAGC-ACAACGGCGAATCTTA-TTTCCCA
1 ATCTTACTTCCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA
** *
313446 GGCGTTGCAGTGGAACAGATCAAATTCACAACGACGA
65 -GCGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
* * * *
313483 ATCTTTCTTCCC-GACATTGCAATGT-AAAAGATTGAAGCCACAACGGCGAATCTTA-TTTC
1 ATCTTACTTCCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC
313542 CCAGGTGATG
Statistics
Matches: 518, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
97 5 0.01
98 82 0.16
99 134 0.26
100 296 0.57
101 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (100 bp):
ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
CGTTGCAGTGGAACAGATTGAAGTCACAACGACGA
Found at i:313226 original size:199 final size:200
Alignment explanation
Indices: 312886--313541 Score: 929
Period size: 199 Copynumber: 3.3 Consensus size: 200
312876 CTAACAGCGG
* *
312886 ATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-
* * * * *
312950 GCAATGCAGAGGAATAGATTGAAG-CTACAACAACGAATCTTACTTCCCTGACATTGCAATTAAA
65 GCATTGCAGTGGAACAGATTGAAGTC-ACAACGACGAATCTTACTTTCCTGACATTGCAATTAAA
*
313014 AAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCG-TGCAGTGAAACAGATTGAAGTCACA
129 AAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACA
313078 ACGACGA
194 ACGACGA
* *
313085 ATCTTACTTCCCTGACATTGAAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
313150 CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTTCCTGACATTGCAATTAAAAA
66 CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTTCCTGACATTGCAATTAAAAA
313215 GATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAAC
131 GATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAAC
313280 GACGA
196 GACGA
313285 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
1 ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
* * ** * *
313350 CGTTGCAGTGGAACAGGTCAAAGTCACAACGACGAATCTCAC-TT-CTCGGCATTGCAATGT-AA
66 CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTTCCT-GACATTGCAAT-TAAA
** * ** ** *
313412 AAGATTGAAGC-ACAACGGCGAATCTTA-TTTCCCAGGCGTTGCAGTGGAACAGATCAAATTCAC
129 AAGATTGAAGCTACAATAGCGGATCTTACTTTCTTA-GCGTTGCAGTGGAACAGATTGAAGTCAC
313475 AACGACGA
193 AACGACGA
* * * *
313483 ATCTTTCTTCCC-GACATTGCAATGT-AAAAGATTGAAGCCACAACGGCGAATCTTA-TTTC
1 ATCTTACTTCCCTGACATTGCAAT-TAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC
313542 CCAGGTGATG
Statistics
Matches: 420, Mismatches: 30, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
196 4 0.01
197 43 0.10
198 60 0.14
199 179 0.43
200 134 0.32
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (200 bp):
ATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG
CATTGCAGTGGAACAGATTGAAGTCACAACGACGAATCTTACTTTCCTGACATTGCAATTAAAAA
GATTGAAGCTACAATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCACAAC
GACGA
Found at i:313356 original size:50 final size:50
Alignment explanation
Indices: 312878--313356 Score: 435
Period size: 50 Copynumber: 9.6 Consensus size: 50
312868 TTCCTGTACT
* *
312878 AACAGCGGATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTAC
1 AACAGCGGATCTTACTTTCCTAGCATTGCAATTAAAAAGATTGAAGCTAC
* ** *
312928 AACAGCGGATCTTACTTTCC-AGGCAATGCAGA-GGAATAGATTGAAGCTAC
1 AACAGCGGATCTTACTTTCCTA-GCATTGCA-ATTAAAAAGATTGAAGCTAC
* * *
312978 AACAACGAATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCTAC
1 AACAGCGGATCTTACTTTCCTAG-CATTGCAATTAAAAAGATTGAAGCTAC
* * * * * *
313028 AATAGCGGATCTTACTTTCTTAGC-GTGCAGTGAAACAGATTGAAG-TCAC
1 AACAGCGGATCTTACTTTCCTAGCATTGCAATTAAAAAGATTGAAGCT-AC
* * *
313077 AAC-GACGAATCTTACTTCCCT-GACATTGAAATTAAAAAGATTGAAGCTAC
1 AACAG-CGGATCTTACTTTCCTAG-CATTGCAATTAAAAAGATTGAAGCTAC
* * * ** *
313127 AATAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAG-TCAC
1 AACAGCGGATCTTACTTTCCTAGCATTGCAATTAAAAAGATTGAAGCT-AC
*
313177 AAC-GACGAATCTTACTTTCCT-GACATTGCAATTAAAAAGATTGAAGCTAC
1 AACAG-CGGATCTTACTTTCCTAG-CATTGCAATTAAAAAGATTGAAGCTAC
* * * * ** *
313227 AATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAG-TCAC
1 AACAGCGGATCTTACTTTCCTAGCATTGCAATTAAAAAGATTGAAGCT-AC
* *
313277 AAC-GACGAATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAGCTAC
1 AACAG-CGGATCTTACTTTCCTAG-CATTGCAATTAAAAAGATTGAAGCTAC
* *
313327 AACAGCGGATCTTACTTTCTTAGCGTTGCA
1 AACAGCGGATCTTACTTTCCTAGCATTGCA
313357 GTGGAACAGG
Statistics
Matches: 336, Mismatches: 68, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
48 3 0.01
49 44 0.13
50 278 0.83
51 11 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (50 bp):
AACAGCGGATCTTACTTTCCTAGCATTGCAATTAAAAAGATTGAAGCTAC
Found at i:313379 original size:50 final size:50
Alignment explanation
Indices: 312878--313465 Score: 341
Period size: 50 Copynumber: 11.8 Consensus size: 50
312868 TTCCTGTACT
* * * * ** *
312878 AACAGCGGATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAG-CTAC
1 AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTC-AC
* * * *
312928 AACAGCGGATCTTACTTTC-CAGGCAATGCAGAGGAATAGATTGAAG-CTAC
1 AACAGCGGATCTTACTTTCTTA-GCATTGCAGTGGAACAGATTGAAGTC-AC
* * * * * ** *
312978 AACAACGAATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAG-CTAC
1 AACAGCGGATCTTACTTTCTTAG-CATTGCAGTGGAACAGATTGAAGTC-AC
* * *
313028 AATAGCGGATCTTACTTTCTTAGC-GTGCAGTGAAACAGATTGAAGTCAC
1 AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
* * * * * ** *
313077 AAC-GACGAATCTTACTTCCCT-GACATTGAAATTAAAAAGATTGAAG-CTAC
1 AACAG-CGGATCTTACTTTCTTAG-CATTGCAGTGGAACAGATTGAAGTC-AC
*
313127 AATAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
1 AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
* * * ** *
313177 AAC-GACGAATCTTACTTTCCT-GACATTGCAATTAAAAAGATTGAAG-CTAC
1 AACAG-CGGATCTTACTTTCTTAG-CATTGCAGTGGAACAGATTGAAGTC-AC
* *
313227 AATAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGTCAC
1 AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
* * * * ** *
313277 AAC-GACGAATCTTACTTCCCT-GACATTGCAATTAAAAAGATTGAAG-CTAC
1 AACAG-CGGATCTTACTTTCTTAG-CATTGCAGTGGAACAGATTGAAGTC-AC
* * **
313327 AACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGGTCAAAGTCAC
1 AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
* * ** * * *
313377 AAC-GACGAATCTCAC-TTCTCGGCATTGCAATGTAAAAGATTGAAG-CAC
1 AACAG-CGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
* * ** *
313425 AACGGCGAATCTTA-TTTCCCAGGCGTTGCAGTGGAACAGAT
1 AACAGCGGATCTTACTTTCTTA-GCATTGCAGTGGAACAGAT
313466 CAAATTCACA
Statistics
Matches: 411, Mismatches: 99, Indels: 57
0.72 0.17 0.10
Matches are distributed among these distances:
48 20 0.05
49 82 0.20
50 299 0.73
51 10 0.02
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (50 bp):
AACAGCGGATCTTACTTTCTTAGCATTGCAGTGGAACAGATTGAAGTCAC
Found at i:315315 original size:3 final size:3
Alignment explanation
Indices: 315246--315306 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
315236 AGTACTTTTG
*
315246 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* *
315291 TAC TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT T
315307 GGTATTATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:315515 original size:35 final size:36
Alignment explanation
Indices: 315436--315515 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
315426 AATTTGTTTA
*
315436 ATATATATACGTATACTCATATTTCTTTTTTATATAT
1 ATATATATACATATAC-CATATTTCTTTTTTATATAT
*
315473 ATCTATATACATATA-CATATTT-TTATTTTATA-AGT
1 ATATATATACATATACCATATTTCTT-TTTTATATA-T
315508 ATATATAT
1 ATATATAT
315516 TTATATGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
34 3 0.08
35 22 0.58
37 13 0.34
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACCATATTTCTTTTTTATATAT
Found at i:315779 original size:18 final size:19
Alignment explanation
Indices: 315742--315780 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
315732 TATACACCTA
315742 TATATATATGTACATATTTT
1 TATATATATG-ACATATTTT
*
315762 TATATATATG-CATCTTTT
1 TATATATATGACATATTTT
315780 T
1 T
315781 TCTTCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (19 bp):
TATATATATGACATATTTT
Found at i:322866 original size:22 final size:23
Alignment explanation
Indices: 322841--322884 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
322831 AAGTTTTTTT
322841 TAAAAAAAT-TATTATTCTTTAC
1 TAAAAAAATATATTATTCTTTAC
322863 TAAAAAAATATATTATTCTTTA
1 TAAAAAAATATATTATTCTTTA
322885 AAGTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAAAATATATTATTCTTTAC
Found at i:330741 original size:25 final size:25
Alignment explanation
Indices: 330713--330764 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
330703 ATGTGCAACG
* *
330713 TTATATATGAATTTTTT-TTGCAATT
1 TTATACATAAATTTTTTATT-CAATT
330738 TTATACATAAATTTTTTATTCAATT
1 TTATACATAAATTTTTTATTCAATT
330763 TT
1 TT
330765 CACAAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (25 bp):
TTATACATAAATTTTTTATTCAATT
Found at i:334612 original size:28 final size:31
Alignment explanation
Indices: 334557--334620 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
334547 GTTCATGTAT
*
334557 TTTTTATATATTTGAAATTTAGATATTTT-A
1 TTTTTATATATTTGAAATTTAGAAATTTTCA
334587 TTTTTAT-T-TTTGAGAATTTA-AAATTTTCA
1 TTTTTATATATTTGA-AATTTAGAAATTTTCA
334616 TTTTT
1 TTTTT
334621 TTAGATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 11 0.35
29 13 0.42
30 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (31 bp):
TTTTTATATATTTGAAATTTAGAAATTTTCA
Found at i:336686 original size:29 final size:30
Alignment explanation
Indices: 336627--336684 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
336617 TCCGAGCCTT
*
336627 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
336657 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
336685 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:336914 original size:13 final size:13
Alignment explanation
Indices: 336896--336927 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
336886 TTTCCAGCAA
336896 TTATGAATTTATT
1 TTATGAATTTATT
336909 TTATGAATTTATT
1 TTATGAATTTATT
*
336922 TGATGA
1 TTATGA
336928 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:337081 original size:50 final size:50
Alignment explanation
Indices: 337022--337317 Score: 450
Period size: 50 Copynumber: 5.8 Consensus size: 50
337012 ATTTGGGTAA
*
337022 AGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
337072 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT--G
337124 AGGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 A-GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
337175 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
337225 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATG
** *
337275 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
337318 TGTTATTATC
Statistics
Matches: 227, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
49 1 0.00
50 140 0.62
51 36 0.16
52 2 0.01
53 48 0.21
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:337202 original size:103 final size:100
Alignment explanation
Indices: 337022--337317 Score: 450
Period size: 103 Copynumber: 2.9 Consensus size: 100
337012 ATTTGGGTAA
*
337022 AGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
337087 GACCATGTCTGGGACATGGCATTGGCACCGAGATGAG
66 GACCATGTCTGGGACATGGCATTGGCACCGAGAT--G
337124 AGGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
1 A-GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTA
*
337189 AGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
65 AGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * **
337225 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAACATCCCATGT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATGAG-AGGTCCCATGT
*
337289 AAGACCATGTCTGGGACATGGCTTTGGCA
64 AAGACCATGTCTGGGACATGGCATTGGCA
337318 TGTTATTATC
Statistics
Matches: 181, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
99 1 0.01
100 44 0.24
101 39 0.22
102 1 0.01
103 96 0.53
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (100 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:348100 original size:15 final size:16
Alignment explanation
Indices: 348067--348102 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
348057 CATTTACTTT
*
348067 ATAATATTTTATAAAA
1 ATAATATTTCATAAAA
348083 ATAATATTTCAT-AAA
1 ATAATATTTCATAAAA
348098 ATAAT
1 ATAAT
348103 TGAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATTTCATAAAA
Found at i:357396 original size:31 final size:31
Alignment explanation
Indices: 357360--357425 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
357350 AAAAAAATTT
*
357360 AATAGTCCAGTGATTTAAATAAAAACTTTGG
1 AATAGTCCAGTGACTTAAATAAAAACTTTGG
* * * *
357391 AATAGTCTAGTGACTTAAATGAAAATTTTTG
1 AATAGTCCAGTGACTTAAATAAAAACTTTGG
357422 AATA
1 AATA
357426 ATTTAATGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (31 bp):
AATAGTCCAGTGACTTAAATAAAAACTTTGG
Found at i:360194 original size:3 final size:3
Alignment explanation
Indices: 360186--360240 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
360176 TTAAATCTAG
360186 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
360234 TAA TAA T
1 TAA TAA T
360241 TGGATCGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:372580 original size:108 final size:108
Alignment explanation
Indices: 372391--372595 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 108
372381 ATCATTGAAG
* *
372391 TGTTAACAAGATTAACCACTACTCTCTTATGTTGTTGACAATTTCGATTATTGATCATGCATTCA
1 TGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCATGCATTCA
*
372456 CTCTTGAATTGGATTTTCCAATGGCTTCAAATAGACATTAAAA
66 CTCTTGAATTGGATTTTCCAATCGCTTCAAATAGACATTAAAA
* *
372499 TGTTAACAAGATTAACCACTACTCTTTTACGTTGTTGACAATTTCAATTATTGATCATTCATTCA
1 TGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCATGCATTCA
* **
372564 TTCTT-AGATTGGATTTTTGAATCGCTTCAAAT
66 CTCTTGA-ATTGGATTTTCCAATCGCTTCAAAT
372596 GAAGGATATC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 1 0.01
108 87 0.99
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (108 bp):
TGTTAACAAGATTAACCACTACTCTCTTACGTTGTTGACAATTTCAATTATTGATCATGCATTCA
CTCTTGAATTGGATTTTCCAATCGCTTCAAATAGACATTAAAA
Found at i:380823 original size:23 final size:22
Alignment explanation
Indices: 380773--380823 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
380763 TTTTAAACGA
* *
380773 TTAACAAATAATATTATAAAAG
1 TTAAAAAATAAAATTATAAAAG
*
380795 TATAAAAAATAAAATTATATCAAG
1 T-TAAAAAATAAAATTATA-AAAG
380819 TTAAA
1 TTAAA
380824 CTACGGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
TTAAAAAATAAAATTATAAAAG
Found at i:395453 original size:11 final size:12
Alignment explanation
Indices: 395439--395470 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
395429 ACCCCATTCC
395439 TTGCCCATAC-T
1 TTGCCCATACAT
395450 TTGCCCATACAT
1 TTGCCCATACAT
395462 TT-CCCATAC
1 TTGCCCATAC
395471 CTACCCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (12 bp):
TTGCCCATACAT
Found at i:396039 original size:18 final size:18
Alignment explanation
Indices: 396016--396094 Score: 104
Period size: 18 Copynumber: 4.4 Consensus size: 18
396006 TACGACCGTT
396016 TACAGTACTATTCACGTA
1 TACAGTACTATTCACGTA
*
396034 TACAGTACTATTTACGTA
1 TACAGTACTATTCACGTA
* * *
396052 TACGGCACTATTCATGTA
1 TACAGTACTATTCACGTA
* *
396070 TACGGTACTGTTCACGTA
1 TACAGTACTATTCACGTA
396088 TACAGTA
1 TACAGTA
396095 GTTGGGATTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (18 bp):
TACAGTACTATTCACGTA
Found at i:400054 original size:11 final size:11
Alignment explanation
Indices: 400034--400086 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
400024 TAGAATATAC
* *
400034 CCCATTCCTTG
1 CCCATACCTTA
400045 CCCATACCTTA
1 CCCATACCTTA
*
400056 CCCATACCTTT
1 CCCATACCTTA
400067 CCCATACC-TA
1 CCCATACCTTA
400077 CCCATACCTT
1 CCCATACCTT
400087 GGAATGGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 28 0.76
ACGTcount: A:0.21, C:0.47, G:0.02, T:0.30
Consensus pattern (11 bp):
CCCATACCTTA
Found at i:400080 original size:21 final size:22
Alignment explanation
Indices: 400034--400087 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
400024 TAGAATATAC
*
400034 CCCATTCCTTGCCCATACCTTA
1 CCCATACCTTGCCCATACCTTA
*
400056 CCCATACCTTTCCCATACC-TA
1 CCCATACCTTGCCCATACCTTA
400077 CCCATACCTTG
1 CCCATACCTTG
400088 GAATGGTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.20, C:0.46, G:0.04, T:0.30
Consensus pattern (22 bp):
CCCATACCTTGCCCATACCTTA
Found at i:405519 original size:31 final size:31
Alignment explanation
Indices: 405484--405551 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
405474 ATTAAAAATT
405484 TTATACATTTCTATTATAAAAAACTGGTCCA
1 TTATACATTTCTATTATAAAAAACTGGTCCA
*
405515 TTATACATTTCTATTATAAAAAACTGTTCCA
1 TTATACATTTCTATTATAAAAAACTGGTCCA
405546 TGTATA
1 T-TATA
405552 TTAGCAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (31 bp):
TTATACATTTCTATTATAAAAAACTGGTCCA
Found at i:407539 original size:48 final size:48
Alignment explanation
Indices: 407445--407539 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
407435 GTAATTACCC
* **
407445 GGGATTTCTTTCGGTTTTTCCTCTTTAAAATGAAAAGGGGGGCAACCT
1 GGGATATCTTTCGGTTTTTCCTCTTTAAAATGAAAAGGGCAGCAACCT
** * *
407493 GGGATATCTTTCGGTTTTTCCTCTTTTCAATGAAAATGGCATCAACC
1 GGGATATCTTTCGGTTTTTCCTCTTTAAAATGAAAAGGGCAGCAACC
407540 GTCCTACAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (48 bp):
GGGATATCTTTCGGTTTTTCCTCTTTAAAATGAAAAGGGCAGCAACCT
Found at i:414821 original size:6 final size:6
Alignment explanation
Indices: 414810--414908 Score: 198
Period size: 6 Copynumber: 16.5 Consensus size: 6
414800 CAATACAGAA
414810 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
414858 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
414906 ATA
1 ATA
414909 TGAGTCAACA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:424062 original size:20 final size:20
Alignment explanation
Indices: 424037--424076 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
424027 ATTCAATAAG
*
424037 AATGTGTAATTTGTAACGTT
1 AATGTGTAATCTGTAACGTT
*
424057 AATGTGTAATCTGTCACGTT
1 AATGTGTAATCTGTAACGTT
424077 CTTATTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (20 bp):
AATGTGTAATCTGTAACGTT
Found at i:425470 original size:16 final size:16
Alignment explanation
Indices: 425451--425482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
425441 AAATGGTACA
425451 AACCCAAAATGACATG
1 AACCCAAAATGACATG
*
425467 AACCCGAAATGACATG
1 AACCCAAAATGACATG
425483 TGCAAGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
AACCCAAAATGACATG
Found at i:430822 original size:28 final size:29
Alignment explanation
Indices: 430782--430839 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
430772 TCAAATAGTA
* *
430782 ATGACGTGGCAACTAAAGTA-GAAAAATG
1 ATGACATGACAACTAAAGTAGGAAAAATG
*
430810 ATGACATGACAACTGAAGTAGGAAAAATG
1 ATGACATGACAACTAAAGTAGGAAAAATG
430839 A
1 A
430840 GAATAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.17
Consensus pattern (29 bp):
ATGACATGACAACTAAAGTAGGAAAAATG
Found at i:431108 original size:19 final size:18
Alignment explanation
Indices: 431061--431095 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
431051 CATTAAGCTC
431061 AAAAAAAAACCTAACCCA
1 AAAAAAAAACCTAACCCA
431079 AAAAAAAAACCTAACCC
1 AAAAAAAAACCTAACCC
431096 CCCCAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.29, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAAACCTAACCCA
Found at i:431257 original size:36 final size:36
Alignment explanation
Indices: 431216--431300 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
431206 GAAATAATAG
431216 AAAATCATGTAAAATATGGCTATAAAAAGCCATTAA
1 AAAATCATGTAAAATATGGCTATAAAAAGCCATTAA
431252 AAAATCATGTAAAATATGGCTATAAAAAGCCATTAA
1 AAAATCATGTAAAATATGGCTATAAAAAGCCATTAA
431288 AAAATCATGTAAA
1 AAAATCATGTAAA
431301 GGGGGGGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (36 bp):
AAAATCATGTAAAATATGGCTATAAAAAGCCATTAA
Found at i:431894 original size:13 final size:13
Alignment explanation
Indices: 431876--431903 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
431866 AATTGCACTT
431876 TTAGCCCCTCCGC
1 TTAGCCCCTCCGC
431889 TTAGCCCCTCCGC
1 TTAGCCCCTCCGC
431902 TT
1 TT
431904 TTTCATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.50, G:0.14, T:0.29
Consensus pattern (13 bp):
TTAGCCCCTCCGC
Found at i:432357 original size:22 final size:22
Alignment explanation
Indices: 432310--432357 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
432300 ATGTTGTTAA
*
432310 TTTATTACTTTATTTTAATATC
1 TTTATTAATTTATTTTAATATC
432332 TTTATTATATTTACTTTT-ATAT-
1 TTTATTA-ATTTA-TTTTAATATC
432354 TTTA
1 TTTA
432358 ATATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATTAATTTATTTTAATATC
Found at i:432532 original size:30 final size:30
Alignment explanation
Indices: 432477--432553 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
432467 TTTATCCCTA
432477 ATAT-TTATGTATTATATAAATA-TTTTAAT
1 ATATATTATGTA-TATATAAATATTTTTAAT
* * **
432506 ATTATATTATGTATATCTATATATTTTTCGT
1 A-TATATTATGTATATATAAATATTTTTAAT
432537 ATATATTATGTATATAT
1 ATATATTATGTATATAT
432554 GTTTTCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 26 0.65
31 13 0.32
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
ATATATTATGTATATATAAATATTTTTAAT
Found at i:432661 original size:19 final size:19
Alignment explanation
Indices: 432637--432673 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
432627 CTATTTTATA
*
432637 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
432656 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
432674 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:432780 original size:20 final size:18
Alignment explanation
Indices: 432744--432783 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
432734 ATTTCTAATA
*
432744 TATATATTATATGTATTT
1 TATATATTATATATATTT
432762 TATATATTATGTATATATTT
1 TATATATTA--TATATATTT
432782 TA
1 TA
432784 ATGTTATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATATTATATATATTT
Found at i:433072 original size:37 final size:35
Alignment explanation
Indices: 433007--433076 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
432997 TTATATATAG
433007 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
433044 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
433077 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:436842 original size:17 final size:14
Alignment explanation
Indices: 436808--436843 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
436798 AAAGAAATTT
436808 TTCTTCTAGTAAAG
1 TTCTTCTAGTAAAG
436822 TTCTTCTAGTAAAG
1 TTCTTCTAGTAAAG
436836 TTCTTCTA
1 TTCTTCTA
436844 ATGAAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (14 bp):
TTCTTCTAGTAAAG
Found at i:444905 original size:72 final size:74
Alignment explanation
Indices: 444638--446165 Score: 1787
Period size: 72 Copynumber: 20.7 Consensus size: 74
444628 TGATGTTTTT
* **
444638 ATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGA
1 ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
444701 GGTATTTTCA
65 GGTATTTTCA
*
444711 ATTTCT-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA--CTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
444773 GTATTTTCA
66 GTATTTTCA
444782 ATTTCTGTTCAATTTTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 A----T-TTC-----TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
444846 ACAC-ATGAGGTATTTTCA
56 ACACGCTGAGGTATTTTCA
444864 ATTTCTGTTTTTCAAAAAA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
444927 GTA-TTTCA
66 GTATTTTCA
* * **
444935 ATTTTTGTTTTCAATTATTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
1 ATTTCTGTTTT---TCA-------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
445000 ACACGCTGAGGTAATTTCA
56 ACACGCTGAGGTATTTTCA
* * *
445019 ATTT-TGTTTGTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-CACGTTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
445080 GTATTTTTTCT
66 GTA--TTTTCA
* * *
445091 GTTCTTTATTTTTCAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATT-TCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
*
445155 GGTAATTTCA
65 GGTATTTTCA
** * *
445165 ATTT-TG--TTT-AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
445226 GTATTTTCA
66 GTATTTTCA
* * *
445235 ATTT-TGTCTTTCAAAAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCAAGACA-GTTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
445297 GTA-TTTCA
66 GTATTTTCA
*
445305 ATTTCTGTTTTCAATTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACGCT
1 ATTTCTGTTTT---TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
445368 GAGGTAATTTCA
63 GAGGTATTTTCA
* *
445380 ATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAAGACA-GCTGA
1 ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
445441 GGTATTTTCA
65 GGTATTTTCA
*
445451 ATTT-TGTCTTTCAAAAAAATCAACTCATATT--GAGAGGTGAGTTGAGCCTCA-GACACGCTGA
1 ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
445512 GGTA-TTTCA
65 GGTATTTTCA
* * *
445521 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGA-ATGAGTTGAGCCTCA-GACACGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
445584 GTAATTTCA
66 GTATTTTCA
* ** **
445593 ATTTCTG-TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GACTTGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
445655 GTATTTTCA
66 GTATTTTCA
* * *
445664 ATTTTTGTCTTTCAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
1 ATTTCTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
445729 AGGTAATTTCA
64 AGGTATTTTCA
* * * ** *
445740 ATTTCTATTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
445805 GTAATTTCA
66 GTATTTTCA
* ** * *
445814 ATTTCTG-TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
445877 GTATTTTCA
66 GTATTTTCA
* *
445886 ATTTCTGTTTTTTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
1 ATTTCTG-TTTTT----CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
445951 CTGAGGTAATTTCA
61 CTGAGGTATTTTCA
* ** * *
445965 ATTTCTG-TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
446028 GTATTTTCA
66 GTATTTTCA
* *
446037 ATTTCTG-TTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCT
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCT
446100 GAGGTATTTTCA
63 GAGGTATTTTCA
* *
446112 ATTTCTGTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
446166 ATCACACACT
Statistics
Matches: 1274, Mismatches: 104, Indels: 150
0.83 0.07 0.10
Matches are distributed among these distances:
69 20 0.02
70 138 0.11
71 220 0.17
72 252 0.20
73 120 0.09
74 120 0.09
75 112 0.09
76 94 0.07
77 8 0.01
78 1 0.00
79 60 0.05
80 1 0.00
81 49 0.04
82 53 0.04
83 17 0.01
84 9 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (74 bp):
ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTATTTTCA
Found at i:445159 original size:146 final size:146
Alignment explanation
Indices: 444953--446160 Score: 1450
Period size: 146 Copynumber: 8.3 Consensus size: 146
444943 TTTCAATTAT
** *
444953 TTTTTC-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
*
445017 CAATTT-TGTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-CACGTTGA
66 CAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGA
** * *
445079 GGTATTTTTTCTGTTCTTTA
130 GGTA--TTTTCAATT-TCTG
*
445099 TTTTTCAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
* ** *
445163 CAATTT-TG-TTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
66 CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
445226 GTATTTTCAATTT-TG
131 GTATTTTCAATTTCTG
* *
445241 TCTTTCAAAAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCAAGACA-GTTGAGGT-ATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
*
445303 CAATTTCTGTTTTCAATTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AG-GACG
66 CAATTTCTGTTTTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
*
445366 CTGAGGTAATTTCAATTTCTG
126 CTGAGGTATTTTCAATTTCTG
* *
445387 -TTGTCAAAAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAAGACA-GCTGAGGTATTT
1 TTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
445448 TCAATTT-TGTCTTTCAAAAAAATCAACTCATATT--GAGAGGTGAGTTGAGCCTC-AGACACGC
65 TCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
445509 TGAGGTA-TTTCAATTTCTG
127 TGAGGTATTTTCAATTTCTG
* * *
445528 TTGTTAAAAAAATCAACTCATATTGCGAGA-ATGAGTTGAGCCTC-AGACACGCTGAGGTAATTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
* ** **
445591 CAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACTTGCTGAG
66 CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
*
445655 GTATTTTCAATTTTTG
131 GTATTTTCAATTTCTG
* * *
445671 TCTTTCAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
1 TTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAAT
* * ** * *
445736 TTCAATTTCTATTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTAAGCCTCAGGACACGC
64 TTCAATTTCTGTT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGC
*
445801 TGAGGTAATTTCAATTTCTG
127 TGAGGTATTTTCAATTTCTG
* ** * *
445821 -TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
* **
445884 CAATTTCTGTTTTTTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
66 CAATTTCTG--TTTT-----CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
445949 CGCTGAGGTAATTTCAATTTCTG
124 CGCTGAGGTATTTTCAATTTCTG
* ** * *
445972 -TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
* * *
446035 CAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGC
66 CAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGC
446099 TGAGGTATTTTCAATTTCTG
127 TGAGGTATTTTCAATTTCTG
*
446119 TCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
446161 TTCAGATCAC
Statistics
Matches: 947, Mismatches: 73, Indels: 81
0.86 0.07 0.07
Matches are distributed among these distances:
140 26 0.03
141 71 0.07
142 122 0.13
143 43 0.05
144 10 0.01
145 151 0.16
146 177 0.19
147 105 0.11
148 8 0.01
149 76 0.08
150 23 0.02
151 135 0.14
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (146 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTT
CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
GTATTTTCAATTTCTG
Found at i:447812 original size:13 final size:13
Alignment explanation
Indices: 447794--447821 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
447784 AATTGCACTT
447794 TTAGCCCCTCCGC
1 TTAGCCCCTCCGC
447807 TTAGCCCCTCCGC
1 TTAGCCCCTCCGC
447820 TT
1 TT
447822 TTTCATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.50, G:0.14, T:0.29
Consensus pattern (13 bp):
TTAGCCCCTCCGC
Found at i:448331 original size:24 final size:23
Alignment explanation
Indices: 448271--448363 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 23
448261 ACTTTTTATA
448271 TTTTAATATTATTATTAT-TATCATG
1 TTTTAATA-TA-TATTATGTAT-ATG
* * *
448296 -ATTACTATATATTAGTGTATATT
1 TTTTAATATATATTA-TGTATATG
*
448319 TTTTATTATATATATATGTATATG
1 TTTTAATATATAT-TATGTATATG
448343 TTTTAATATAT-TTATGTATAT
1 TTTTAATATATATTATGTATAT
448364 ACTTATGTAG
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
22 14 0.25
23 6 0.11
24 35 0.61
25 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTAATATATATTATGTATATG
Found at i:448363 original size:12 final size:12
Alignment explanation
Indices: 448301--448372 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
448291 TCATGATTAC
448301 TATATA-TTAGTG
1 TATATATTTA-TG
*
448313 TATATTTTTTAT-
1 TATA-TATTTATG
*
448325 TATATATATATG
1 TATATATTTATG
*
448337 TATATGTTT-T-
1 TATATATTTATG
*
448347 AATATATTTATG
1 TATATATTTATG
*
448359 TATATACTTATG
1 TATATATTTATG
448371 TA
1 TA
448373 GCATTATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 7 0.15
11 7 0.15
12 27 0.59
13 2 0.04
14 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.57
Consensus pattern (12 bp):
TATATATTTATG
Found at i:448364 original size:24 final size:23
Alignment explanation
Indices: 448301--448364 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 23
448291 TCATGATTAC
448301 TATATATTAGTGTATAT-TTTTTATTA
1 TATAT-TTA-TGTATATATTTTTA--A
* *
448327 TATATATATGTATAT-GTTTTAA
1 TATATTTATGTATATATTTTTAA
448349 TATATTTATGTATATA
1 TATATTTATGTATATA
448365 CTTATGTAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 15 0.44
24 12 0.35
25 2 0.06
26 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (23 bp):
TATATTTATGTATATATTTTTAA
Found at i:448582 original size:19 final size:19
Alignment explanation
Indices: 448558--448594 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
448548 CTATTTTATA
*
448558 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
448577 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
448595 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:448914 original size:37 final size:35
Alignment explanation
Indices: 448849--448918 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
448839 TTATATATAG
448849 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
448886 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
448919 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:451190 original size:11 final size:11
Alignment explanation
Indices: 451174--451200 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
451164 TGGTTTTGGA
451174 TTTCTTTCGTC
1 TTTCTTTCGTC
451185 TTTCTTTCGTC
1 TTTCTTTCGTC
451196 TTTCT
1 TTTCT
451201 CCATAGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTCTTTCGTC
Found at i:452487 original size:20 final size:20
Alignment explanation
Indices: 452464--452504 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
452454 AATTCCAAAT
452464 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
* *
452484 TAAAATCCTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
452504 T
1 T
452505 TAAGAGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:456608 original size:16 final size:16
Alignment explanation
Indices: 456587--456618 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
456577 TTATTGTTGG
456587 GTGAGACGTGTCTATT
1 GTGAGACGTGTCTATT
456603 GTGAGACGTGTCTATT
1 GTGAGACGTGTCTATT
456619 ATGGCAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
GTGAGACGTGTCTATT
Found at i:458757 original size:2 final size:2
Alignment explanation
Indices: 458750--458777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
458740 ACATCCATGC
458750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
458778 CAGCCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:459111 original size:26 final size:26
Alignment explanation
Indices: 459082--459145 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 26
459072 TATCAAAGAT
459082 TTTATTGATTAA-AAAATATATATT-TA
1 TTTATT-ATTAAGAAAAT-TATATTATA
* *
459108 TTTAATAATTAAGTAAATTATATTATA
1 TTT-ATTATTAAGAAAATTATATTATA
459135 TTATATTATTA
1 TT-TATTATTA
459146 TTATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 14 0.45
27 16 0.52
28 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TTTATTATTAAGAAAATTATATTATA
Found at i:460820 original size:39 final size:39
Alignment explanation
Indices: 460713--460847 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
460703 GACCTCGAGT
* * *
460713 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
460754 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
460792 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
460831 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
460848 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:475185 original size:16 final size:16
Alignment explanation
Indices: 475164--475195 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
475154 TGGGTCAAGT
475164 TGATTTTGGATCGATC
1 TGATTTTGGATCGATC
475180 TGATTTTGGATCGATC
1 TGATTTTGGATCGATC
475196 AATCTGGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
TGATTTTGGATCGATC
Found at i:476720 original size:30 final size:30
Alignment explanation
Indices: 476658--476718 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
476648 TATAGTCAAC
* *
476658 AAATAATTTAAAATTTATAAAAGTATTAAA
1 AAATAAATTAAAATTTATAAAAGCATTAAA
476688 AAATAAATTAAAATTT-TAAAA-CATTAAA
1 AAATAAATTAAAATTTATAAAAGCATTAAA
476716 AAA
1 AAA
476719 AAGCATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.31
29 5 0.17
30 15 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATAAATTAAAATTTATAAAAGCATTAAA
Found at i:482857 original size:20 final size:20
Alignment explanation
Indices: 482832--482871 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
482822 CATGACGGAA
482832 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
482852 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
482872 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:490720 original size:12 final size:12
Alignment explanation
Indices: 490700--490738 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
490690 GAAAAGAAAA
490700 AAAAACAAAATC
1 AAAAACAAAATC
*
490712 AAAATCAAAATC
1 AAAAACAAAATC
* *
490724 AAAAATAAAAAC
1 AAAAACAAAATC
490736 AAA
1 AAA
490739 GAGAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAACAAAATC
Found at i:492524 original size:44 final size:44
Alignment explanation
Indices: 492476--492790 Score: 196
Period size: 44 Copynumber: 7.2 Consensus size: 44
492466 GACAAAAGAT
* *
492476 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * *
492520 CTTGCC-TCTTTCGATTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTTC-ATTGACA-GCGAAGCAGGTCGAAGACACAA-AC
* *
492564 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* * ** * * * *
492608 CTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTTC-ATTGACA-GCGAAGCAGGTCGAAGACACAA-AC
* * *
492652 CTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* * ** ** * * * *
492696 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTTC-ATTGACAGCGAAGCAGGTCGAAGACACAA-AC
* *
492740 CTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
492784 CTTGCCT
1 CTTGCCT
492791 CTCTCGGTTG
Statistics
Matches: 192, Mismatches: 63, Indels: 32
0.67 0.22 0.11
Matches are distributed among these distances:
43 55 0.29
44 81 0.42
45 56 0.29
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:492574 original size:88 final size:88
Alignment explanation
Indices: 492420--492900 Score: 695
Period size: 88 Copynumber: 5.5 Consensus size: 88
492410 ACAGATCAAT
* * *
492420 GAAGTCACAAACCTTGCCTCTCTCGGTTGT-AGTGGAGCTGGTTAAAGACAAAAGATCTTGCCTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
*
492484 CCTACATTGACAGCGAAGCAGATC
65 CCTGCATTGACAGCGAAGCAGATC
*
492508 GAAGACACAAACCTTGCCTCTTTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
*
492573 CTACATTGACAGCGAAGCAGATC
66 CTGCATTGACAGCGAAGCAGATC
*
492596 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
492661 CTGCATTGACAGCGAAGCAGATC
66 CTGCATTGACAGCGAAGCAGATC
*
492684 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
* *
492749 CTGCATTGACAGTGAAGCAGGTC
66 CTGCATTGACAGCGAAGCAGATC
* * **
492772 GAAGACACAAACCTTGCCTCTCTCGGTTGT-AGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTT
1 GAAGACACAAACCTTGCCTCTTTCGGTTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
* * *
492835 CTTGCATTAACAGCAAAGCAGATC
65 CCTGCATTGACAGCGAAGCAGATC
* ** *
492859 -AA-AAACAAAGCCTTGCCTCCATCGGTTG-CATTGGAGCTGGTT
1 GAAGACACAAA-CCTTGCCTCTTTCGGTTGTGA-TGGAGCTGGTT
492901 AAAGGTTACA
Statistics
Matches: 364, Mismatches: 25, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
85 6 0.02
86 30 0.08
87 33 0.09
88 294 0.81
89 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (88 bp):
GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
CTGCATTGACAGCGAAGCAGATC
Done.