Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007410.1 Hibiscus syriacus cultivar Beakdansim tig00020021_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 274377
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:738 original size:21 final size:21
Alignment explanation
Indices: 699--738 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
689 AAGGAAGATT
*
699 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
720 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
739 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:785 original size:21 final size:20
Alignment explanation
Indices: 760--798 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
750 GGTTGCGAAT
760 TGATGGTCTTGATGGATGAGA
1 TGATGGTCTTGAT-GATGAGA
*
781 TGATGGTGTTGATGATGA
1 TGATGGTCTTGATGATGA
799 AATGGAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.36
Consensus pattern (20 bp):
TGATGGTCTTGATGATGAGA
Found at i:3396 original size:35 final size:37
Alignment explanation
Indices: 3327--3406 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
3317 ATACTATTTC
* * *
3327 CATCCCCATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
3364 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
3399 CATCACCA
1 CATCACCA
3407 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:9035 original size:35 final size:37
Alignment explanation
Indices: 8967--9046 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
8957 ATACTATTTC
* *
8967 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
9004 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
9039 CATCACCA
1 CATCACCA
9047 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:14705 original size:1 final size:1
Alignment explanation
Indices: 14701--14744 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
14691 GCTTTTTGGC
14701 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14745 GAAAAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16247 original size:19 final size:21
Alignment explanation
Indices: 16196--16239 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
16186 GAAACCCCCT
16196 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
16217 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
16236 TGAA
1 TGAA
16240 GATGCATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:19396 original size:8 final size:8
Alignment explanation
Indices: 19383--19417 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
19373 GAATTTCTTT
19383 TTCTTTTC
1 TTCTTTTC
19391 TTCTTTTC
1 TTCTTTTC
19399 -T-TTTTC
1 TTCTTTTC
19405 TTCTTTTC
1 TTCTTTTC
19413 TTCTT
1 TTCTT
19418 CATTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.20
7 2 0.08
8 18 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:19396 original size:14 final size:14
Alignment explanation
Indices: 19377--19440 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
19367 CTTTTTGAAT
19377 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
19391 TTC-TTTTCTTTTTC
1 TTCTTTTTC-TTTTC
19405 TTC-TTTTCTTCTTC
1 TTCTTTTTCTT-TTC
* *
19419 AT-TTTTTATTTTC
1 TTCTTTTTCTTTTC
19432 TTTCTTTTT
1 -TTCTTTTT
19441 GTACTCCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 10 0.24
14 27 0.64
15 5 0.12
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:19400 original size:19 final size:19
Alignment explanation
Indices: 19376--19439 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
19366 TCTTTTTGAA
19376 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
19395 TTTCTTTTTCTTCTT-TTCT
1 TTTCTTTTTCTT-TTCTTCT
*
19414 TCTTCATTTTTTATTTTCTTTCT
1 T-TTC--TTTTTCTTTTC-TTCT
19437 TTT
1 TTT
19440 TGTACTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 17 0.45
20 5 0.13
21 2 0.05
22 9 0.24
23 5 0.13
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:19424 original size:22 final size:20
Alignment explanation
Indices: 19375--19425 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
19365 TTCTTTTTGA
19375 ATTTCTTTTTCTTTTCTTCTT
1 ATTT-TTTTTCTTTTCTTCTT
*
19396 TTCTTTTTCTTCTTTTCTTCTT
1 AT-TTTTT-TTCTTTTCTTCTT
19418 CATTTTTT
1 -ATTTTTT
19426 ATTTTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 20 0.80
23 1 0.04
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTTTTCTTTTCTTCTT
Found at i:20200 original size:19 final size:21
Alignment explanation
Indices: 20150--20201 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20140 GAAACCCCCT
20150 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
20171 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
20190 T-AAAGATACATG
1 TGAAA-ATACATG
20202 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 4 0.13
21 13 0.43
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:35281 original size:13 final size:12
Alignment explanation
Indices: 35265--35292 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35255 TTTTTTTTTG
35265 TTTTTTTGCCTT
1 TTTTTTTGCCTT
35277 TTTTTTTGCCTT
1 TTTTTTTGCCTT
35289 TTTT
1 TTTT
35293 GTTTTTTGAA
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:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:35299 original size:21 final size:20
Alignment explanation
Indices: 35248--35293 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
35238 TGTTTTGAAA
* *
35248 TTTTGGCTTTTTTTTTGTTT
1 TTTTGCCTTTTTTTTTGCTT
35268 TTTTGCCTTTTTTTTTGCCTT
1 TTTTGCCTTTTTTTTTG-CTT
35289 TTTTG
1 TTTTG
35294 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTTGCCTTTTTTTTTGCTT
Found at i:52652 original size:21 final size:21
Alignment explanation
Indices: 52606--52667 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
52596 CTTTTTGAAT
52606 TTCTTTTTC--TTTTCTTTT-
1 TTCTTTTTCTATTTTCTTTTC
* * * *
52624 ATCGTTTTCTGTTTTTTTTTC
1 TTCTTTTTCTATTTTCTTTTC
*
52645 TTCTTTTTGTATTTTCTTTTC
1 TTCTTTTTCTATTTTCTTTTC
52666 TT
1 TT
52668 TTTGCACTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 7 0.21
20 8 0.24
21 18 0.55
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (21 bp):
TTCTTTTTCTATTTTCTTTTC
Found at i:62563 original size:5 final size:5
Alignment explanation
Indices: 62548--62610 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
62538 TCCTTTTGAA
62548 TTTCTT TTTCT TTTCT TTTC- TTT-T TTTCT GTTT-T TTTCT GATTT-T
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTTCT --TTTCT
*
62593 TGTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTT
62611 TGCACTCCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
4 11 0.23
5 26 0.54
6 8 0.17
7 3 0.06
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:62568 original size:10 final size:9
Alignment explanation
Indices: 62552--62611 Score: 59
Period size: 10 Copynumber: 6.2 Consensus size: 9
62542 TTTGAATTTC
62552 TTTTTCTTT
1 TTTTTCTTT
62561 TCTTTTC-TT
1 T-TTTTCTTT
62570 TTTTTCTGTT
1 TTTTTCT-TT
62580 TTTTTCTGATT
1 TTTTTCT--TT
*
62591 TTTGTCTTT
1 TTTTTCTTT
62600 TCTTTTCTTT
1 T-TTTTCTTT
62610 TT
1 TT
62612 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.12
9 8 0.19
10 22 0.51
11 8 0.19
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:62592 original size:21 final size:21
Alignment explanation
Indices: 62552--62607 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 21
62542 TTTGAATTTC
62552 TTTT-TCTTTTCTTTTCT--T
1 TTTTGTCTTTTCTTTTCTGAT
62570 TTTT-TCTGTTT-TTTTCTGAT
1 TTTTGTCT-TTTCTTTTCTGAT
62590 TTTTGTCTTTTCTTTTCT
1 TTTTGTCTTTTCTTTTCT
62608 TTTTGCACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
20 8 0.24
21 9 0.27
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (21 bp):
TTTTGTCTTTTCTTTTCTGAT
Found at i:62952 original size:22 final size:21
Alignment explanation
Indices: 62926--62966 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
62916 GCTGTGGAAT
62926 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
62948 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
62967 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:66146 original size:19 final size:21
Alignment explanation
Indices: 66103--66154 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
66093 GAAACCCCTT
66103 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
66124 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
66143 TGAAGATACATG
1 TGAAAATACATG
66155 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:70246 original size:18 final size:20
Alignment explanation
Indices: 70204--70254 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
70194 GAAACCCCTT
70204 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGAC-TTTAAA
70225 TGAAAATACATGA-TTT-AA
1 TGAAAATACATGACTTTAAA
*
70243 TGAAGATACATG
1 TGAAAATACATG
70255 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.45
19 3 0.10
21 13 0.45
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGACTTTAAA
Found at i:73293 original size:14 final size:15
Alignment explanation
Indices: 73259--73305 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
73249 AATTTGGAGT
73259 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
73274 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
73288 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
73305 G
1 G
73306 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:82078 original size:15 final size:15
Alignment explanation
Indices: 82058--82105 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
82048 TTTGATATCA
82058 TTTCTTTCCATTTCT
1 TTTCTTTCCATTTCT
*
82073 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCT
82088 TTTCTTCTTCCATTTCT
1 TTTC-T-TTCCATTTCT
82105 T
1 T
82106 ATTTCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 16 0.59
16 3 0.11
17 8 0.30
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTCCATTTCT
Found at i:83559 original size:22 final size:22
Alignment explanation
Indices: 83531--83574 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
83521 AAGAGGAGAA
83531 TGAAGAACATATTTTAACTAAC
1 TGAAGAACATATTTTAACTAAC
83553 TGAAGAACATATTTTAACTAAC
1 TGAAGAACATATTTTAACTAAC
83575 CTTATTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
TGAAGAACATATTTTAACTAAC
Found at i:89950 original size:11 final size:13
Alignment explanation
Indices: 89918--89947 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
89908 TGGCCAAAGA
89918 TGAAAAGGTATGT
1 TGAAAAGGTATGT
89931 TGAAAAGGTATG-
1 TGAAAAGGTATGT
89943 TGAAA
1 TGAAA
89948 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:94733 original size:19 final size:18
Alignment explanation
Indices: 94709--94744 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
94699 CGGACAAGAG
94709 CATGTATCTTCATTAAAAT
1 CATGTATCTTCA-TAAAAT
*
94728 CATGTATTTTCATAAAA
1 CATGTATCTTCATAAAA
94745 AAAACATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (18 bp):
CATGTATCTTCATAAAAT
Found at i:94745 original size:19 final size:20
Alignment explanation
Indices: 94709--94760 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
94699 CGGACAAGAG
* * *
94709 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAA
94728 CATGTATTTTCATAAAAAAAA
1 CATGTATTTTCAT-AAAAAAA
94749 CATGTATTTTCA
1 CATGTATTTTCA
94761 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAA
Found at i:96590 original size:20 final size:22
Alignment explanation
Indices: 96561--96600 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
96551 GGGAGAGCTT
96561 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
96581 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
96601 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:104624 original size:52 final size:53
Alignment explanation
Indices: 104493--104624 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
104483 TTGCATTTAT
* *
104493 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
104547 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
104599 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
104625 ATAAATCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:108486 original size:55 final size:55
Alignment explanation
Indices: 108424--108792 Score: 569
Period size: 55 Copynumber: 6.7 Consensus size: 55
108414 ACATGTTCAC
*
108424 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * * * *
108479 TCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
108534 TCCTTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* *
108589 TCCCTATTCCTTCAGAGAGTATGAGACTCAAACAATCTTCAATAATCGTGTTTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
108644 TCCCTATTCTTTCAGAGAGTATGACACTCGAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
108699 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTATGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
*
108754 TCCCTATTCTTTCAGAGAGTATGAGACTCGAAC-ATCTTC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTC
108793 TTCTTACAGG
Statistics
Matches: 284, Mismatches: 30, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 6 0.02
55 278 0.98
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
Found at i:108812 original size:54 final size:53
Alignment explanation
Indices: 108754--109909 Score: 993
Period size: 54 Copynumber: 21.8 Consensus size: 53
108744 TCGTGTATGT
* ** * *
108754 TCCCTATTCTTTCAGAGAGTATGAG-ACTCGAACATCTTCTTCTTACAGGTTCAC
1 TCCCTCTT-TTTCAG-GAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * **
108808 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCAAAAAATCGTCTTCTTACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTC-GAACATCTTCTTCAAACGGGTTCGC
*
108863 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGAACATCTTTTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * * *
108917 TCCCTCTTTCTCTAGGGAGTATG-GAATTTGGACATATTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
108971 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGAGTTCCC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
109025 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
109079 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAACGAGTTCCC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
109133 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* ** *
109187 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
109238 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGGACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
109289 TCCCTCTTTCTCTAGGGAGTAT-AGAACTC-AGACATTTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGA-ACATCTTCTTCAAACGGGTTCGC
* ** * *
109343 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCTC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
109394 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGGACA---TCTTCAAACGGGTTCGT
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
109445 TCCCTCTTTCTCTAGGGAGTAT-AGAACTTGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
109499 TCCCTCTTTCCTT-AGGGAGTATG-GAACTCGAACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT--TTCA-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * *
109553 TCCCTCTTTCTTTAGGAATTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* * * *
109607 TCCCTCTTTCTCTAGGGAGTATG-GAACTCGAACATCTTCTTCAAATGAGTTCCC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
109661 TCCCTCTTTCTTCAGGAAGTAT-AGAACTCGGACATCTTCTTCAAACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* ** *
109715 TCCCTCTTTCTTCAGGAAGTAT-AGAACTC-CA-AT-AACTTCACACGGGTTCGC
1 TCCCTCTTT-TTCAGG-AGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
* *
109766 TCCCTCTTTCTCTAGGGAGTATG-GAAATCGAACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
*
109817 TCCCTCTTTCTCTAGGGAGTATG-GAAAC-C-AGACA---TCTTCAAACGGGTTCGC
1 TCCCTCTTTTTC-A-GGAGTATGAG-AACTCGA-ACATCTTCTTCAAACGGGTTCGC
* * *
109868 TCCCTCTTTCTCTAGGGAGTATG-GTACTCAAACATCTTCTTC
1 TCCCTCTTTTTC-A-GGAGTATGAGAACTCGAACATCTTCTTC
109910 TGCTTCACTA
Statistics
Matches: 954, Mismatches: 87, Indels: 122
0.82 0.07 0.10
Matches are distributed among these distances:
50 9 0.01
51 285 0.30
52 18 0.02
53 28 0.03
54 550 0.58
55 63 0.07
56 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.32
Consensus pattern (53 bp):
TCCCTCTTTTTCAGGAGTATGAGAACTCGAACATCTTCTTCAAACGGGTTCGC
Found at i:108998 original size:108 final size:107
Alignment explanation
Indices: 108770--109909 Score: 1341
Period size: 108 Copynumber: 10.7 Consensus size: 107
108760 TTCTTTCAGA
** * *
108770 GAGTAT-GAGACTCGAACATCTTCTTCTTACAGGTTCACTCCCTCTTTCT-TCAGGAAGTATAGA
1 GAGTATGGA-ACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGA
** * * **
108833 ACTCAAAAAATCGTCTTCTTACGGGTTCGCTCCCTCTTTCT-TCAGG
63 ACTC-GGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * *
108879 AAGTATAGAACTCGAACATCTTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAT
1 GAGTATGGAACTCGAACATC-TTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAAC
* *
108944 TTGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
65 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
108987 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCT-TCAGGAAGTATAGAA
1 GAGTATGGAACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAA
109051 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
64 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
109095 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCT-TCAGGAAGTATAGAA
1 GAGTATGGAACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAA
109159 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
64 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * * * * *
109203 AAGTATAGAACTCCAATAAC--TTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT
1 GAGTATGGAACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACT
109266 CGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
66 CGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
109305 GAGTATAGAACTC-AGACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGA
1 GAGTATGGAACTCGA-ACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGA
* ** * *
109368 ACTC-CA-AT-AACTTCACACGGGTTCTCTCCCTCTTTCTCTAGG
63 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
109410 GAGTATGGAACTCGGACATC--TTCAAACGGGTTCGTTCCCTCTTTCTCTAGGGAGTATAGAACT
1 GAGTATGGAACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACT
*
109473 TGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-CTTAGG
66 CGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC-TAGG
* *
109515 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGAATTATAGAAC
1 GAGTATGGAACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAAC
109580 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
65 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
109623 GAGTATGGAACTCGAACATCTTCTTCAAATGAGTTCCCTCCCTCTTTCT-TCAGGAAGTATAGAA
1 GAGTATGGAACTCGAACATCTT-TTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGAAGTATAGAA
109687 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
64 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * * * * * *
109731 AAGTATAGAACTCCAATAAC--TTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAAT
1 GAGTATGGAACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACT
*
109794 C-GA-A-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
66 CGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
109833 GAGTATGGAAAC-C-AGACATC--TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGTA
1 GAGTATGG-AACTCGA-ACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAA
**
109894 CTCAAACATCTTCTTC
64 CTCGGACATCTTCTTC
109910 TGCTTCACTA
Statistics
Matches: 907, Mismatches: 89, Indels: 74
0.85 0.08 0.07
Matches are distributed among these distances:
101 2 0.00
102 167 0.18
103 10 0.01
104 8 0.01
105 215 0.24
106 2 0.00
107 6 0.01
108 440 0.49
109 52 0.06
110 5 0.01
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (107 bp):
GAGTATGGAACTCGAACATCTTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACT
CGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:119604 original size:25 final size:25
Alignment explanation
Indices: 119576--119636 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
119566 AATCATCCTG
119576 AAAAAAAAATCCGAAAATTAAAAAA
1 AAAAAAAAATCCGAAAATTAAAAAA
* * *
119601 AAAACAGATTCCGAAAATTAAAAAA
1 AAAAAAAAATCCGAAAATTAAAAAA
119626 AGAAAAGAAAA
1 A-AAAA-AAAA
119637 GAAAGTTCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 23 0.82
26 3 0.11
27 2 0.07
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.11
Consensus pattern (25 bp):
AAAAAAAAATCCGAAAATTAAAAAA
Found at i:122415 original size:52 final size:53
Alignment explanation
Indices: 122284--122415 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
122274 TTGCATTTAT
* *
122284 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
122338 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
122390 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
122416 ATAACTCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:124055 original size:4 final size:4
Alignment explanation
Indices: 124046--124070 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
124036 ATTACTTTCA
124046 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
124071 GTCCTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:124570 original size:13 final size:12
Alignment explanation
Indices: 124551--124615 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
124541 ATATAGGCGT
124551 GATATGGTGATG
1 GATATGGTGATG
124563 GAATATGGTGAT-
1 G-ATATGGTGATG
*
124575 GATATAGGCG-T-
1 GATAT-GGTGATG
124586 GATAATGGTGATG
1 GAT-ATGGTGATG
124599 GACTATGGTGAT-
1 GA-TATGGTGATG
124611 GATAT
1 GATAT
124616 AAGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:124606 original size:36 final size:36
Alignment explanation
Indices: 124533--124637 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
124523 ATTTATAAGT
* *
124533 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
124568 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
124604 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
124638 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:129209 original size:11 final size:11
Alignment explanation
Indices: 129193--129230 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
129183 TTGGAGTGCA
129193 AAAAGAAGAAG
1 AAAAGAAGAAG
129204 AAAAGAAGAAAAG
1 AAAAGAAG--AAG
129217 AAAAGAA-AAG
1 AAAAGAAGAAG
129227 AAAA
1 AAAA
129231 AGAATTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.28
11 8 0.32
13 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:129217 original size:5 final size:5
Alignment explanation
Indices: 129193--129230 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
129183 TTGGAGTGCA
129193 AAAAG AAGAAG AAAAG --AAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
129231 AGAATTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:129224 original size:18 final size:19
Alignment explanation
Indices: 129193--129228 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
129183 TTGGAGTGCA
129193 AAAAGAAGAAGAAAAGAAG
1 AAAAGAAGAAGAAAAGAAG
129212 AAAAGAA-AAGAAAAGAA
1 AAAAGAAGAAGAAAAGAA
129229 AAAGAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAGAAAAGAAG
Found at i:129231 original size:11 final size:11
Alignment explanation
Indices: 129192--129234 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
129182 ATTGGAGTGC
129192 AAAAAGAAGAAG
1 AAAAAGAA-AAG
129204 AAAAGAAGAAAAG
1 -AAA-AAGAAAAG
129217 -AAAAGAAAAG
1 AAAAAGAAAAG
129227 AAAAAGAA
1 AAAAAGAA
129235 TTCAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
13 6 0.21
14 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:139460 original size:13 final size:12
Alignment explanation
Indices: 139441--139505 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
139431 ATATAGGCGT
139441 GATATGGTGATG
1 GATATGGTGATG
139453 GAATATGGTGAT-
1 G-ATATGGTGATG
*
139465 GATATAGGCG-T-
1 GATAT-GGTGATG
139476 GATAATGGTGATG
1 GAT-ATGGTGATG
139489 GACTATGGTGAT-
1 GA-TATGGTGATG
139501 GATAT
1 GATAT
139506 AAGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:139496 original size:36 final size:36
Alignment explanation
Indices: 139423--139527 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
139413 ATTTATAAGT
* *
139423 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
139458 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
139494 TGGTGATGATATAAGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
139528 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:146040 original size:52 final size:53
Alignment explanation
Indices: 145909--146040 Score: 185
Period size: 52 Copynumber: 2.5 Consensus size: 53
145899 TTGCATTTAT
* *
145909 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGAGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGAGCACCCAC
* *
145963 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGAGCACCCAC
* * *
146015 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
146041 ATAACTCATG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
52 37 0.53
53 29 0.41
54 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGAGCACCCAC
Found at i:147584 original size:4 final size:4
Alignment explanation
Indices: 147575--147641 Score: 102
Period size: 4 Copynumber: 17.0 Consensus size: 4
147565 ATTACTTTCA
*
147575 TCTT TCTT TCTT TCTT TC-T TCTT TCTT TCTT T-TT CTTTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT -TCTT TCTT TCTT
147622 TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT
147642 GTCCTTTGAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
3 5 0.08
4 52 0.88
5 2 0.03
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:154742 original size:52 final size:53
Alignment explanation
Indices: 154611--154742 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
154601 TTGCATTTAT
* *
154611 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
154665 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
154717 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
154743 ATAACTCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:156380 original size:4 final size:4
Alignment explanation
Indices: 156371--156439 Score: 129
Period size: 4 Copynumber: 17.2 Consensus size: 4
156361 ATTACTTTCA
*
156371 TCTT TCTT TCTT TATT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
156419 TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT T
156440 GTCCTTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:162620 original size:82 final size:79
Alignment explanation
Indices: 162453--162661 Score: 175
Period size: 79 Copynumber: 2.6 Consensus size: 79
162443 ATCATCATGT
* * * *
162453 AGCACGTCTTGCACTCATATTAAACAAAACATCATGTTTATCCTTTATTTTAATTAACTCATGTG
1 AGCACGTCTTGAACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
* * *
162518 TATTCCCATTGTTA
66 CATTCACATTGATA
* * * ** * *
162532 AACACGTCTTGAACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCAT
1 AGCACGTCTTGAACTCATATTAAACAAAACAACATGTTTATCATTT-ATTATAATTA--ACTCAT
*
162597 GTGCATTCATATTGATA
63 GTGCATTCACATTGATA
* * * * * * *
162614 AGCACGTTTTTTGCATTTATATTCAACATAACAGCATGTTTATCATTT
1 AGCACG--TCTTGAACTCATATTAAACAAAACAACATGTTTATCATTT
162662 GTTTTGTTAA
Statistics
Matches: 101, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
79 37 0.37
80 9 0.09
82 23 0.23
84 32 0.32
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (79 bp):
AGCACGTCTTGAACTCATATTAAACAAAACAACATGTTTATCATTTATTATAATTAACTCATGTG
CATTCACATTGATA
Found at i:162765 original size:52 final size:53
Alignment explanation
Indices: 162634--162765 Score: 194
Period size: 52 Copynumber: 2.5 Consensus size: 53
162624 TTGCATTTAT
* *
162634 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
162688 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
162740 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
162766 ATAACTCATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 38 0.54
53 29 0.41
54 4 0.06
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:166106 original size:21 final size:21
Alignment explanation
Indices: 166066--166107 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
166056 TCAGAGAATA
* *
166066 TTACCAAGGTATTTCATCCTC
1 TTACCAAGGTAATCCATCCTC
*
166087 TTACCAAGGTAATCCTTCCTC
1 TTACCAAGGTAATCCATCCTC
166108 ATCTTCTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.36
Consensus pattern (21 bp):
TTACCAAGGTAATCCATCCTC
Found at i:169771 original size:25 final size:24
Alignment explanation
Indices: 169742--169799 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
169732 CTTCACTTCT
169742 TTTTTCTTTGAATTTTTTTCTCTTA
1 TTTTTCTTTGAA-TTTTTTCTCTTA
*
169767 TTTTTCGTTGAATTTTTTCTCTTA
1 TTTTTCTTTGAATTTTTTCTCTTA
169791 TTTTTCTTT
1 TTTTTCTTT
169800 TCTTTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTTCTTTGAATTTTTTCTCTTA
Found at i:169865 original size:25 final size:25
Alignment explanation
Indices: 169835--169925 Score: 168
Period size: 25 Copynumber: 3.7 Consensus size: 25
169825 TGTAGGAGTT
169835 TTTCTTTTGCTTTTTGTTTTTTGTC
1 TTTCTTTTGCTTTTTGTTTTTTGTC
169860 TTTCTTTTGCTTTTTGTTTTTTGTC
1 TTTCTTTTGCTTTTTGTTTTTTGTC
169885 TTTCTTTTGCTTTTTG--TTTTGTC
1 TTTCTTTTGCTTTTTGTTTTTTGTC
169908 TTTCTTTTGCTTTTTGTT
1 TTTCTTTTGCTTTTTGTT
169926 GCAGCACTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.36
25 41 0.64
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (25 bp):
TTTCTTTTGCTTTTTGTTTTTTGTC
Found at i:170337 original size:35 final size:35
Alignment explanation
Indices: 170292--170393 Score: 159
Period size: 35 Copynumber: 2.9 Consensus size: 35
170282 TGGTAAGGGA
*
170292 ATGGTGATGATATGGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* * *
170327 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
170362 ATGGTGATGATATAGGCGTGAAAATGGTGATA
1 ATGGTGATGATATAGGCGTG-AAATGGTGATA
170394 AACATATAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 50 0.85
36 9 0.15
ACGTcount: A:0.32, C:0.04, G:0.37, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:182609 original size:24 final size:21
Alignment explanation
Indices: 182574--182616 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
182564 GGCACATTCT
*
182574 TTTGAATTTCAAGAGGTACATCA
1 TTTGAATCTCAA-AGG-ACATCA
182597 TTTGAAATCTCAAAGGACAT
1 TTTG-AATCTCAAAGGACAT
182617 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TTTGAATCTCAAAGGACATCA
Found at i:184799 original size:24 final size:23
Alignment explanation
Indices: 184772--184829 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
184762 AAGAAAAATC
*
184772 AGAAAAAAATTGAAGCACTCCAAA
1 AGAAAAAAATTCAAGCACT-CAAA
* * *
184796 AGAAGAAATTTCCAGCACTCAAA
1 AGAAAAAAATTCAAGCACTCAAA
184819 AGAAAGAAAAT
1 AGAAA-AAAAT
184830 CAATGAAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (23 bp):
AGAAAAAAATTCAAGCACTCAAA
Found at i:189767 original size:32 final size:33
Alignment explanation
Indices: 189706--189772 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
189696 ACAAAATTAA
* *
189706 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
189738 AAGAAAGGAAATGA-TAACAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
189771 AA
1 AA
189773 ATATTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.01, G:0.24, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:193649 original size:17 final size:17
Alignment explanation
Indices: 193627--193660 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
193617 CGGCTTAAAA
193627 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
193644 AAATGGTTATGGTATAG
1 AAATGGTTAGGGTATAG
193661 GGGTAGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:194196 original size:32 final size:33
Alignment explanation
Indices: 194135--194201 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
194125 ACAAAATTAA
* *
194135 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
194167 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
194200 AA
1 AA
194202 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:198796 original size:20 final size:19
Alignment explanation
Indices: 198760--198798 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
198750 AGTAAAGATG
* *
198760 TGAAAACATATATTATGCA
1 TGAAAACATAAAGTATGCA
198779 TGAAAATCATAAAGTATGCA
1 TGAAAA-CATAAAGTATGCA
198799 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (19 bp):
TGAAAACATAAAGTATGCA
Found at i:201239 original size:28 final size:28
Alignment explanation
Indices: 201207--201272 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
201197 CTTGGCTTGC
201207 TTTC-TCTTTT-TAAATTTCTTTC-TCT
1 TTTCTTCTTTTCTAAATTTCTTTCTTCT
* *
201232 TTTCTTCTTTTCTGAATTTTTTTCTTCT
1 TTTCTTCTTTTCTAAATTTCTTTCTTCT
**
201260 TTTGGTCTTTTCT
1 TTTCTTCTTTTCT
201273 TTTCCTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.12
26 6 0.18
27 10 0.29
28 14 0.41
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.70
Consensus pattern (28 bp):
TTTCTTCTTTTCTAAATTTCTTTCTTCT
Found at i:202029 original size:19 final size:20
Alignment explanation
Indices: 201991--202033 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
201981 GAAACCCCTT
*
201991 TGAAAATACATGATTTTTAA
1 TGAAAATACATGAATTTTAA
202011 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
202030 TGAA
1 TGAA
202034 GATAAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAATTTTAA
Found at i:205783 original size:19 final size:20
Alignment explanation
Indices: 205759--205807 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
205749 TATCCTTTCT
205759 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
205778 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
205798 -TATTATTATT
1 TTATT-TTATT
205808 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:209614 original size:23 final size:23
Alignment explanation
Indices: 209582--209634 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
209572 CCCTAGATGG
*
209582 AGGGAAATGATCCTTGGCCGAAT
1 AGGGAGATGATCCTTGGCCGAAT
*
209605 AGGGAGATGATGCTTGGCCGAAT
1 AGGGAGATGATCCTTGGCCGAAT
209628 AGGGAGA
1 AGGGAGA
209635 GGGCTCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.38, T:0.19
Consensus pattern (23 bp):
AGGGAGATGATCCTTGGCCGAAT
Found at i:219575 original size:15 final size:16
Alignment explanation
Indices: 219549--219580 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
219539 GTGACCTTTG
219549 ATGAATGATGCTGCCC
1 ATGAATGATGCTGCCC
219565 ATGAA-GATGCTGCCC
1 ATGAATGATGCTGCCC
219580 A
1 A
219581 AACGTTCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (16 bp):
ATGAATGATGCTGCCC
Found at i:220472 original size:19 final size:20
Alignment explanation
Indices: 220448--220496 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
220438 TATCCTTTCT
220448 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
220467 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
220487 -TATTATTATT
1 TTATT-TTATT
220497 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:222836 original size:720 final size:723
Alignment explanation
Indices: 221449--222889 Score: 2161
Period size: 720 Copynumber: 2.0 Consensus size: 723
221439 CACCATCATC
* * *
221449 ATCACTACTTAGGACGCTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTCTTCGCGA
1 ATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTCTTCGCAA
221514 ATAGTTGCCACCTCAAGAGGTACCTTTTCACAAGGAGCTGCCCAAACGTTCACCATGTCACAAAT
66 ATAGTTGCCACCTCAAGAGGTACCTTTTCACAAGGAGCTGCCCAAACGTTCACCATGTCACAAAT
* * *** *
221579 CATCTATGGCCAGCTCCCCTTTAGCTCATTCACACCATAAGCAGCTCAAACATGAAGGGACACCT
131 CATCTAAGGCCAGCTCACCACCAGCTCATTCACACCATAAGCAGCTCAAACATGAAGGGACACCC
* * *
221644 TTCTCAAACATTGTGACCTTTGATGAATGATGCTGCCCATGAAGATGCCTTTTCATCTAGGAGCA
196 TTCTCAAACATTGTGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCATCAAGGAACA
** * * *
221709 CGTTGGTGAAGGAATTGCTAGCATTGGAAGCTTAAATCACCAAGAGACATGAGATAGAGCTCCAA
261 CGTTGGTGAAGGAATCACTACCATTGGAAGCTTAAATCACCAAGAGACATGAGATAAAGATCCAA
** * * * *
221774 GCCTATTCGGTAACACCACATGCCTTGCACATGGAAGCTTTGGTGCCAAACATGATAAGGCACAT
326 GCCTATTCGACAACACCACATGCCATGCACATGGAAGCTTTGGCGCCAAACATGATAAGACACAC
* * *
221839 GACTATTCGGCCAAGGAGAGGAAATTGGCGCCAAGATGAACAAGCATGAACCATTCGGCCAAGGG
391 CACCATTCGGCCAAGGAGAGGAAAATGGCGCCAAGATGAACAAGCATGAACCATTCGGCCAAGGG
*
221904 AGATGTCTCTCCACCCTTTGACCGAATCATTAAGGACTTTCATGAAGAGTTAGCCAAACCATCAC
456 AGATGTCTCTCCACCCTTAGACCGAATCATTAAGGACTTTCATGAAGAGTTAGCCAAACCATCAC
*
221969 AAGCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAAAGACATGTATCTAGCC
521 AAGCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAAAGACATGTATCTAGAC
* * *
222034 GAAACATCATGTAACTATTCGGCCAAGCCATCTCATTTCCTATAAATAGAGTGGCTTGCCTACAT
586 GAAACAACATGTAACCATTCGGCCAAGCCATCTAATTTCCTATAAATAGAGTGGCTTGCCTACAT
* *
222099 TTGTAATCATCTCATCTCTTATATAAAACATACTCTTGTGAGTTATTTCTCTTCAAAGTTCTTTG
651 TTGTAACCATCTCATCTCTTATATAAAACATACTCTTGTCAGTTATTTCTCTTCAAAGTTCTTTG
222164 TGAACTAA
716 TGAACTAA
* *
222172 ATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATTGTACCTTTTCGCAA
1 ATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTCTTCGCAA
* *
222237 ATAGTTGCCACCTCAAGAGGTACCTTTTCACAAGGAGCTGCCCAAACGTTCACCATGTTACAAGT
66 ATAGTTGCCACCTCAAGAGGTACCTTTTCACAAGGAGCTGCCCAAACGTTCACCATGTCACAAAT
* * * * **
222302 CATCTAAGGCCAGCTCACCACCATCTCATTGACACCCA-AAGTAGCTTAAACATGAAGGGTTACC
131 CATCTAAGGCCAGCTCACCACCAGCTCATTCACA-CCATAAGCAGCTCAAACATGAAGGGACACC
222366 CTTC-CAAACATTGTGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAAT-AAGGAA
195 CTTCTCAAACATTGTGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTC-ATCAAGGAA
* *
222429 CACG-TGGATGAA-GAGATCAC-ACCTATTGGAAGCTTAAATCACCAAGAGATATGAGCTAAAGG
259 CACGTTGG-TGAAGGA-ATCACTACC-ATTGGAAGCTTAAATCACCAAGAGACATGAGATAAA-G
* * *
222491 ATCCATGCCTATTCGACCACATCACATGCCATGCACAT-GAGAGTCTTTGGCGCCAAACATGA-A
320 ATCCAAGCCTATTCGACAACACCACATGCCATGCACATGGA-AG-CTTTGGCGCCAAACATGATA
* *
222554 GAGACACACCACCATTCGGCCAAGGA-A-GAAAATGGCGCCATGATGAACAAGCATG-CCCATTC
383 -AGACACACCACCATTCGGCCAAGGAGAGGAAAATGGCGCCAAGATGAACAAGCATGAACCATTC
* *
222616 GGCCAAGGGAGATGTCT-TCCCATCCTTAG-CCGAATCATTAAGGCCTTTCATGAAGAGTTAGCC
447 GGCCAAGGGAGATGTCTCT-CCACCCTTAGACCGAATCATTAAGGACTTTCATGAAGAGTTAGCC
* *
222679 GAACCATCACAAGCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAGAGACAT
511 AAACCATCACAAGCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAAAGACAT
* *
222744 GTATCTAGACGAAACAACTTGTAACCATTCGGCCAAGCCCTCTAATTTCCTATAAATAGAGTGGC
576 GTATCTAGACGAAACAACATGTAACCATTCGGCCAAGCCATCTAATTTCCTATAAATAGAGTGGC
* * * *
222809 TTTCCTTCATTTGTACCCATCTCATCTCTTATATAAAATATACTCTTGTCAGTTATTTCTCTTCA
641 TTGCCTACATTTGTAACCATCTCATCTCTTATATAAAACATACTCTTGTCAGTTATTTCTCTTCA
222874 AAGTTCTTTGTGAACT
706 AAGTTCTTTGTGAACT
222890 TTATCGATTA
Statistics
Matches: 648, Mismatches: 60, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
720 231 0.36
721 38 0.06
722 125 0.19
723 213 0.33
724 41 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (723 bp):
ATCACCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTCTTCGCAA
ATAGTTGCCACCTCAAGAGGTACCTTTTCACAAGGAGCTGCCCAAACGTTCACCATGTCACAAAT
CATCTAAGGCCAGCTCACCACCAGCTCATTCACACCATAAGCAGCTCAAACATGAAGGGACACCC
TTCTCAAACATTGTGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCATCAAGGAACA
CGTTGGTGAAGGAATCACTACCATTGGAAGCTTAAATCACCAAGAGACATGAGATAAAGATCCAA
GCCTATTCGACAACACCACATGCCATGCACATGGAAGCTTTGGCGCCAAACATGATAAGACACAC
CACCATTCGGCCAAGGAGAGGAAAATGGCGCCAAGATGAACAAGCATGAACCATTCGGCCAAGGG
AGATGTCTCTCCACCCTTAGACCGAATCATTAAGGACTTTCATGAAGAGTTAGCCAAACCATCAC
AAGCCCAAAGGACTTATTCATTCATCTCAAGCATTATGTATTTTCCTAAAGACATGTATCTAGAC
GAAACAACATGTAACCATTCGGCCAAGCCATCTAATTTCCTATAAATAGAGTGGCTTGCCTACAT
TTGTAACCATCTCATCTCTTATATAAAACATACTCTTGTCAGTTATTTCTCTTCAAAGTTCTTTG
TGAACTAA
Found at i:223170 original size:19 final size:20
Alignment explanation
Indices: 223146--223194 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
223136 TATCCTTTCT
223146 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
223165 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
223185 -TATTATTATT
1 TTATT-TTATT
223195 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:223702 original size:23 final size:25
Alignment explanation
Indices: 223662--223715 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
223652 TTCTTTTCTT
223662 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
223687 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
223710 TTTCTT
1 TTTCTT
223716 TCGTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:240367 original size:18 final size:19
Alignment explanation
Indices: 240328--240367 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
240318 AATCAGAAAA
* *
240328 AAAGCCCTCAAAAAGATTG
1 AAAGCACTCAAAAAGATAG
240347 AAAGCACTCAAAAAGA-AG
1 AAAGCACTCAAAAAGATAG
240365 AAA
1 AAA
240368 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAGCACTCAAAAAGATAG
Found at i:245452 original size:33 final size:33
Alignment explanation
Indices: 245373--245476 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
245363 ATACAATCTG
* *
245373 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
245409 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
245442 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
245475 TC
1 TC
245477 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:245839 original size:26 final size:26
Alignment explanation
Indices: 245800--245867 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
245790 CCCTAGAACA
*
245800 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
245826 CCCATGTGCCTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
245852 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
245868 GTGGTTCTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.18, C:0.34, G:0.19, T:0.29
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGATCAGCC
Found at i:266231 original size:24 final size:24
Alignment explanation
Indices: 266179--266245 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
266169 AAAGAAAGTG
*
266179 AAGCACTCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAGAAAGAAAAAAC
* *
266203 CAGCACTCAAACG-AAGAAAAAAC
1 AAGCACTCAAAAGAAAGAAAAAAC
***
266226 AAAGCAAAGAAAAGAAAGAA
1 -AAGCACTCAAAAGAAAGAA
266246 GTTGAAGCAC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
23 9 0.27
24 19 0.58
25 5 0.15
ACGTcount: A:0.64, C:0.16, G:0.15, T:0.04
Consensus pattern (24 bp):
AAGCACTCAAAAGAAAGAAAAAAC
Done.