Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003924.1 Hibiscus syriacus cultivar Beakdansim tig00008483_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: 1466330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 5
Found at i:1027 original size:16 final size:16
Alignment explanation
Indices: 1006--1037 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
996 GAGAAAAATC
*
1006 AGAAAAGAAGAAGAAA
1 AGAAAAGAAAAAGAAA
1022 AGAAAAGAAAAAGAAA
1 AGAAAAGAAAAAGAAA
1038 GTTCAAAAAG
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:7414 original size:13 final size:13
Alignment explanation
Indices: 7396--7420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7386 ATTTGTAGCT
7396 CATAACATGAACC
1 CATAACATGAACC
7409 CATAACATGAAC
1 CATAACATGAAC
7421 ATGCATGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
CATAACATGAACC
Found at i:15806 original size:30 final size:30
Alignment explanation
Indices: 15731--15816 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 30
15721 ACTGTTTGTG
* *
15731 AGCTGTCA-ATGTCTCCCAAATGTTCCACTA
1 AGCTGT-ATATGTCTTCCAAATGCTCCACTA
*
15761 AGCTCTATA--TCTTCCAAATGCTCCACTA
1 AGCTGTATATGTCTTCCAAATGCTCCACTA
*
15789 AGCTGTATATGTCTTCCAAGTGCTCCAC
1 AGCTGTATATGTCTTCCAAATGCTCCAC
15817 GAAGTTGTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 25 0.52
29 1 0.02
30 22 0.46
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (30 bp):
AGCTGTATATGTCTTCCAAATGCTCCACTA
Found at i:18831 original size:35 final size:37
Alignment explanation
Indices: 18763--18841 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
18753 TACTATTTCT
*
18763 ATCACCATAATCCATCTTCCATTATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
*
18800 ATCACCATAGTCCATC-ACCA-TATCACGCCTATATC
1 ATCACCATAATCCATCTACCATTATCACGCCTATATC
18835 ATCACCA
1 ATCACCA
18842 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
ATCACCATAATCCATCTACCATTATCACGCCTATATC
Found at i:28001 original size:15 final size:15
Alignment explanation
Indices: 27981--28028 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
27971 TTTTATATCA
27981 TTTCTTTCCATTTCT
1 TTTCTTTCCATTTCT
*
27996 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCT
28011 TTTCTTCTTCCATTTCT
1 TTTC-T-TTCCATTTCT
28028 T
1 T
28029 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:29473 original size:22 final size:22
Alignment explanation
Indices: 29445--29488 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29435 AAGAGGAGAA
29445 TGAAGAACATATTTTAACTAAC
1 TGAAGAACATATTTTAACTAAC
29467 TGAAGAACATATTTTAACTAAC
1 TGAAGAACATATTTTAACTAAC
29489 CTTATTCTTT
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:33437 original size:19 final size:20
Alignment explanation
Indices: 33413--33463 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
33403 CGGACAAGAG
* * *
33413 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAA
33432 CATGTATTTTCATAAAAAAA
1 CATGTATTTTCATAAAAAAA
33452 CATGTATTTTCA
1 CATGTATTTTCA
33464 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAA
Found at i:33861 original size:19 final size:20
Alignment explanation
Indices: 33833--33872 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
33823 GGGTAATAAT
33833 ATAAGTAATGAATAT-AAATA
1 ATAAGTAATGAA-ATGAAATA
33853 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
33872 A
1 A
33873 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.63
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:40550 original size:8 final size:8
Alignment explanation
Indices: 40539--40570 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
40529 ATTTTGGCTT
40539 TTTTTTTG
1 TTTTTTTG
40547 TTTTTTTTG
1 -TTTTTTTG
40556 TTTTTTTG
1 TTTTTTTG
40564 TTTTTTT
1 TTTTTTT
40571 TCTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (8 bp):
TTTTTTTG
Found at i:40550 original size:9 final size:9
Alignment explanation
Indices: 40538--40581 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
40528 AATTTTGGCT
40538 TTTTTTTTG
1 TTTTTTTTG
40547 TTTTTTTTG
1 TTTTTTTTG
40556 -TTTTTTTG
1 TTTTTTTTG
*
40564 TTTTTTTTC
1 TTTTTTTTG
40573 TTATTTTTT
1 TT-TTTTTT
40582 TGAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 8 0.25
9 18 0.56
10 6 0.19
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:40559 original size:17 final size:17
Alignment explanation
Indices: 40539--40571 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40529 ATTTTGGCTT
40539 TTTTTTTGTTTTTTTTG
1 TTTTTTTGTTTTTTTTG
40556 TTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
40572 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTG
Found at i:40579 original size:17 final size:17
Alignment explanation
Indices: 40542--40579 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40532 TTGGCTTTTT
* *
40542 TTTTGTTTTTTTTGTTT
1 TTTTGTTTTTTTTCTTA
40559 TTTTGTTTTTTTTCTTA
1 TTTTGTTTTTTTTCTTA
40576 TTTT
1 TTTT
40580 TTTGAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.87
Consensus pattern (17 bp):
TTTTGTTTTTTTTCTTA
Found at i:50861 original size:21 final size:21
Alignment explanation
Indices: 50832--50872 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50822 GTGAGGTTTA
* *
50832 TTTTTTGTTGATTTTTCTTTC
1 TTTTATGTTGATTTTACTTTC
*
50853 TTTTATGTTTATTTTACTTT
1 TTTTATGTTGATTTTACTTT
50873 AAAATTTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTATGTTGATTTTACTTTC
Found at i:56294 original size:19 final size:20
Alignment explanation
Indices: 56270--56309 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
56260 TATTCTTTCT
56270 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
56289 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
56309 T
1 T
56310 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:56578 original size:10 final size:9
Alignment explanation
Indices: 56563--56623 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 9
56553 ATTGGAGTGC
56563 AAAAAGAAA
1 AAAAAGAAA
56572 GAAAAAGACAA
1 -AAAAAGA-AA
56583 AAGAAGAGAAA
1 AA-AA-AGAAA
**
56594 AATCAGAAAA
1 AAAAAG-AAA
56604 AAAAAGAAA
1 AAAAAGAAA
56613 AGAAAAGAAA
1 A-AAAAGAAA
56623 A
1 A
56624 GAAATTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 6 0.14
10 25 0.60
11 8 0.19
12 3 0.07
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:56608 original size:5 final size:5
Alignment explanation
Indices: 56598--56627 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
56588 GAGAAAAATC
*
56598 AGAAA AAAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
56628 TTCAAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:60358 original size:19 final size:20
Alignment explanation
Indices: 60334--60374 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
60324 TATCCTTTCT
60334 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
60353 TTATTTCATTTCATTACTTA
1 TTATTTCATTTCATTACTTA
60373 TT
1 TT
60375 TTATTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:61009 original size:16 final size:16
Alignment explanation
Indices: 60990--61044 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
60980 CATTTCTATC
60990 CATTTCCTTTTCTTAT
1 CATTTCCTTTTCTTAT
61006 CATTTCCTTTCTTCTT-T
1 CATTTCC-TT-TTCTTAT
61023 CATATT-CTATTT-TTAT
1 CAT-TTCCT-TTTCTTAT
61039 CATTTC
1 CATTTC
61045 TTTCTTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 4 0.12
16 14 0.42
17 8 0.24
18 7 0.21
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCCTTTTCTTAT
Found at i:61052 original size:15 final size:15
Alignment explanation
Indices: 60998--61052 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
60988 TCCATTTCCT
60998 TTTC-TTATCATTTCC
1 TTTCTTTATCATTT-C
*
61013 TTTCTTCTTTCATATTC
1 TTTCTT-TATCAT-TTC
61030 TATT-TTTATCATTTC
1 T-TTCTTTATCATTTC
61045 TTTCTTTA
1 TTTCTTTA
61053 ATTTTTGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 2 0.06
15 12 0.36
16 6 0.18
17 9 0.27
18 4 0.12
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTATCATTTC
Found at i:62704 original size:21 final size:21
Alignment explanation
Indices: 62678--62727 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
62668 ATTCATCTTG
62678 AAAAAAAATATTCCGAAAATT
1 AAAAAAAATATTCCGAAAATT
*
62699 AAAAAACATATTCCGAAAATT
1 AAAAAAAATATTCCGAAAATT
62720 AAAAAAAA
1 AAAAAAAA
62728 AAAGTTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.66, C:0.10, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAAAAATATTCCGAAAATT
Found at i:68651 original size:30 final size:31
Alignment explanation
Indices: 68599--68658 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
68589 CTTAGCTTTA
**
68599 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
68629 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
68659 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:72865 original size:42 final size:44
Alignment explanation
Indices: 72811--72909 Score: 159
Period size: 43 Copynumber: 2.3 Consensus size: 44
72801 CTTTGGAACC
*
72811 CAAAAGACGTGTCC-TTGAAAAGCAAAAGGACA-AATTTTCATT
1 CAAAAGATGTGTCCATTGAAAAGCAAAAGGACACAATTTTCATT
72853 CAAAAGATGTGTCCATTGAAAAGCAAAAGGACATCAATTTTCATT
1 CAAAAGATGTGTCCATTGAAAAGCAAAAGGACA-CAATTTTCATT
72898 C-AAAGATGTGTC
1 CAAAAGATGTGTC
72910 TTTAGAAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
42 13 0.25
43 18 0.34
44 11 0.21
45 11 0.21
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (44 bp):
CAAAAGATGTGTCCATTGAAAAGCAAAAGGACACAATTTTCATT
Found at i:75390 original size:19 final size:21
Alignment explanation
Indices: 75366--75417 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
75356 CGGCCAAGAG
*
75366 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
75385 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
75406 CATGTATTTTCA
1 CATGTATTTTCA
75418 AGGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:76177 original size:47 final size:46
Alignment explanation
Indices: 76092--76203 Score: 104
Period size: 50 Copynumber: 2.3 Consensus size: 46
76082 AGGATTATAT
*
76092 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAATA-TTATCTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAATATTTA-CTTTA-TTA
*
76142 TTATTATTTTATTAGGAATT-A-GAGTTAAGACATATTTAGTTTATTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAA-A-ATATTTACTTTATTA
*
76188 TTATTTTTTTCATTAG
1 TTATTATTTT-ATTAG
76204 TGATCTAAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
45 6 0.11
46 13 0.24
47 12 0.22
48 3 0.05
49 1 0.02
50 20 0.36
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAATATTTACTTTATTA
Found at i:78314 original size:21 final size:20
Alignment explanation
Indices: 78276--78325 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
78266 CTATTTTTTA
**
78276 AAAACAAAAAACAAAAAAGGC
1 AAAA-AAAAAACAAAAAACAC
78297 AAAAAAAAAACAAAAAAACAC
1 AAAAAAAAAAC-AAAAAACAC
78318 AAAAAAAA
1 AAAAAAAA
78326 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACAAAAAACAC
Found at i:78321 original size:20 final size:20
Alignment explanation
Indices: 78276--78325 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
78266 CTATTTTTTA
*
78276 AAAACAAAAAACAAAAAAGGC
1 AAAA-AAAAAACAAAAAAGAC
78297 AAAAAAAAAACAAAAAA-AC
1 AAAAAAAAAACAAAAAAGAC
78316 ACAAAAAAAA
1 A-AAAAAAAA
78326 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACAAAAAAGAC
Found at i:82911 original size:11 final size:10
Alignment explanation
Indices: 82894--82932 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
82884 AGAAAAATAC
82894 AAAAAGAAGA
1 AAAAAGAAGA
82904 AGAAAAGAAGA
1 A-AAAAGAAGA
82915 AAAGAA-AAGA
1 AAA-AAGAAGA
82925 AAAAAGAA
1 AAAAAGAA
82933 TTCAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 12 0.46
11 12 0.46
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:95117 original size:16 final size:16
Alignment explanation
Indices: 95098--95137 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
95088 TACGATTAAA
95098 ATAAAATAAACAAAAG
1 ATAAAATAAACAAAAG
**
95114 AT-AAATAAATGAAAG
1 ATAAAATAAACAAAAG
95129 ATAAAATAA
1 ATAAAATAA
95138 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
ATAAAATAAACAAAAG
Found at i:96443 original size:17 final size:16
Alignment explanation
Indices: 96422--96493 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 16
96412 ATTGGAGTGC
96422 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
96438 ACAAAAGAAGAGAAAAATC
1 A-AAAAGAA-AGAAAAA-G
96457 AGAAAAG-AAG-AAAAG
1 A-AAAAGAAAGAAAAAG
*
96472 AAAAGAAAAAGAAAAAG
1 AAAA-AGAAAGAAAAAG
96489 AAAAA
1 AAAAA
96494 TTCAAAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 3 0.07
15 2 0.04
16 9 0.20
17 18 0.39
18 8 0.17
19 6 0.13
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:96445 original size:7 final size:6
Alignment explanation
Indices: 96428--96493 Score: 55
Period size: 6 Copynumber: 10.5 Consensus size: 6
96418 GTGCAAAAAG
* *
96428 AAAGAA AAAGACA AAAG-A AGAGAA AAATCAGA AAAGAA GAAA-AGA AAAGAA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAA-GA-A AAAGAA -AAAGA-A AAAGAA
96479 AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAA
96494 TTCAAAAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
5 4 0.08
6 29 0.59
7 12 0.24
8 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:96462 original size:19 final size:18
Alignment explanation
Indices: 96423--96467 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
96413 TTGGAGTGCA
*
96423 AAAAGAA-AGAAAAAGAC
1 AAAAGAAGAGAAAAACAC
*
96440 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAA-CAC
96459 AAAAGAAGA
1 AAAAGAAGA
96468 AAAGAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAGAAAAACAC
Found at i:96476 original size:39 final size:40
Alignment explanation
Indices: 96428--96504 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 40
96418 GTGCAAAAAG
*
96428 AAAGAAAAAGACAAAAG-AAGAGAAAAA-TCAGAAAAGAAGA
1 AAAGAAAAAGA-AAAAGAAAAAGAAAAATTCA-AAAAGAAGA
96468 AAAG-AAAAGAAAAAGAAAAAGAAAAATTCAAAAAGAA
1 AAAGAAAAAGAAAAAGAAAAAGAAAAATTCAAAAAGAA
96505 AGCAATCCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 5 0.15
39 22 0.65
40 7 0.21
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (40 bp):
AAAGAAAAAGAAAAAGAAAAAGAAAAATTCAAAAAGAAGA
Found at i:98778 original size:84 final size:84
Alignment explanation
Indices: 98637--98804 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
98627 AGAAAGTACT
98637 TCCCTGAATTGTTTTGCCTTTGCACGAGTGATAGGTCCAATGGGCATGACTTCAGGATCTATTTG
1 TCCCTGAATTGTTTTGCCTTTGCACGAGTGATAGGTCCAATGGGCATGACTTCAGGATCTATTTG
98702 TGTAGTTGTGATTACATCA
66 TGTAGTTGTGATTACATCA
98721 TCCCTGAATTGTTTTGCCTTTGCACGAGTGATAGGTCCAATGGGCATGACTTCAGGATCTATTTG
1 TCCCTGAATTGTTTTGCCTTTGCACGAGTGATAGGTCCAATGGGCATGACTTCAGGATCTATTTG
98786 TGTAGTTGTGATTACATCA
66 TGTAGTTGTGATTACATCA
98805 CATTTACTCT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (84 bp):
TCCCTGAATTGTTTTGCCTTTGCACGAGTGATAGGTCCAATGGGCATGACTTCAGGATCTATTTG
TGTAGTTGTGATTACATCA
Found at i:102852 original size:22 final size:22
Alignment explanation
Indices: 102818--102862 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
102808 AATTCCAGCA
102818 AAGAAAATCAAAGCACTCAAAG
1 AAGAAAATCAAAGCACTCAAAG
* *
102840 AAGAAATTGAAAGCACTCAAAG
1 AAGAAAATCAAAGCACTCAAAG
102862 A
1 A
102863 GGAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (22 bp):
AAGAAAATCAAAGCACTCAAAG
Found at i:102875 original size:21 final size:21
Alignment explanation
Indices: 102822--102875 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
102812 CCAGCAAAGA
*
102822 AAATCAAAGCACTCAAAGAAG
1 AAATAAAAGCACTCAAAGAAG
* *
102843 AAATTGAAAGCACTCAAAGAGG
1 AAA-TAAAAGCACTCAAAGAAG
102865 AAGA-AAAAGCA
1 AA-ATAAAAGCA
102876 AAGAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.32
22 18 0.64
23 1 0.04
ACGTcount: A:0.57, C:0.15, G:0.19, T:0.09
Consensus pattern (21 bp):
AAATAAAAGCACTCAAAGAAG
Found at i:103597 original size:6 final size:6
Alignment explanation
Indices: 103586--103618 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
103576 GATGTAGGAG
103586 TCTTTT TC-TTT TCTTTT TCTTTT T-TTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT
103619 CTTGTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TCTTTT
Found at i:103602 original size:11 final size:11
Alignment explanation
Indices: 103586--103635 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
103576 GATGTAGGAG
103586 TCTTTTTCTTT
1 TCTTTTTCTTT
103597 TCTTTTTCTTT
1 TCTTTTTCTTT
*
103608 TTTTTTTC-TT
1 TCTTTTTCTTT
*
103618 TCTTGTTGCTTT
1 TCTT-TTTCTTT
103630 T-TTTTT
1 TCTTTTT
103636 GTAGAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 7 0.21
11 23 0.70
12 3 0.09
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:103608 original size:17 final size:17
Alignment explanation
Indices: 103586--103618 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
103576 GATGTAGGAG
103586 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
*
103603 TCTTTTTTTTTTCTTT
1 TCTTTTTCTTTTCTTT
103619 CTTGTTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:103614 original size:22 final size:22
Alignment explanation
Indices: 103588--103635 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
103578 TGTAGGAGTC
*
103588 TTTTTCTTTTCTT-TTTCTTTTT
1 TTTTTC-TTTCTTGTTGCTTTTT
103610 TTTTTCTTTCTTGTTGCTTTTT
1 TTTTTCTTTCTTGTTGCTTTTT
103632 TTTT
1 TTTT
103636 GTAGAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTCTTGTTGCTTTTT
Found at i:104040 original size:13 final size:13
Alignment explanation
Indices: 104022--104133 Score: 57
Period size: 13 Copynumber: 9.2 Consensus size: 13
104012 TATAGGCGTG
104022 ATATGGTGATGGA
1 ATATGGTGATGGA
104035 ATATGGTGAT-G-
1 ATATGGTGATGGA
*
104046 ATATAGGCG-T-G-
1 ATAT-GGTGATGGA
104057 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
*
104071 CTATGGTGAT-G-
1 ATATGGTGATGGA
*
104082 ATATAGG-CAT-G-
1 ATAT-GGTGATGGA
104093 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
*
104107 AGATGGTGATGGA
1 ATATGGTGATGGA
* *
104120 A-ATAGTAATGGA
1 ATATGGTGATGGA
104132 AT
1 AT
104134 GTTGATGGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
11 21 0.27
12 24 0.30
13 32 0.41
14 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.29
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:104076 original size:36 final size:36
Alignment explanation
Indices: 104003--104117 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
103993 ATTTAGAAGT
*
104003 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
104038 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
104074 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
104110 TGGTGATG
1 TGGTGATG
104118 GAAATAGTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.27
36 54 0.73
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:104140 original size:72 final size:71
Alignment explanation
Indices: 104003--104142 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 71
103993 ATTTAGAAGT
* * * ** *
104003 TGGTGATAATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATAATATAGGCATGATATGGTGATGGAAGATGGTGATGAAATAGGAATGAGAATGGTGAT
104068 GGACTA
66 GGACTA
* * *
104074 TGGTGATGATATAGGCATGATAATGGTGATGGAAGATGGTGATGGAAATAGTAATG-GAATGTTG
1 TGGTGATAATATAGGCATGAT-ATGGTGATGGAAGATGGTGAT-GAAATAGGAATGAGAATGGTG
104138 ATGGA
64 ATGGA
104143 GTTGGCGTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
71 19 0.33
72 31 0.53
73 8 0.14
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.30
Consensus pattern (71 bp):
TGGTGATAATATAGGCATGATATGGTGATGGAAGATGGTGATGAAATAGGAATGAGAATGGTGAT
GGACTA
Found at i:106077 original size:2 final size:2
Alignment explanation
Indices: 106070--106110 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
106060 TAGTAGCGGA
106070 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
106111 AGTTGGTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110210 original size:28 final size:28
Alignment explanation
Indices: 110178--110240 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
110168 TTTCTTTTCT
* *
110178 TTTCTTTGCTTT-TTTTTAAGTGCTGGAA
1 TTTCTTT-CTTTCTTTTGAAGTGCTGCAA
* *
110206 TTTCTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTCTTTCTTTTGAAGTGCTGCAA
110234 TTTCTTT
1 TTTCTTT
110241 TTTTTCTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.60
Consensus pattern (28 bp):
TTTCTTTCTTTCTTTTGAAGTGCTGCAA
Found at i:112335 original size:35 final size:36
Alignment explanation
Indices: 112296--112375 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
112286 AAATGGAATT
* **
112296 TGGTGATGATATAGGCTTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
*
112331 TGGTGATGATATAGTCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
112367 TGGTGATGA
1 TGGTGATGA
112376 ACAGATTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 19 0.47
36 21 0.52
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:116432 original size:21 final size:19
Alignment explanation
Indices: 116390--116433 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
116380 TGTAGGAGTC
* *
116390 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTTTCTTGTTGCT
116409 TTTTTCTTCTATCTTGTTGCT
1 TTTTTCTT-T-TCTTGTTGCT
116430 TTTT
1 TTTT
116434 GTTATAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 1 0.05
21 12 0.57
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTCTTTTCTTGTTGCT
Found at i:116838 original size:11 final size:11
Alignment explanation
Indices: 116822--116859 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
116812 AATTTGGTGA
116822 TGATATAGGCG
1 TGATATAGGCG
*
116833 TGATAT-GGTG
1 TGATATAGGCG
116843 ATGATATAGGCG
1 -TGATATAGGCG
116855 TGATA
1 TGATA
116860 ATGGTGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (11 bp):
TGATATAGGCG
Found at i:116844 original size:22 final size:23
Alignment explanation
Indices: 116816--116868 Score: 99
Period size: 22 Copynumber: 2.3 Consensus size: 23
116806 AAATGGAATT
116816 TGGTGATGATATAGGCGTGAT-A
1 TGGTGATGATATAGGCGTGATAA
116838 TGGTGATGATATAGGCGTGATAA
1 TGGTGATGATATAGGCGTGATAA
116861 TGGTGATG
1 TGGTGATG
116869 GAAGATGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.32
Consensus pattern (23 bp):
TGGTGATGATATAGGCGTGATAA
Found at i:119366 original size:130 final size:132
Alignment explanation
Indices: 119202--119466 Score: 498
Period size: 133 Copynumber: 2.0 Consensus size: 132
119192 ATCACATATC
*
119202 ATTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATAT-T-TTC
1 ATTCTTAGGAAATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATATATTC
119265 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
119330 TT
131 TT
119332 ATTCTTAGGAAATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATT
1 ATTCTTAGGAAATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATAT-ATATT
119397 CATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGT
65 CATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGT
119462 CTT
130 CTT
119465 AT
1 AT
119467 AATCATTATG
Statistics
Matches: 131, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
130 58 0.44
132 1 0.01
133 72 0.55
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (132 bp):
ATTCTTAGGAAATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATATATTC
ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
TT
Found at i:121044 original size:10 final size:10
Alignment explanation
Indices: 121029--121054 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
121019 ACTCAAAAAG
121029 AAGAAAAGGA
1 AAGAAAAGGA
121039 AAGAAAAGGA
1 AAGAAAAGGA
121049 AAGAAA
1 AAGAAA
121055 GAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:123531 original size:133 final size:133
Alignment explanation
Indices: 123293--123559 Score: 516
Period size: 133 Copynumber: 2.0 Consensus size: 133
123283 TACATATCAT
123293 TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGCTATATGATATTC
1 TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGCTATATGATATTC
123358 AAGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 AAGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
123423 TTA
131 TTA
*
123426 TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGTTATATGATATTC
1 TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGCTATATGATATTC
*
123491 ATGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
66 AAGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
123556 TTA
131 TTA
123559 T
1 T
123560 AATCATATGC
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (133 bp):
TTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGAATACCATGCTATATGATATTC
AAGCATACAACATATACCCTATCTTTATGATTGATACACAATGTTATAAGCATATTAGGATAGTC
TTA
Found at i:126230 original size:30 final size:31
Alignment explanation
Indices: 126194--126253 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
126184 CTTAGCTTTA
126194 TATTATGTTTACATATGT-TTTAGAT-TCATT
1 TATTATGTTTACATAT-TATTTAGATATCATT
*
126224 TATTATGTTTGCATATTATTTAGATATCAT
1 TATTATGTTTACATATTATTTAGATATCAT
126254 GGCAACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 22 0.81
31 4 0.15
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATTATTTAGATATCATT
Found at i:127128 original size:19 final size:21
Alignment explanation
Indices: 127104--127155 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
127094 CGGCCAAGAG
*
127104 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
127123 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
127144 CATGTATTTTCA
1 CATGTATTTTCA
127156 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:127583 original size:19 final size:20
Alignment explanation
Indices: 127559--127598 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
127549 TATCCTTTCT
127559 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
127578 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
127598 T
1 T
127599 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:132341 original size:12 final size:12
Alignment explanation
Indices: 132306--132340 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
132296 TTTGAACTTC
132306 TCTTT-TTCTTT
1 TCTTTCTTCTTT
132317 TCTTTCTTCTTT
1 TCTTTCTTCTTT
132329 TC-TTCTTCTTT
1 TCTTTCTTCTTT
132340 T
1 T
132341 TGATTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TCTTTCTTCTTT
Found at i:132347 original size:18 final size:18
Alignment explanation
Indices: 132309--132351 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
132299 GAACTTCTCT
*
132309 TTTTCTT-TTCTTTCTTC
1 TTTTCTTCTTCTTTCTTA
132326 TTTTCTTCTTCTTT-TTGA
1 TTTTCTTCTTCTTTCTT-A
132344 TTTTCTTC
1 TTTTCTTC
132352 CTTTTTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTCTTCTTCTTTCTTA
Found at i:133766 original size:75 final size:75
Alignment explanation
Indices: 133672--133819 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
133662 ACAACCACGT
133672 TTCCAAGCACCAAACTCTTTACAAAACCAAAGTTCATGATCCCGTC-TTCAAAGGAGACAACGAT
1 TTCCAAGCACCAAACTCTTTACAAAACCAAAGTTCATGATCCCGTCTTTCAAAGGAGACAACGAT
133736 CCAGACAGTA
66 CCAGACAGTA
133746 TTCCAAGCACCCAAACTCTTTACAAAACCAAAGTTCATGATCCCGTCTTTCAAAGGAGACAACGA
1 TTCCAAGCA-CCAAACTCTTTACAAAACCAAAGTTCATGATCCCGTCTTTCAAAGGAGACAACGA
133811 TCCAGACAG
65 TCCAGACAG
133820 GTACATCGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 9 0.12
75 37 0.51
76 26 0.36
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (75 bp):
TTCCAAGCACCAAACTCTTTACAAAACCAAAGTTCATGATCCCGTCTTTCAAAGGAGACAACGAT
CCAGACAGTA
Found at i:141921 original size:13 final size:13
Alignment explanation
Indices: 141903--141938 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
141893 ACGCCTATAT
141903 CATCACCATAGTC
1 CATCACCATAGTC
141916 CATCACCATAGTC
1 CATCACCATAGTC
141929 CATCACCATA
1 CATCACCATA
141939 TCACGCCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.39, G:0.06, T:0.22
Consensus pattern (13 bp):
CATCACCATAGTC
Found at i:141953 original size:48 final size:50
Alignment explanation
Indices: 141864--141958 Score: 140
Period size: 48 Copynumber: 1.9 Consensus size: 50
141854 AGATACTATT
* * *
141864 TCCATCCCCATAATCCATCTTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATAACCATAG
*
141914 TCCATCACCATAGTCCATC-ACCA-TATCACGCCTATATCATAACCA
1 TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATAACCA
141959 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 21 0.51
49 3 0.07
50 17 0.41
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.27
Consensus pattern (50 bp):
TCCATCACCATAATCCATCTACCATTATCACGCCTATATCATAACCATAG
Found at i:142435 original size:14 final size:15
Alignment explanation
Indices: 142401--142447 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
142391 AATTTGGAGT
142401 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
142416 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
142430 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
142447 G
1 G
142448 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:147707 original size:47 final size:45
Alignment explanation
Indices: 147637--147762 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
147627 TATAAAATCT
*
147637 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
147682 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
147729 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
147763 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:149237 original size:30 final size:30
Alignment explanation
Indices: 149180--149243 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
149170 TTCTTCATCA
* * *
149180 TTTTCCAAAATTTACGAATTTATCCCAAAC
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
* *
149210 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
149239 TTTTC
1 TTTTC
149244 TAAGGCTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCAAAC
Found at i:150563 original size:35 final size:37
Alignment explanation
Indices: 150495--150570 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
150485 ATACTATTTC
* *
150495 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
150532 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
150567 CATC
1 CATC
150571 CCCAAATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 18 0.50
36 3 0.08
37 15 0.42
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:151859 original size:25 final size:22
Alignment explanation
Indices: 151815--151860 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
151805 AAGATGATGC
151815 ATTATATTTTAGGATTAGATTT
1 ATTATATTTTAGGATTAGATTT
*
151837 ATTATTTTATTAGGAATTAAGATT
1 ATTATATT-TTAGG-ATT-AGATT
151861 GGGTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
ATTATATTTTAGGATTAGATTT
Found at i:152365 original size:22 final size:22
Alignment explanation
Indices: 152340--152381 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
152330 CAATTTATTT
152340 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
152362 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
152382 CTAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:152742 original size:10 final size:10
Alignment explanation
Indices: 152708--152733 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
152698 TCAAAAGAAC
152708 AAAAAAGGCA
1 AAAAAAGGCA
152718 AAAAAAGGCA
1 AAAAAAGGCA
152728 AAAAAA
1 AAAAAA
152734 AAGCCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGGCA
Found at i:156950 original size:22 final size:22
Alignment explanation
Indices: 156925--156966 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
156915 CAATTCATTT
156925 ATCTT-TTATTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
156947 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
156967 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:159113 original size:24 final size:25
Alignment explanation
Indices: 159086--159139 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
159076 AAAATCATTG
*
159086 CTTTTGGAA-AACCAAAAGATGTGA
1 CTTTTGGAAGAACCAAAAGATATGA
* *
159110 CTTTT-GAAGAACCAATAGGTATGA
1 CTTTTGGAAGAACCAAAAGATATGA
159134 CTTTTG
1 CTTTTG
159140 CTGATTCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGATATGA
Found at i:160463 original size:19 final size:20
Alignment explanation
Indices: 160425--160467 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
160415 GAAACCCCTT
*
160425 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
160445 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
160464 TGAA
1 TGAA
160468 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:167564 original size:11 final size:11
Alignment explanation
Indices: 167550--167621 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
167540 TTTTTTAAAA
167550 TTTTGGCTTTT
1 TTTTGGCTTTT
167561 TTTTGGCTTTT
1 TTTTGGCTTTT
*
167572 TTGTTTG--TTT
1 TT-TTGGCTTTT
*
167582 TTTTGCCTTTTT
1 TTTTGGC-TTTT
*
167594 TCTTTGCCTTTT
1 T-TTTGGCTTTT
**
167606 TTTTGTTTTTT
1 TTTTGGCTTTT
167617 TTTTG
1 TTTTG
167622 AAAAAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 26 0.51
12 12 0.24
13 6 0.12
ACGTcount: A:0.00, C:0.10, G:0.14, T:0.76
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:167582 original size:21 final size:22
Alignment explanation
Indices: 167558--167621 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
167548 AATTTTGGCT
*
167558 TTTTTTTGGCTTTTTTGTTTG-
1 TTTTTTTGGCTTTTTTCTTTGC
*
167579 TTTTTTTGCCTTTTTTCTTTGCC
1 TTTTTTTGGCTTTTTTCTTTG-C
* *
167602 TTTTTTTTG-TTTTTTTTTTG
1 TTTTTTTGGCTTTTTTCTTTG
167622 AAAAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.53
22 10 0.28
23 7 0.19
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (22 bp):
TTTTTTTGGCTTTTTTCTTTGC
Found at i:167592 original size:32 final size:32
Alignment explanation
Indices: 167550--167617 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
167540 TTTTTTAAAA
* *
167550 TTTTGGCTTTTTT-TTGGCTTTTTTGTTTGTTT
1 TTTTGCCTTTTTTCTTGGCCTTTTT-TTTGTTT
*
167582 TTTTGCCTTTTTTCTTTGCCTTTTTTTTGTTT
1 TTTTGCCTTTTTTCTTGGCCTTTTTTTTGTTT
167614 TTTT
1 TTTT
167618 TTTGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.76
Consensus pattern (32 bp):
TTTTGCCTTTTTTCTTGGCCTTTTTTTTGTTT
Found at i:169224 original size:14 final size:15
Alignment explanation
Indices: 169190--169236 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
169180 AATTTGGAGT
169190 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
169205 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
169219 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
169236 G
1 G
169237 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:176659 original size:13 final size:13
Alignment explanation
Indices: 176637--176666 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
176627 ACTAAACACC
176637 TTTC-ACATACCT
1 TTTCAACATACCT
176649 TTTCAACATACCT
1 TTTCAACATACCT
176662 TTTCA
1 TTTCA
176667 TCTTTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:181574 original size:19 final size:20
Alignment explanation
Indices: 181550--181589 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
181540 TATCCTTTCT
181550 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
181569 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
181589 T
1 T
181590 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:190728 original size:23 final size:24
Alignment explanation
Indices: 190686--190738 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
190676 TTTCTTTCTT
190686 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
190710 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
190733 TTTCTT
1 TTTCTT
190739 TGCTGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:191588 original size:30 final size:31
Alignment explanation
Indices: 191554--191613 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
191544 CTTAGCTTTA
**
191554 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
191584 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
191614 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:192526 original size:19 final size:20
Alignment explanation
Indices: 192502--192552 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
192492 CGGCCAAGAG
* *
192502 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
192521 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
192541 CATGTATTTTCA
1 CATGTATTTTCA
192553 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:195118 original size:24 final size:22
Alignment explanation
Indices: 195073--195125 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
195063 CACTTCAATT
* *
195073 GGCACATTCTTTTGAATTTCAAGA
1 GGCACA-TCCTTTGAATGTCAA-A
195097 GGCACATCCTTTGAAATGTCAAA
1 GGCACATCCTTTG-AATGTCAAA
195120 GG-ACAT
1 GGCACAT
195126 GTCTTGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
GGCACATCCTTTGAATGTCAAA
Found at i:197421 original size:19 final size:21
Alignment explanation
Indices: 197397--197448 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
197387 CAGCCAAGAG
*
197397 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
197416 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
197437 CATGTATTTTCA
1 CATGTATTTTCA
197449 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:201719 original size:19 final size:18
Alignment explanation
Indices: 201695--201754 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
201685 TTTTTCAAAA
201695 AAAAAAACAAAAAAATGCC
1 AAAAAAACAAAAAAA-GCC
* *
201714 AAAAAAGGCAAAAAAA-CA
1 AAAAAA-ACAAAAAAAGCC
*
201732 AAAAAAAGCCAAAAAAGCC
1 AAAAAAA-CAAAAAAAGCC
201751 AAAA
1 AAAA
201755 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 14 0.42
19 11 0.33
20 8 0.24
ACGTcount: A:0.75, C:0.15, G:0.08, T:0.02
Consensus pattern (18 bp):
AAAAAAACAAAAAAAGCC
Found at i:201745 original size:9 final size:9
Alignment explanation
Indices: 201704--201754 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
201694 AAAAAAAACA
201704 AAAAAATGCC
1 AAAAAA-GCC
*
201714 AAAAAAGGC
1 AAAAAAGCC
* *
201723 AAAAAAACAA
1 AAAAAAGC-C
201733 AAAAAAGCC
1 AAAAAAGCC
201742 AAAAAAGCC
1 AAAAAAGCC
201751 AAAA
1 AAAA
201755 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 21 0.62
10 13 0.38
ACGTcount: A:0.73, C:0.16, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:201764 original size:28 final size:28
Alignment explanation
Indices: 201695--201754 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
201685 TTTTTCAAAA
* *
201695 AAAAAAACAAAAAAATGCCAAAAAAGGC
1 AAAAAAACAAAAAAAAGCCAAAAAAGCC
201723 AAAAAAACAAAAAAAAGCCAAAAAAGCC
1 AAAAAAACAAAAAAAAGCCAAAAAAGCC
201751 AAAA
1 AAAA
201755 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.75, C:0.15, G:0.08, T:0.02
Consensus pattern (28 bp):
AAAAAAACAAAAAAAAGCCAAAAAAGCC
Found at i:208705 original size:19 final size:21
Alignment explanation
Indices: 208681--208732 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
208671 CAGCCAAGAG
*
208681 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
208700 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
208721 CATGTATTTTCA
1 CATGTATTTTCA
208733 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:209821 original size:18 final size:17
Alignment explanation
Indices: 209800--209879 Score: 51
Period size: 18 Copynumber: 4.6 Consensus size: 17
209790 CCTTGGCTTG
209800 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
* *
209818 CTTTTTCTTTTCATTTATT
1 CTTTCT-TTTTGATTT-TT
*
209837 C--T-TTTCTGATTTTT
1 CTTTCTTTTTGATTTTT
*
209851 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
209869 CTTTCTTTTTG
1 CTTTCTTTTTG
209880 CACTCCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
14 3 0.06
15 7 0.15
16 1 0.02
17 9 0.19
18 21 0.44
19 7 0.15
ACGTcount: A:0.06, C:0.16, G:0.05, T:0.72
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:209871 original size:32 final size:32
Alignment explanation
Indices: 209801--209872 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
209791 CTTGGCTTGC
*
209801 TTTCTTTTTGAATTTTTCTTTTTCTTTTCATT
1 TTTCTTTTTGAATTTTTCTTTTTCTTGTCATT
209833 TATTCTTTTCTG-ATTTTTCTCTTCTT-TTGTC-TT
1 T-TTCTTTT-TGAATTTTTCT-TT-TTCTTGTCATT
209866 TTTCTTT
1 TTTCTTT
209873 CTTTTTGCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
32 7 0.20
33 18 0.51
34 8 0.23
35 2 0.06
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTGAATTTTTCTTTTTCTTGTCATT
Found at i:210006 original size:21 final size:21
Alignment explanation
Indices: 209980--210021 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
209970 GATTACCGCT
209980 TGATGTAAGGCGAATCCACAC
1 TGATGTAAGGCGAATCCACAC
*
210001 TGATGTAAGGCGAATCTACAC
1 TGATGTAAGGCGAATCCACAC
210022 ACTTTGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (21 bp):
TGATGTAAGGCGAATCCACAC
Found at i:210178 original size:16 final size:14
Alignment explanation
Indices: 210156--210190 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
210146 AATAAAGGGT
210156 AATAATAAGTAATGA
1 AATAATAAG-AATGA
210171 ATATAATAAGAATGA
1 A-ATAATAAGAATGA
210186 AATAA
1 AATAA
210191 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 7 0.37
16 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (14 bp):
AATAATAAGAATGA
Found at i:214791 original size:20 final size:20
Alignment explanation
Indices: 214758--214801 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
214748 GGGTAATAAT
* *
214758 ATAAGTAATGAATATAAATA
1 ATAAGTAATGAATAAAAAAA
214778 ATAAG-AATGAAATAAAAAAA
1 ATAAGTAATG-AATAAAAAAA
214798 ATAA
1 ATAA
214802 AAAAAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAATAAAAAAA
Found at i:219225 original size:36 final size:36
Alignment explanation
Indices: 219178--219279 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
219168 GATACAATCT
219178 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
219214 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
219250 TTCCATCACTA-TATCACGCCCATATTATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
219280 TCAACTTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:219679 original size:12 final size:11
Alignment explanation
Indices: 219652--219695 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
219642 CTACAACAAA
219652 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
219665 AAAGAAGAAAAG
1 AAA-AAGAAAAG
219677 AAAAGAGAAAAG
1 AAAA-AGAAAAG
219689 AAAAAGA
1 AAAAAGA
219696 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:219751 original size:14 final size:15
Alignment explanation
Indices: 219717--219763 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
219707 AATTTGGAGT
219717 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
219732 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
219746 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
219763 G
1 G
219764 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:224931 original size:36 final size:36
Alignment explanation
Indices: 224884--224985 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
224874 GATACAATCT
224884 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
224920 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
224956 TTCCATCACTA-TATCACGCCCATATTATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
224986 TCAACTTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:228554 original size:19 final size:19
Alignment explanation
Indices: 228507--228551 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
228497 TCTCTATCCT
228507 TTCTT-TTATTTCATTTCA
1 TTCTTATTATTTCATTTCA
*
228525 TTCTTATTATTTCTTTTCA
1 TTCTTATTATTTCATTTCA
228544 TTACTTAT
1 TT-CTTAT
228552 ATTATTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCTTATTATTTCATTTCA
Found at i:228845 original size:25 final size:25
Alignment explanation
Indices: 228817--228864 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
228807 GCAAAAAGAA
228817 AGAAAAGACA-AAAAGAAAAAAAATC
1 AGAAAAGA-AGAAAAGAAAAAAAATC
* *
228842 AGAATAGAAGAAAATAAAAAAAA
1 AGAAAAGAAGAAAAGAAAAAAAA
228865 AGAAGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.06
Consensus pattern (25 bp):
AGAAAAGAAGAAAAGAAAAAAAATC
Found at i:234130 original size:19 final size:20
Alignment explanation
Indices: 234106--234145 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
234096 TATCATTTCT
234106 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
234125 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
234145 T
1 T
234146 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:234148 original size:19 final size:18
Alignment explanation
Indices: 234102--234148 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
234092 TCTCTATCAT
234102 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
234119 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
234138 TTACTTATATT
1 TT-CTTATATT
234149 ATTATTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:239730 original size:11 final size:11
Alignment explanation
Indices: 239716--239771 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
239706 TCTTTTTGAA
239716 TTCTTTTTCTT
1 TTCTTTTTCTT
239727 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
239740 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
239753 TGTCTTTTTC-T
1 T-TCTTTTTCTT
239764 TTCTTTTT
1 TTCTTTTT
239772 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:239740 original size:19 final size:18
Alignment explanation
Indices: 239716--239771 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
239706 TCTTTTTGAA
239716 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
239734 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
239753 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
239771 T
1 T
239772 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:240527 original size:19 final size:20
Alignment explanation
Indices: 240486--240536 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
240476 GAAACCCCTT
*
240486 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
240506 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
240525 TGAAGATACATG
1 TGAAAATACATG
240537 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:242859 original size:15 final size:15
Alignment explanation
Indices: 242839--242869 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
242829 GGGCTGGCTG
242839 AACCAACATGTACTT
1 AACCAACATGTACTT
242854 AACCAACATGTACTT
1 AACCAACATGTACTT
242869 A
1 A
242870 TTCGGCCAAG
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:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
AACCAACATGTACTT
Found at i:243564 original size:30 final size:31
Alignment explanation
Indices: 243530--243589 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
243520 CTTAGCTTTA
**
243530 TATTATGCTTACATATGTTTTAGAT-TCATT
1 TATTATGCTTACATATCATTTAGATATCATT
* *
243560 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGCTTACATATCATTTAGATATCAT
243590 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGCTTACATATCATTTAGATATCATT
Found at i:253830 original size:18 final size:18
Alignment explanation
Indices: 253798--253833 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
253788 AAAAAAATGG
**
253798 CAAAAAAAAGGCAAAAAA
1 CAAAAAAAAAACAAAAAA
253816 CAAAAAAAAAACAAAAAA
1 CAAAAAAAAAACAAAAAA
253834 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAACAAAAAA
Found at i:265994 original size:13 final size:12
Alignment explanation
Indices: 265975--266039 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
265965 AAATAGGCGT
265975 GATATGGTGATG
1 GATATGGTGATG
265987 GAATATGGTGAT-
1 G-ATATGGTGATG
*
265999 GATATAGGCG-T-
1 GATAT-GGTGATG
266010 GATAATGGTGATG
1 GAT-ATGGTGATG
266023 GACTATGGTGAT-
1 GA-TATGGTGATG
266035 GATAT
1 GATAT
266040 AGGCGTGATA
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:266030 original size:36 final size:36
Alignment explanation
Indices: 265957--266057 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
265947 ATTTATAAGT
* *
265957 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
265992 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
266028 TGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
266058 TGACAGATTG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 19 0.31
36 43 0.69
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:271120 original size:26 final size:26
Alignment explanation
Indices: 271081--271148 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
271071 CCCTAGAACA
*
271081 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
271107 CCCATGTGCCTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGATCAGCC
*
271133 CCTATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
271149 GTGGTTCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.31
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGATCAGCC
Found at i:271979 original size:27 final size:28
Alignment explanation
Indices: 271927--271991 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
271917 AAAGAAAATT
*
271927 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
271955 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
271982 AGAAAAGAAA
1 AGAAAAGAAA
271992 AAAAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:282888 original size:24 final size:24
Alignment explanation
Indices: 282836--282902 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
282826 AAAGAAAGTG
*
282836 AAGCACTCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAGAAAGAAAAAAC
* *
282860 CAGCACTCAAACG-AAGAAAAAAC
1 AAGCACTCAAAAGAAAGAAAAAAC
***
282883 AAAGCAAAGAAAAGAAAGAA
1 -AAGCACTCAAAAGAAAGAA
282903 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
Found at i:296197 original size:52 final size:53
Alignment explanation
Indices: 296066--296197 Score: 185
Period size: 52 Copynumber: 2.5 Consensus size: 53
296056 TTGCATTTAT
* * *
296066 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCTCTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
296120 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * *
296172 ATTCACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
296198 ATAAATCATG
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:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:305702 original size:55 final size:55
Alignment explanation
Indices: 305640--306008 Score: 587
Period size: 55 Copynumber: 6.7 Consensus size: 55
305630 ACATGTTCAC
*
305640 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * * * *
305695 TCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAATAATAGTGTCTGC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
305750 TCCTTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
305805 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* * *
305860 TCCCTATTCTTTCAGAGAGTATGACACTCGAACAATCTTCAATAATTGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* *
305915 TCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTGT
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
* *
305970 TCCCTATTCTTTCAGAGAGTATGAGACTCAAAC-ATCTTC
1 TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTC
306009 TTCTTACGGG
Statistics
Matches: 288, Mismatches: 26, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
54 6 0.02
55 282 0.98
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTGT
Found at i:306028 original size:54 final size:54
Alignment explanation
Indices: 305987--307038 Score: 822
Period size: 54 Copynumber: 19.9 Consensus size: 54
305977 TCTTTCAGAG
*
305987 AGTAT-GAGACTCAAACATCTTCTTCTTACGGGTTCACTCCCTCTTTCTTCAGGA
1 AGTATAGA-ACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* * * *
306041 AGTATAGAACTCAAAAAATCGTCTTCTTACAGGTTTGCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTC-AAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* * ** *
306096 AGTATAGAACTCGAACATCTTTTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* * *** ** *
306150 AGTATGGAATTTGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* * ** * *
306204 AGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* ** ** *
306258 AATATAGAACTCGGACATCTTCTTCACACGGG---G-TCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* * ** * *
306308 AGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
** ** *
306362 AGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAAGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* * * * *
306416 AGTATAGAACTCCAATAACTTC-AC--ACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* ** * * *
306467 AGTATGGAACTCGGACA---TCTTC-AAAGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
** * **
306517 AGTATAGAACTCGGACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* * * * * * *
306571 AGTATAGAACTCCAATAACTTC-AC--ACAGGTTCTCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* ** ** *
306622 AGTATGGAACTCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
** ** * *
306673 AGTATAGAACTCGGACATCTTCTTCAAATGGGTTCGCTCCCTCTTTCCTT-AGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTT-CTTCAGGA
* * **
306727 AGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
** ** *
306781 AGTATAGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* * ** * *
306835 AGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* **
306889 AGTATAGAACTCAGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGA
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
* * * *
306943 AGTATAGAACTCCAATATCTTC-AC--ACGGGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGA
* * ** **
306994 AGTATGGAAATCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTCT
1 AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCT
307039 CTAGGGAGTA
Statistics
Matches: 857, Mismatches: 106, Indels: 72
0.83 0.10 0.07
Matches are distributed among these distances:
48 6 0.01
49 5 0.01
50 88 0.10
51 165 0.19
53 15 0.02
54 517 0.60
55 60 0.07
56 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (54 bp):
AGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGA
Found at i:306219 original size:108 final size:108
Alignment explanation
Indices: 305986--307053 Score: 1309
Period size: 108 Copynumber: 10.1 Consensus size: 108
305976 TTCTTTCAGA
* ** *
305986 GAGTAT-GAGACTCAAACATCTTCTTCTTACGGGTTCACTCCCTCTTTCTTCAGGAAGTATAGAA
1 GAGTATGGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAA
** * * ** * *
306050 CTCAAAAAATCGTCTTCTTACAGGTTTGCTCCCTCTTTCT-TCAGG
65 CTC-GGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * *
306095 AAGTATAGAACTCGAACATCTTTTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
* *
306159 TTTGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
306203 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAATATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
*
306268 TCGGACATCTTCTTCACACGGG---G-TCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
306307 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
*
306372 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAAG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * ** * * *
306415 AAGTATAGAACTC-CA-AT-AACTTCACACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
306476 CTCGGACA---TCTTCAAA-GGGTTCGCTCCCTCTTTCTCTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
306516 GAGTATAGAACTCGGACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
* ** * * *
306581 TC-CA-AT-AACTTCACACAGGTTCTCTCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
306621 GAGTATGGAACTCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
*
306682 CTCGGACATCTTCTTCAAATGGGTTCGCTCCCTCTTTC-CTTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC-TAGG
306726 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
306791 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
306834 GAGTATGGAACTCGAACATCTTCTTCAAACGAGTTCCCTCCCTCTTTCTTCAGGAAGTATAGAAC
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
*
306899 TCAGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
66 TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * * * * *
306942 AAGTATAGAACTC-CA-AT-ATCTTCACACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAA
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAGAA
*
307003 ATCGGACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
65 CTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
307044 GAGTATGGAA
1 GAGTATGGAA
307054 TCGCTCTCTT
Statistics
Matches: 845, Mismatches: 83, Indels: 69
0.85 0.08 0.07
Matches are distributed among these distances:
101 35 0.04
102 92 0.11
103 5 0.01
104 153 0.18
105 168 0.20
106 4 0.00
107 5 0.01
108 324 0.38
109 57 0.07
110 2 0.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (108 bp):
GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAAC
TCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:316794 original size:22 final size:21
Alignment explanation
Indices: 316749--316797 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 21
316739 ATTCATCCTG
316749 AAAAAAAATTCCGAAAATTAA
1 AAAAAAAATTCCGAAAATTAA
316770 AAAAAACAGATTCCGAAAATTAA
1 AAAAAA-A-ATTCCGAAAATTAA
316793 AAAAA
1 AAAAA
316798 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 6 0.23
22 1 0.04
23 19 0.73
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.16
Consensus pattern (21 bp):
AAAAAAAATTCCGAAAATTAA
Found at i:320110 original size:11 final size:11
Alignment explanation
Indices: 320094--320120 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
320084 TATTTTTTTT
320094 AAAAAAAAAAC
1 AAAAAAAAAAC
320105 AAAAAAAAAAC
1 AAAAAAAAAAC
320116 AAAAA
1 AAAAA
320121 GGCAAAAAAA
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:320136 original size:17 final size:17
Alignment explanation
Indices: 320094--320165 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
320084 TATTTTTTTT
320094 AAAAAAAAAA--CAAAAA
1 AAAAAAAAAAGGC-AAAA
320110 AAAAACAAAAAGGCAAAA
1 AAAAA-AAAAAGGCAAAA
*
320128 AAAAAAAAACGGCAAAA
1 AAAAAAAAAAGGCAAAA
*
320145 AAAAAAAAAGAGCCAAAA
1 AAAAAAAAA-AGGCAAAA
320163 AAA
1 AAA
320166 GCCAAAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
16 5 0.10
17 25 0.51
18 18 0.37
19 1 0.02
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGGCAAAA
Found at i:320136 original size:33 final size:34
Alignment explanation
Indices: 320094--320165 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
320084 TATTTTTTTT
320094 AAAAAAAAAAC-AAAAAAAAAACAAAAAG-GCAAA
1 AAAAAAAAAACGAAAAAAAAAA-AAAAAGAGCAAA
** *
320127 AAAAAAAAAACGGCAAAAAAAAAAAAAGAGCCAA
1 AAAAAAAAAACGAAAAAAAAAAAAAAAGAGCAAA
320161 AAAAA
1 AAAAA
320166 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAACGAAAAAAAAAAAAAAAGAGCAAA
Found at i:331886 original size:52 final size:53
Alignment explanation
Indices: 331755--331886 Score: 185
Period size: 52 Copynumber: 2.5 Consensus size: 53
331745 TTGCATTTAT
* *
331755 ATTCAACATAACAGCATGTTTATCATTTGTTTTGTTAAATTCACGTGCACTCAC
1 ATTC-ACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
*
331809 ATTCACATAACAGCATGTTCATCATTTGTTTAGTT-AATTCACGTGCACCCAC
1 ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
* * * *
331861 ATTTACTTTACAGCATGTTTTTCATT
1 ATTCACATAACAGCATGTTTATCATT
331887 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:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (53 bp):
ATTCACATAACAGCATGTTTATCATTTGTTTAGTTAAATTCACGTGCACCCAC
Found at i:333582 original size:20 final size:21
Alignment explanation
Indices: 333553--333592 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
333543 TTTTTTTCAA
*
333553 AAAAACAAAAGGCAAAAAAAC
1 AAAAACAAAAGCCAAAAAAAC
333574 AAAAA-AAAAGCCAAAAAAA
1 AAAAACAAAAGCCAAAAAAA
333593 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAGCCAAAAAAAC
Found at i:335272 original size:21 final size:21
Alignment explanation
Indices: 335232--335273 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
335222 TCAGAGAATA
* *
335232 TTACCAAGGTATTTCATCCTC
1 TTACCAAGGTAATCCATCCTC
*
335253 TTACCAAGGTAATCCTTCCTC
1 TTACCAAGGTAATCCATCCTC
335274 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:339181 original size:35 final size:37
Alignment explanation
Indices: 339135--339214 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
339125 TTTGAGAATT
*
339135 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
339170 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
339207 TGGGGATG
1 TGGTGATG
339215 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Done.