Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007913.1 Hibiscus syriacus cultivar Beakdansim tig00110315_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: 425440
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 2
Found at i:3070 original size:11 final size:13
Alignment explanation
Indices: 3038--3067 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3028 TGGCCAAAGA
3038 TGAAAAGGTATGT
1 TGAAAAGGTATGT
3051 TGAAAAGGTATG-
1 TGAAAAGGTATGT
3063 TGAAA
1 TGAAA
3068 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:7905 original size:24 final size:24
Alignment explanation
Indices: 7870--7916 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
7860 ATACTAGAGG
*
7870 CAGGAGGCAGATCGGTCGGGCTCA
1 CAGGAGGAAGATCGGTCGGGCTCA
*
7894 CAGGAGGAAGATCTGTCGGGCTC
1 CAGGAGGAAGATCGGTCGGGCTC
7917 GTATGAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.40, T:0.15
Consensus pattern (24 bp):
CAGGAGGAAGATCGGTCGGGCTCA
Found at i:15971 original size:25 final size:25
Alignment explanation
Indices: 15920--15979 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
15910 GAGTCGAGCT
* * *
15920 GAGCTAAGACAAGCCGAGCTGAGCC
1 GAGCTAAGCCAAGCCAAGCTGAACC
* *
15945 GAGCTAAGCCATGCCAAGTTGAACC
1 GAGCTAAGCCAAGCCAAGCTGAACC
*
15970 GAGCTGAGCC
1 GAGCTAAGCC
15980 GAGTTAAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (25 bp):
GAGCTAAGCCAAGCCAAGCTGAACC
Found at i:16051 original size:15 final size:15
Alignment explanation
Indices: 16033--16073 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16023 CCGAATCGAT
* *
16033 CCGAGCCGAGTCAAG
1 CCGAGCCAAGCCAAG
16048 CCGAGCCAAGCCAAG
1 CCGAGCCAAGCCAAG
*
16063 CCGAACCAAGC
1 CCGAGCCAAGC
16074 TGAGCCGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.39, G:0.27, T:0.02
Consensus pattern (15 bp):
CCGAGCCAAGCCAAG
Found at i:22476 original size:16 final size:16
Alignment explanation
Indices: 22452--22491 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
22442 TTACAAAGCC
*
22452 AAGCAACACTTTTGCA
1 AAGCCACACTTTTGCA
22468 AAGCCACACTTTTGCA
1 AAGCCACACTTTTGCA
22484 AAGCCACA
1 AAGCCACA
22492 GTTCATCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (16 bp):
AAGCCACACTTTTGCA
Found at i:27312 original size:24 final size:24
Alignment explanation
Indices: 27285--27360 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
27275 TCCGATTTGA
* *
27285 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACCTGACCTGG
*
27309 ATTCTGATCTGATA-CTGACATGG
1 ATTCTGATCTGATACCTGACCTGG
*
27332 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACCTGACCTGG
27356 ATTCT
1 ATTCT
27361 AATATAATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 22 0.48
24 24 0.52
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACCTGACCTGG
Found at i:40698 original size:20 final size:21
Alignment explanation
Indices: 40672--40726 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
40662 TTGGATTAAG
40672 GGTTTAGGGTTTA-TAGTTTAT
1 GGTTTAGGGTTTAGTA-TTTAT
*
40693 -GTTTAGGGTCTAGTATTTAT
1 GGTTTAGGGTTTAGTATTTAT
40713 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAG
40727 GGCTCATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (21 bp):
GGTTTAGGGTTTAGTATTTAT
Found at i:40701 original size:27 final size:28
Alignment explanation
Indices: 40670--40728 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
40660 AATTGGATTA
* * *
40670 AGGGTTTAGGGTTTATAGTTTA-TGTTT
1 AGGGTCTAGGATTTATAGTTTAGGGTTT
* *
40697 AGGGTCTAGTATTTATGGTTTAGGGTTT
1 AGGGTCTAGGATTTATAGTTTAGGGTTT
40725 AGGG
1 AGGG
40729 CTCATTGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.46
Consensus pattern (28 bp):
AGGGTCTAGGATTTATAGTTTAGGGTTT
Found at i:45517 original size:20 final size:20
Alignment explanation
Indices: 45492--45538 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
45482 AGTCGATCCA
45492 AGCTGAGCCAAGCCGAG-CTG
1 AGCTGAGCCAAGCCGAGTC-G
*
45512 AGCTGAGCCGAGCCGAGTCG
1 AGCTGAGCCAAGCCGAGTCG
45532 AGCTGAG
1 AGCTGAG
45539 TCGATTCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.11
Consensus pattern (20 bp):
AGCTGAGCCAAGCCGAGTCG
Found at i:45534 original size:15 final size:15
Alignment explanation
Indices: 45492--45534 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
45482 AGTCGATCCA
*
45492 AGCTGAGCCAAGCCG
1 AGCTGAGCCGAGCCG
*
45507 AGCTGAGCTGAGCCG
1 AGCTGAGCCGAGCCG
* *
45522 AGCCGAGTCGAGC
1 AGCTGAGCCGAGC
45535 TGAGTCGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.37, T:0.09
Consensus pattern (15 bp):
AGCTGAGCCGAGCCG
Found at i:48598 original size:2 final size:2
Alignment explanation
Indices: 48591--48620 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48581 GTTCTTATGC
48591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48621 AGATTCTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58799 original size:24 final size:24
Alignment explanation
Indices: 58772--58823 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
58762 AACGGATATA
*
58772 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
58796 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
58820 TCAA
1 TCAA
58824 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:58824 original size:24 final size:24
Alignment explanation
Indices: 58792--58909 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
58782 AAACATAAAT
*
58792 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
58816 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
58840 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
58864 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
58888 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
58910 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:58926 original size:48 final size:47
Alignment explanation
Indices: 58795--58926 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
58785 CATAAATCAG
* *
58795 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
58843 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
58891 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
58927 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:61243 original size:15 final size:15
Alignment explanation
Indices: 61223--61256 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
61213 GGTCAACTCC
61223 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
61238 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
61253 GGTC
1 GGTC
61257 GGGTAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:61256 original size:8 final size:7
Alignment explanation
Indices: 61222--61253 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
61212 TGGTCAACTC
61222 CGGTCAA
1 CGGTCAA
61229 CGGTCAA
1 CGGTCAA
61236 CGGGTCAA
1 C-GGTCAA
61244 CGGTCAA
1 CGGTCAA
61251 CGG
1 CGG
61254 GTCGGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:61274 original size:18 final size:18
Alignment explanation
Indices: 61251--61296 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
61241 CAACGGTCAA
*
61251 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
*
61269 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
61287 CGGGTCGGGT
1 CGGGTCGGGT
61297 TATGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:63478 original size:24 final size:24
Alignment explanation
Indices: 63451--63502 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
63441 AACGGATATA
*
63451 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
63475 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
63499 TCAA
1 TCAA
63503 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:63503 original size:24 final size:24
Alignment explanation
Indices: 63471--63588 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
63461 AAACATAAAT
*
63471 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
63495 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
63519 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
63543 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
63567 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
63589 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:63605 original size:48 final size:47
Alignment explanation
Indices: 63474--63605 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
63464 CATAAATCAG
* *
63474 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
63522 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
63570 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
63606 GTAAAACATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:66046 original size:7 final size:7
Alignment explanation
Indices: 66034--66079 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
66024 TGGTCAACTC
66034 CGGTCAA
1 CGGTCAA
66041 CGGTCAA
1 CGGTCAA
66048 CGGTCAA
1 CGGTCAA
66055 CGGTCAA
1 CGGTCAA
66062 CGGGTCAA
1 C-GGTCAA
66070 CGGTCAA
1 CGGTCAA
66077 CGG
1 CGG
66080 GTCGGGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:66069 original size:15 final size:15
Alignment explanation
Indices: 66035--66095 Score: 92
Period size: 15 Copynumber: 4.3 Consensus size: 15
66025 GGTCAACTCC
66035 GGTCAACGGTCAAC-
1 GGTCAACGGTCAACG
66049 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
66064 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
66079 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
66092 GGTC
1 GGTC
66096 GGGTAAATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
13 12 0.27
14 14 0.31
15 19 0.42
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:66071 original size:29 final size:28
Alignment explanation
Indices: 66035--66095 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
66025 GGTCAACTCC
66035 GGTCAACGGTCAAC-GGTCAACGGTCAACG
1 GGTCAACGGTCAACGGGTC--CGGTCAACG
*
66064 GGTCAACGGTCAACGGGTCGGGTCAACG
1 GGTCAACGGTCAACGGGTCCGGTCAACG
66092 GGTC
1 GGTC
66096 GGGTAAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.40
29 14 0.47
30 4 0.13
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (28 bp):
GGTCAACGGTCAACGGGTCCGGTCAACG
Found at i:66111 original size:18 final size:18
Alignment explanation
Indices: 66090--66135 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
66080 GTCGGGTCAA
*
66090 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
*
66108 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
66126 CGGGTCGGGT
1 CGGGTCGGGT
66136 TATGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:66131 original size:13 final size:13
Alignment explanation
Indices: 66056--66113 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
66046 AACGGTCAAC
*
66056 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
66071 GGTCAACGGGTCG
1 GGTCAACGGGTCG
66084 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
66097 GGTAAATGGGTCG
1 GGTCAACGGGTCG
66110 GGTC
1 GGTC
66114 GGGTCAACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 27 0.69
15 12 0.31
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:123596 original size:20 final size:19
Alignment explanation
Indices: 123566--123607 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
123556 AAGAAAACTT
123566 TAAAACCACTAACATAACA
1 TAAAACCACTAACATAACA
123585 TAAAATCCACTAACATAACA
1 TAAAA-CCACTAACATAACA
123605 TAA
1 TAA
123608 CATCATGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAACCACTAACATAACA
Found at i:125120 original size:29 final size:29
Alignment explanation
Indices: 125080--125199 Score: 163
Period size: 29 Copynumber: 4.1 Consensus size: 29
125070 CCGGGGTGAC
125080 ATTTTGGGAA-TTAATTCAAAATAGGTGCT
1 ATTTTGGGAATTTAATTCAAAA-AGGTGCT
*
125109 ATTTTGGTAATTTAATTCAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAGGTGCT
*
125138 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
* * *
125168 ATTTTGGTAA-TTATTTTAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAGGTGCT
125196 ATTT
1 ATTT
125200 CTGTAAAATG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
28 14 0.17
29 38 0.46
30 30 0.37
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCAAAAAGGTGCT
Found at i:127941 original size:24 final size:24
Alignment explanation
Indices: 127914--128004 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
127904 CATAATTCAA
* *
127914 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
127938 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
* *
127962 GTCAA-TATCAGATCAAAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
* * *
127985 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
128005 TCAAATTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:127994 original size:47 final size:48
Alignment explanation
Indices: 127914--128004 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 48
127904 CATAATTCAA
* * * *
127914 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAGGTCAGGTATCAGAACAGAATCCAT
* * *
127962 GTCAA-TATCAGATCAAAATCTATGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAAAATCCAGGTCAGGTATCAGAACAGAAT
128005 TCAAATTAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 31 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:132471 original size:35 final size:35
Alignment explanation
Indices: 132401--132473 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
132391 CACGTACAGC
* * *
132401 AAGGCCCTGAGCACACAGCCGATGAGCCGACAAGT
1 AAGGCCCTGAGCACAAAGCCGAGGAGCCCACAAGT
* *
132436 AAGGCCCTGAGCACAAAGTCGGGGAGCCTCA-AAGT
1 AAGGCCCTGAGCACAAAGCCGAGGAGCC-CACAAGT
132471 AAG
1 AAG
132474 CTTCCTCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.30, T:0.10
Consensus pattern (35 bp):
AAGGCCCTGAGCACAAAGCCGAGGAGCCCACAAGT
Found at i:132577 original size:24 final size:24
Alignment explanation
Indices: 132550--132640 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
132540 CATAATTCAA
132550 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAG
* * *
132574 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAAAATCCAG
*
132598 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAAAATCCAG
* *
132621 GTCAGGTATCATAACAAAAT
1 GTCAAGTATCATATCAAAAT
132641 TCAAATAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAG
Found at i:134357 original size:27 final size:29
Alignment explanation
Indices: 134300--134357 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 29
134290 AGTTATTAAT
*
134300 CAACTTCAAGGGTCAATTCTTGACATCTTA
1 CAACTTCAAGGGT-AATTCTTGAAATCTTA
* *
134330 CAACTT-AAGGGT-ATTTTTGAAATTTTA
1 CAACTTCAAGGGTAATTCTTGAAATCTTA
134357 C
1 C
134358 CCTACCAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 13 0.52
29 6 0.24
30 6 0.24
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (29 bp):
CAACTTCAAGGGTAATTCTTGAAATCTTA
Found at i:135131 original size:13 final size:13
Alignment explanation
Indices: 135113--135137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135103 GTGGTCAATG
135113 GTCAACGGGTCGA
1 GTCAACGGGTCGA
135126 GTCAACGGGTCG
1 GTCAACGGGTCG
135138 GGTCGGGTTA
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:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:135141 original size:18 final size:18
Alignment explanation
Indices: 135118--135199 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
135108 CAATGGTCAA
*
135118 CGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
135136 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
** *
135154 TAGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
*
135172 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
*
135190 TGGGTCGGGT
1 CGGGTCGGGT
135200 TGTAACCGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.23
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:135169 original size:36 final size:36
Alignment explanation
Indices: 135120--135200 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
135110 ATGGTCAACG
* * *
135120 GGTCGAGTCAACGGGTCGGGTCGGGTTAACGGGTTA
1 GGTCGGGTTAACGGGTCGGGTCGGGTCAACGGGTTA
* *
135156 GGTCGGGTTAACGGGTCGGGTCGGGTCAATGGGTTG
1 GGTCGGGTTAACGGGTCGGGTCGGGTCAACGGGTTA
135192 GGTCGGGTT
1 GGTCGGGTT
135201 GTAACCGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.12, C:0.15, G:0.48, T:0.25
Consensus pattern (36 bp):
GGTCGGGTTAACGGGTCGGGTCGGGTCAACGGGTTA
Found at i:137273 original size:24 final size:24
Alignment explanation
Indices: 137246--137329 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
137236 CATAATTCAT
*
137246 GTCAAGTACCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * * *
137270 GTCATGTATCATATCATAATCTAT
1 GTCAAGTATCATATCAGAATCCAG
*
137294 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
137317 GTCAAGTATCATA
1 GTCAAGTATCATA
137330 ACAAAATTGA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.40
24 29 0.60
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:137317 original size:47 final size:48
Alignment explanation
Indices: 137236--137329 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 48
137226 AAAATCAAAA
* *
137236 CATAATTCATGTCAAGTACCATATCAGAATCCAGGTCATGTATCATAT
1 CATAATTCATGTCAAGTACCAGATCAGAATCCAGGTCAAGTATCATAT
*
137284 CATAA-TCTATGTCAA-TATCAGATCAGAATCCAGGTCAAGTATCATA
1 CATAATTC-ATGTCAAGTACCAGATCAGAATCCAGGTCAAGTATCATA
137330 ACAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 30 0.71
48 12 0.29
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (48 bp):
CATAATTCATGTCAAGTACCAGATCAGAATCCAGGTCAAGTATCATAT
Found at i:139605 original size:23 final size:23
Alignment explanation
Indices: 139568--139635 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
139558 AAAATAATTA
139568 ATGTCAAGTATCATATCAGAATCC
1 ATGTCAA-TATCATATCAGAATCC
139592 ATGTCAATATCATATCAGAATCC
1 ATGTCAATATCATATCAGAATCC
* * *
139615 AGGTCAGGTATCATAACAGAA
1 ATGTCA-ATATCATATCAGAA
139636 CTCAAATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (23 bp):
ATGTCAATATCATATCAGAATCC
Found at i:149025 original size:23 final size:24
Alignment explanation
Indices: 148989--149034 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
148979 AATTGAATAT
*
148989 AATTTTTTAGCATATTTATGTTTA
1 AATTTTTTAGCATATTAATGTTTA
*
149013 AATTTTTT-TCATATTAATGTTT
1 AATTTTTTAGCATATTAATGTTT
149035 CTACTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (24 bp):
AATTTTTTAGCATATTAATGTTTA
Found at i:163204 original size:9 final size:9
Alignment explanation
Indices: 163192--163235 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
163182 TTTTGGTTCT
163192 TTTTTTTTG
1 TTTTTTTTG
163201 -TTTTTTTG
1 TTTTTTTTG
**
163209 CCTTTTTTG
1 TTTTTTTTG
*
163218 TTTTTTTTT
1 TTTTTTTTG
163227 TTTTTTTTG
1 TTTTTTTTG
163236 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:163206 original size:8 final size:8
Alignment explanation
Indices: 163193--163231 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
163183 TTTGGTTCTT
163193 TTTTTTTG
1 TTTTTTTG
163201 TTTTTTTG
1 TTTTTTTG
*
163209 CCTTTTTTG
1 -TTTTTTTG
163218 TTTTTTT-
1 TTTTTTTG
163225 TTTTTTT
1 TTTTTTT
163232 TTTGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:163208 original size:31 final size:28
Alignment explanation
Indices: 163173--163234 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
163163 TTTTTTGAAA
*
163173 TTTTGGATTTTTTGGTTCTTTTTTTTTGTTT
1 TTTTGCATTTTTT-GTT-TTTTTTTTT-TTT
*
163204 TTTTGCCTTTTTTGTTTTTTTTTTTTTT
1 TTTTGCATTTTTTGTTTTTTTTTTTTTT
163232 TTT
1 TTT
163235 GAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 9 0.31
30 3 0.10
31 11 0.38
ACGTcount: A:0.02, C:0.05, G:0.11, T:0.82
Consensus pattern (28 bp):
TTTTGCATTTTTTGTTTTTTTTTTTTTT
Found at i:163213 original size:20 final size:20
Alignment explanation
Indices: 163190--163227 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
163180 TTTTTTGGTT
163190 CTTTTTT-TTTGTTTTTTTGC
1 CTTTTTTGTTT-TTTTTTTGC
163210 CTTTTTTGTTTTTTTTTT
1 CTTTTTTGTTTTTTTTTT
163228 TTTTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (20 bp):
CTTTTTTGTTTTTTTTTTGC
Found at i:167663 original size:35 final size:35
Alignment explanation
Indices: 167592--167664 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
167582 ACACATCATA
* **
167592 TAAGGCCCTGAGCACAAAGCCGAGGAACTTGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
*
167627 TAAGGCCCTGAGCACACAGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
167662 TAA
1 TAA
167665 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.27, G:0.26, T:0.12
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCTCCAAG
Found at i:167774 original size:24 final size:23
Alignment explanation
Indices: 167746--167832 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
167736 ATTCAAATCA
*
167746 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
167769 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
* * *
167793 AATATTAGATCAGAATCTAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* *
167816 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
167833 TCAAATTTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:170083 original size:24 final size:24
Alignment explanation
Indices: 170056--170153 Score: 65
Period size: 24 Copynumber: 4.1 Consensus size: 24
170046 TATATCAAAA
*
170056 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAAGTCAAGT
* *
170080 ATCATATCAAAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAAGTCAAGT
* * * *
170104 ATCAGATCAAAATCTATGTC-AGAT
1 ATCAAAACAAAATCCAAGTCAAG-T
* * * *
170128 ATCAGATCATAATCCATGTCAAGT
1 ATCAAAACAAAATCCAAGTCAAGT
170152 AT
1 AT
170154 TAGATCAGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.10
24 55 0.87
25 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (24 bp):
ATCAAAACAAAATCCAAGTCAAGT
Found at i:170158 original size:24 final size:24
Alignment explanation
Indices: 170073--170160 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
170063 CATAAATCAG
* *
170073 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
*
170097 GTCAAGTATCAGATCAAAATCTAT
1 GTCAAGTATCAGATCAAAATCCAT
*
170121 GTC-AGATATCAGATCATAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
*
170145 GTCAAGTATTAGATCA
1 GTCAAGTATCAGATCA
170161 GAATTCAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:172635 original size:8 final size:8
Alignment explanation
Indices: 172594--172651 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
172584 TCAAAGTTTT
172594 GGTCAACAG
1 GGTCAAC-G
172603 TGGTCAACG
1 -GGTCAACG
172612 CCGGTCAAC-
1 --GGTCAACG
172621 GGTCAACG
1 GGTCAACG
*
172629 AGTCAACG
1 GGTCAACG
*
172637 GGTAAACG
1 GGTCAACG
172645 GGTCAAC
1 GGTCAAC
172652 AGTGGTCGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.46
9 1 0.02
10 14 0.34
ACGTcount: A:0.29, C:0.26, G:0.31, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:174720 original size:24 final size:24
Alignment explanation
Indices: 174693--174768 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
174683 TATATCAAAA
174693 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
174717 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
174741 ATCAGATCAGAATCCAAGACAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
174765 ATCA
1 ATCA
174769 GATCAGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:174769 original size:24 final size:24
Alignment explanation
Indices: 174710--174824 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
174700 CATAAATCAG
* * *
174710 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
174734 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
* *
174758 GACAAGTATCAGATCAGAAT-TAT
1 GTCAAGTATCAGATCAGAATCCAT
*
174781 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
174805 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
174825 TCAAATAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.03
23 16 0.21
24 58 0.74
25 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:177198 original size:13 final size:13
Alignment explanation
Indices: 177177--177206 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
177167 AACAGTCAAT
*
177177 GGGTCAATGGGTC
1 GGGTAAATGGGTC
177190 GGGTAAATGGGTC
1 GGGTAAATGGGTC
177203 GGGT
1 GGGT
177207 TATGACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.23
Consensus pattern (13 bp):
GGGTAAATGGGTC
Found at i:177244 original size:21 final size:21
Alignment explanation
Indices: 177220--177263 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
177210 GACCGATCAT
177220 ACCGGTCAACTAT-ACACCAAA
1 ACCGGTCAACTATGA-ACCAAA
177241 ACCGGTCAACTATGAACCAAA
1 ACCGGTCAACTATGAACCAAA
177262 AC
1 AC
177264 TGGACAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.14
Consensus pattern (21 bp):
ACCGGTCAACTATGAACCAAA
Found at i:179013 original size:8 final size:8
Alignment explanation
Indices: 178983--179032 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
178973 GGTCAATTGT
178983 GGTCAACG
1 GGTCAACG
178991 TCGGTCAAC-
1 --GGTCAACG
179000 GGTCAACG
1 GGTCAACG
179008 GGTCAACG
1 GGTCAACG
179016 GGTC-A--
1 GGTCAACG
179021 GGTCAACG
1 GGTCAACG
179029 GGTC
1 GGTC
179033 GGGTCGAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 8 0.22
8 16 0.44
10 7 0.19
ACGTcount: A:0.22, C:0.26, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:179026 original size:13 final size:13
Alignment explanation
Indices: 179008--179037 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
178998 ACGGTCAACG
179008 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
179021 GGTCAACGGGTCG
1 GGTCAACGGGTCA
179034 GGTC
1 GGTC
179038 GAGTCGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:181091 original size:35 final size:35
Alignment explanation
Indices: 181020--181092 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
181010 ATACATCATA
**
181020 TAAGGCCCTGAGCACAAAGCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
* *
181055 TAAGGCCCTGAGCACACAGCCGAGGAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
181090 TAA
1 TAA
181093 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.29, G:0.27, T:0.10
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGGAACCGCCAAG
Found at i:181202 original size:24 final size:23
Alignment explanation
Indices: 181174--181253 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
181164 ATTCAAATCA
*
181174 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAAGTC
*
181197 ATGTATCAGATCAGAAT-CAATGTC
1 A-GTATCATATCAGAATCCAA-GTC
* *
181221 AATATCATATTAGAATCCAAGTC
1 AGTATCATATCAGAATCCAAGTC
181244 AGGTATCATA
1 A-GTATCATA
181254 ACATAATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 19 0.40
24 28 0.60
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAAGTC
Found at i:208238 original size:24 final size:24
Alignment explanation
Indices: 208139--208226 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
208129 AATATAATAA
* *
208139 ATCAAAACAGAATTCATAACAGAT
1 ATCATAACAGAATTCATATCAGAT
* *
208163 ATCATAACATAATCCATATCAGAT
1 ATCATAACAGAATTCATATCAGAT
* * ** * *
208187 ATCAGAATAGAATTCAGGTTAGGT
1 ATCATAACAGAATTCATATCAGAT
208211 ATCATAACAGAATTCA
1 ATCATAACAGAATTCA
208227 AGTCAGAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCATAACAGAATTCATATCAGAT
Found at i:212838 original size:12 final size:12
Alignment explanation
Indices: 212821--212877 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
212811 CATAAATTAA
212821 AACAGAATTCAG
1 AACAGAATTCAG
212833 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
212845 AACAGAATCCAG
1 AACAGAATTCAG
* * *
212857 ATCAGAAATCAT
1 AACAGAATTCAG
*
212869 AATAGAATT
1 AACAGAATT
212878 TAGGTCATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:212857 original size:24 final size:24
Alignment explanation
Indices: 212821--212876 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
212811 CATAAATTAA
* *
212821 AACAGAATTCAGAACAGATATCAG
1 AACAGAATCCAGAACAGAAATCAG
* *
212845 AACAGAATCCAGATCAGAAATCAT
1 AACAGAATCCAGAACAGAAATCAG
*
212869 AATAGAAT
1 AACAGAAT
212877 TTAGGTCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (24 bp):
AACAGAATCCAGAACAGAAATCAG
Found at i:217567 original size:24 final size:24
Alignment explanation
Indices: 217538--217603 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
217528 GAAATATTAT
*
217538 AAATCAAAATAGAATTCAGAAT-AG
1 AAATCAAAACAGAATTCAG-ATCAG
* * *
217562 ATATCATAACAGAATCCAGATCAG
1 AAATCAAAACAGAATTCAGATCAG
*
217586 AAATCAGAACAGAATTCA
1 AAATCAAAACAGAATTCA
217604 TGTCATGTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATCAG
Found at i:223670 original size:23 final size:24
Alignment explanation
Indices: 223620--223672 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
223610 CTTTATTTCT
* * *
223620 TTTCTTCTTTTTGAGTGATTGACT
1 TTTCTTCTTTTGGAGTGATTCACA
*
223644 TTTCTTCTTTTGGAGTGCTTCA-A
1 TTTCTTCTTTTGGAGTGATTCACA
223667 TTTCTT
1 TTTCTT
223673 TGTTGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGATTCACA
Found at i:223708 original size:11 final size:11
Alignment explanation
Indices: 223692--223716 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
223682 TTGTTTTTCT
223692 TTCACTTGCAC
1 TTCACTTGCAC
223703 TTCACTTGCAC
1 TTCACTTGCAC
223714 TTC
1 TTC
223717 TTTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:224632 original size:24 final size:24
Alignment explanation
Indices: 224604--224660 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
224594 TCAAGGTAAG
*
224604 CTAGGTGAGTGTCTTGGTAGCTAG
1 CTAGGTGAGTGTCTTGGTAGCTAA
*
224628 TTAGGTGAGTGTCTTGGTAGCTAA
1 CTAGGTGAGTGTCTTGGTAGCTAA
224652 CTAGGTGAG
1 CTAGGTGAG
224661 CTATAGCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.37, T:0.33
Consensus pattern (24 bp):
CTAGGTGAGTGTCTTGGTAGCTAA
Found at i:227516 original size:6 final size:6
Alignment explanation
Indices: 227505--227530 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
227495 ATTAAGAAAA
227505 GAAATG GAAATG GAAATG GAAATG GA
1 GAAATG GAAATG GAAATG GAAATG GA
227531 TAGAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAATG
Found at i:231466 original size:24 final size:24
Alignment explanation
Indices: 231412--231466 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
231402 GAAAAATCAG
*
231412 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
231435 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
231459 AAAAGAAA
1 AAAAGAAA
231467 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:232719 original size:24 final size:21
Alignment explanation
Indices: 232685--232727 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
232675 TGCACAAGAT
*
232685 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
232707 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
232728 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:236336 original size:16 final size:16
Alignment explanation
Indices: 236287--236351 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
236277 AAGGTTAAGA
*
236287 AAAGAATAAGGTAATG
1 AAAGAATAAGGAAATG
* *
236303 AAATAAGAA--AAGATG
1 AAAGAATAAGGAA-ATG
236318 AAAGAATAAGGAAATG
1 AAAGAATAAGGAAATG
* * *
236334 AAATAGTAAGAAAATG
1 AAAGAATAAGGAAATG
236350 AA
1 AA
236352 GATACTTACA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 10 0.26
16 25 0.66
17 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (16 bp):
AAAGAATAAGGAAATG
Found at i:236573 original size:14 final size:14
Alignment explanation
Indices: 236551--236592 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
236541 TGTAGAAGTC
236551 TGTTCTTTTCTTTT
1 TGTTCTTTTCTTTT
* *
236565 TGTTTTTTTCTTTC
1 TGTTCTTTTCTTTT
*
236579 T-TTGTTTTCTTTT
1 TGTTCTTTTCTTTT
236592 T
1 T
236593 TTTGCAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (14 bp):
TGTTCTTTTCTTTT
Found at i:236838 original size:10 final size:10
Alignment explanation
Indices: 236825--236850 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
236815 GGAAAGAATT
236825 GAAATGGATA
1 GAAATGGATA
236835 GAAATGGATA
1 GAAATGGATA
236845 GAAATG
1 GAAATG
236851 TTATCAAAGA
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:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (10 bp):
GAAATGGATA
Found at i:255474 original size:49 final size:48
Alignment explanation
Indices: 255421--255534 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 48
255411 GGGGAGACAT
*
255421 CTCCCTTGGCTGAATGGTGCATTCTTGTTCATCTTGGCACCACAGTTA
1 CTCCCTTGGCTGAATGGTGCATGCTTGTTCATCTTGGCACCACAGTTA
* *
255469 CCTCCCTTGGCTGAATGGTGCATGCTTGTTCATCTTGGCGCCATAGTTA
1 -CTCCCTTGGCTGAATGGTGCATGCTTGTTCATCTTGGCACCACAGTTA
*
255518 CTGCCCTTGGCCGAATG
1 CT-CCCTTGGCTGAATG
255535 ATGATGTGCC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 2 0.03
49 58 0.97
ACGTcount: A:0.15, C:0.28, G:0.24, T:0.33
Consensus pattern (48 bp):
CTCCCTTGGCTGAATGGTGCATGCTTGTTCATCTTGGCACCACAGTTA
Found at i:259699 original size:23 final size:24
Alignment explanation
Indices: 259664--259717 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
259654 ATATCCAACA
259664 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
259687 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
259711 AAGAAAA
1 AAGAAAA
259718 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:263818 original size:23 final size:24
Alignment explanation
Indices: 263783--263844 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 24
263773 ATATCCAACA
263783 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
263806 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
263830 AAGGAAAAATCAAAG
1 AA-G-AAAATCAAAG
263845 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 16 0.50
24 7 0.22
25 1 0.03
26 8 0.25
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.10
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:268132 original size:24 final size:23
Alignment explanation
Indices: 268087--268132 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
268077 AAAATCAAAG
**
268087 CACTCAAAAGAAGAAATTGAAAC
1 CACTCAAAAGAAGAAAAAGAAAC
268110 CACTCAAAAAGAAGAAAAAGAAA
1 CACTC-AAAAGAAGAAAAAGAAA
268133 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.63, C:0.15, G:0.13, T:0.09
Consensus pattern (23 bp):
CACTCAAAAGAAGAAAAAGAAAC
Found at i:268147 original size:13 final size:14
Alignment explanation
Indices: 268116--268150 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
268106 AAACCACTCA
*
268116 AAAAGAAGAAAAAG
1 AAAAGAAAAAAAAG
268130 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
268144 -AAAGAAA
1 AAAAGAAA
268151 GTTGAAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:272718 original size:26 final size:24
Alignment explanation
Indices: 272664--272718 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
272654 AAAAAAAGTG
*
272664 AAGCACTAAAAAAAAGAAAAAATA
1 AAGCACTAAAAAAAAGAAAAAACA
* *
272688 CAGCACTCAAAAAAAGAAGAAAAGCA
1 AAGCACTAAAAAAAAGAA-AAAA-CA
272714 AAGCA
1 AAGCA
272719 AAGAAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 16 0.64
25 4 0.16
26 5 0.20
ACGTcount: A:0.67, C:0.15, G:0.13, T:0.05
Consensus pattern (24 bp):
AAGCACTAAAAAAAAGAAAAAACA
Found at i:275483 original size:11 final size:13
Alignment explanation
Indices: 275451--275480 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
275441 TATCCAAAGA
275451 TGAAAAGGTATGT
1 TGAAAAGGTATGT
275464 TGAAAAGGTATG-
1 TGAAAAGGTATGT
275476 TGAAA
1 TGAAA
275481 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:281534 original size:17 final size:18
Alignment explanation
Indices: 281518--281555 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
281508 CCTCTTTTCT
281518 TTTTCTGAATATTTTCTTC
1 TTTTCTGAAT-TTTTCTTC
281537 TTTTCTGAATTTTT-TTC
1 TTTTCTGAATTTTTCTTC
281554 TT
1 TT
281556 CTTTTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTCTGAATTTTTCTTC
Found at i:281537 original size:20 final size:21
Alignment explanation
Indices: 281514--281561 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
281504 AATTCCTCTT
281514 TTCTTTTTCTGAA-TATTTTC
1 TTCTTTTTCTGAATTATTTTC
*
281534 TTC-TTTTCTGAATTTTTTTC
1 TTCTTTTTCTGAATTATTTTC
281554 TTCTTTTT
1 TTCTTTTT
281562 ATCTTTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.10, C:0.15, G:0.04, T:0.71
Consensus pattern (21 bp):
TTCTTTTTCTGAATTATTTTC
Found at i:287173 original size:22 final size:23
Alignment explanation
Indices: 287134--287176 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
287124 AAATCCAGCA
287134 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
287157 AAGAAATTGAAAG-ACTCAAA
1 AAGAAAATCAAAGCACTCAAA
287177 GTGGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:289937 original size:11 final size:13
Alignment explanation
Indices: 289905--289934 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
289895 TGGCCAAAGA
289905 TGAAAAGGTATGT
1 TGAAAAGGTATGT
289918 TGAAAAGGTATG-
1 TGAAAAGGTATGT
289930 TGAAA
1 TGAAA
289935 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:296386 original size:24 final size:24
Alignment explanation
Indices: 296354--296441 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
296344 TATTATTATA
* * * *
296354 ATACATGACCTGAATTCTGATCGG
1 ATACTTGACTTGAATTTTGATCAG
* *
296378 ATACTTGACTTGGATTTTGATCAA
1 ATACTTGACTTGAATTTTGATCAG
* * *
296402 ATACTTGACATGGATTTTGATCTG
1 ATACTTGACTTGAATTTTGATCAG
296426 ATACTTGACTTGAATT
1 ATACTTGACTTGAATT
296442 ATGTTTTGAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
ATACTTGACTTGAATTTTGATCAG
Found at i:303552 original size:6 final size:6
Alignment explanation
Indices: 303529--303569 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
303519 GTGCTGCAAC
*
303529 AAAAGA AAAA-A AAGAGA AAAAGA AAAA-A GAAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA
303570 CTCCTACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 5 0.17
6 24 0.80
7 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:303564 original size:18 final size:17
Alignment explanation
Indices: 303529--303569 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
303519 GTGCTGCAAC
*
303529 AAAAGAAAAAAAAGAGA
1 AAAAGAAAAAAAAAAGA
303546 AAAAGAAAAAAGAAAAGA
1 AAAAGAAAAAA-AAAAGA
303564 AAAAGA
1 AAAAGA
303570 CTCCTACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGA
Found at i:303629 original size:25 final size:28
Alignment explanation
Indices: 303601--303653 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
303591 GCAAAAGAAA
303601 AAAAGAAAA-GAAG-AAAATT-CAAAGC
1 AAAAGAAAAGGAAGCAAAATTGCAAAGC
303626 AAAAGAAAAGTGAAGCAAAATTGCAAAG
1 AAAAGAAAAG-GAAGCAAAATTGCAAAG
303654 TACACTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.38
27 4 0.17
28 6 0.25
29 5 0.21
ACGTcount: A:0.64, C:0.08, G:0.19, T:0.09
Consensus pattern (28 bp):
AAAAGAAAAGGAAGCAAAATTGCAAAGC
Found at i:305711 original size:19 final size:21
Alignment explanation
Indices: 305668--305719 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
305658 GAAACCCTTT
305668 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
305689 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
305708 TGAAGATACATG
1 TGAAAATACATG
305720 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:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:306656 original size:30 final size:31
Alignment explanation
Indices: 306617--306676 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
306607 ACATGCTGCC
**
306617 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
306648 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
306677 TAAAGCTAAG
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:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:309076 original size:31 final size:31
Alignment explanation
Indices: 309041--309102 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
309031 GGTAGAGCAC
*
309041 TTTTCCTTAGC-TTTCTTTCTTTT-TGATTTT
1 TTTTTCTTAGCTTTTCTTT-TTTTCTGATTTT
**
309071 TTTTTCTTTTCTTTTCTTTTTTTCTGATTTT
1 TTTTTCTTAGCTTTTCTTTTTTTCTGATTTT
309102 T
1 T
309103 CTCTTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (31 bp):
TTTTTCTTAGCTTTTCTTTTTTTCTGATTTT
Found at i:309078 original size:17 final size:17
Alignment explanation
Indices: 309056--309131 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
309046 CTTAGCTTTC
309056 TTTCTTTTTGATTTTTT
1 TTTCTTTTTGATTTTTT
* *
309073 TTTC-TTTT-CTTTTCT
1 TTTCTTTTTGATTTTTT
*
309088 TTT-TTTCTGATTTTTCT
1 TTTCTTTTTGATTTTT-T
*
309105 CTTC-TTTTG-TCTTTTT
1 TTTCTTTTTGAT-TTTTT
309121 CTTTCTTTTTG
1 -TTTCTTTTTG
309132 CACTCCAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
15 11 0.25
16 10 0.23
17 18 0.41
18 5 0.11
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTGATTTTTT
Found at i:309129 original size:27 final size:27
Alignment explanation
Indices: 309071--309122 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
309061 TTTTGATTTT
* *
309071 TTTTTCTTTTCTTTTCTTTTTTTCTGA
1 TTTTTCTCTTCTTTTCTCTTTTTCTGA
*
309098 TTTTTCTCTTCTTTTGTCTTTTTCT
1 TTTTTCTCTTCTTTTCTCTTTTTCT
309123 TTCTTTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTTCTCTTCTTTTCTCTTTTTCTGA
Found at i:309424 original size:19 final size:20
Alignment explanation
Indices: 309396--309435 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
309386 GAATAATAAT
309396 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
309416 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
309435 A
1 A
309436 ATAAAGGATA
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:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:310724 original size:30 final size:31
Alignment explanation
Indices: 310685--310744 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
310675 ACATGCTGCC
**
310685 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
310716 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
310745 TAAAGCTAAG
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:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:316423 original size:18 final size:20
Alignment explanation
Indices: 316398--316446 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
316388 TTCGGCCAAG
316398 AGCATGTATCTT-CATTAAA
1 AGCATGTATCTTCCATTAAA
316417 A-CATGTAT-TTCCATTAAA
1 AGCATGTATCTTCCATTAAA
316435 AGTCATGTATCT
1 AG-CATGTATCT
316447 AGCAGAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 1 0.04
20 7 0.27
21 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (20 bp):
AGCATGTATCTTCCATTAAA
Found at i:316867 original size:19 final size:20
Alignment explanation
Indices: 316843--316882 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
316833 TATCCATTCT
316843 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
316862 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
316882 T
1 T
316883 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:329274 original size:33 final size:33
Alignment explanation
Indices: 329232--329300 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
329222 GTTGATGAAT
*
329232 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
329265 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
329298 GAA
1 GAA
329301 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:334950 original size:33 final size:33
Alignment explanation
Indices: 334908--334976 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
334898 GTTGATGAAT
*
334908 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
334941 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
334974 GAA
1 GAA
334977 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:342832 original size:14 final size:14
Alignment explanation
Indices: 342813--342857 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
342803 ACGGTGATAC
*
342813 AAGATGGTGATGAA
1 AAGATGGTGATGGA
*
342827 AAGATGGTGTTGGA
1 AAGATGGTGATGGA
342841 AAGATGGTGATGGA
1 AAGATGGTGATGGA
342855 AAG
1 AAG
342858 GTAGTATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (14 bp):
AAGATGGTGATGGA
Found at i:344908 original size:14 final size:14
Alignment explanation
Indices: 344889--344919 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
344879 GTTGAATTAA
344889 ATGAATGAATCTTC
1 ATGAATGAATCTTC
*
344903 ATGAATGTATCTTC
1 ATGAATGAATCTTC
344917 ATG
1 ATG
344920 GCTGAATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (14 bp):
ATGAATGAATCTTC
Found at i:345838 original size:14 final size:14
Alignment explanation
Indices: 345810--345846 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
345800 TGGCATGAAA
*
345810 GTGATGG-ATGATG
1 GTGATGGAAAGATG
345823 GTGATGGAAAGATG
1 GTGATGGAAAGATG
345837 GTGATGGAAA
1 GTGATGGAAA
345847 TAGTATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.24
Consensus pattern (14 bp):
GTGATGGAAAGATG
Found at i:346762 original size:19 final size:20
Alignment explanation
Indices: 346719--346762 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
346709 AAGTGAATAA
346719 AAAT-ATAAGTAATGAAAAG
1 AAATAATAAGTAATGAAAAG
*
346738 AAATAATAA-TAATGAAATG
1 AAATAATAAGTAATGAAAAG
346757 AAATAA
1 AAATAA
346763 AGAAAGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (20 bp):
AAATAATAAGTAATGAAAAG
Found at i:350964 original size:18 final size:17
Alignment explanation
Indices: 350943--351022 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
350933 CCTTGGCTTG
350943 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
350961 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
350977 C-TTCTTTTCTGATTTTT
1 CTTTCTTTT-TGATTTTT
*
350994 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
351012 CTTTCTTTTTG
1 CTTTCTTTTTG
351023 CACTCCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
15 5 0.10
16 8 0.16
17 12 0.24
18 23 0.45
19 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:350981 original size:13 final size:12
Alignment explanation
Indices: 350957--351015 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
350947 CTTTTTGAAT
350957 TTTTC-TTTTTC
1 TTTTCTTTTTTC
350968 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
350981 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
350995 TCTTCTTTTGTC
1 TTTTCTTTTTTC
351007 TTTTTCTTT
1 -TTTTCTTT
351016 CTTTTTGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 8 0.20
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:350981 original size:19 final size:19
Alignment explanation
Indices: 350959--351015 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
350949 TTTTGAATTT
350959 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
*
350978 TTC-TTTTCTGATTT-TTCTC
1 TTCTTTTTCT--TTTCTTTTC
350997 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
351016 CTTTTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 9 0.30
21 4 0.13
22 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:351317 original size:14 final size:13
Alignment explanation
Indices: 351278--351319 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
351268 TAATAAAGAG
*
351278 AATAATAATAT-A
1 AATAATAAAATGA
*
351290 AGTAATAAAATGA
1 AATAATAAAATGA
351303 AATAATAAGAATGA
1 AATAATAA-AATGA
351317 AAT
1 AAT
351320 GAAATAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.36
13 8 0.32
14 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (13 bp):
AATAATAAAATGA
Found at i:351319 original size:19 final size:20
Alignment explanation
Indices: 351287--351326 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
351277 GAATAATAAT
351287 ATAAGTAATAAAATGAAATA
1 ATAAGTAATAAAATGAAATA
*
351307 ATAAG-AATGAAATGAAATA
1 ATAAGTAATAAAATGAAATA
351326 A
1 A
351327 AGAAAGGGAT
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:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (20 bp):
ATAAGTAATAAAATGAAATA
Found at i:355012 original size:14 final size:14
Alignment explanation
Indices: 354993--355019 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
354983 AAAATTCTTA
354993 AAAAACATTTTTCT
1 AAAAACATTTTTCT
355007 AAAAACATTTTTC
1 AAAAACATTTTTC
355020 GATAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAACATTTTTCT
Found at i:356647 original size:29 final size:29
Alignment explanation
Indices: 356609--356842 Score: 294
Period size: 29 Copynumber: 8.2 Consensus size: 29
356599 ACGGTAAACT
* * *
356609 ATTACGAAAATAACACTTTTTTAAAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
*
356638 ATTACAAAAATATCAC-TTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
* **
356666 ATTACCAAAATATCATTTTTTTTGAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
* **
356695 ATTACCAAAATATCATTTTTTTTGAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
* *
356724 ATTATCAAAATATCACTTTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
*
356753 ATTACCAAAATATCATTTTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
*
356782 ATTACCAAAATATCAC-TTTTTCGAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
* *
356810 ATTATCAAAATATCA-ATTTTTCAAAATA
1 ATTACCAAAATATCACTTTTTTCAAAATA
*
356838 TTTAC
1 ATTAC
356843 GAAACTAACA
Statistics
Matches: 184, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
28 64 0.35
29 120 0.65
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTACCAAAATATCACTTTTTTCAAAATA
Found at i:372932 original size:19 final size:19
Alignment explanation
Indices: 372910--372953 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
372900 TGAAGCACTC
372910 AAAAGAAGAAAAAAAAGAA
1 AAAAGAAGAAAAAAAAGAA
* * *
372929 AAAAAAAGAATAGAAAGAA
1 AAAAGAAGAAAAAAAAGAA
372948 ACAAAG
1 A-AAAG
372954 TTGAAGCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAAAAAAAGAA
Found at i:379001 original size:29 final size:29
Alignment explanation
Indices: 378959--379015 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
378949 GGAAAGTAAA
378959 ATATAATGTAAAAAGGGAGGCTTAGAAAC
1 ATATAATGTAAAAAGGGAGGCTTAGAAAC
* *
378988 ATATAATGTGAAAAGGGTGGCTTAGAAA
1 ATATAATGTAAAAAGGGAGGCTTAGAAA
379016 TAGAAAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (29 bp):
ATATAATGTAAAAAGGGAGGCTTAGAAAC
Found at i:379182 original size:21 final size:22
Alignment explanation
Indices: 379165--379211 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
379155 TTTCTTTATC
379165 TTCCT-TTTTGAGTGCTTTCAAT
1 TTCCTCTTTTGAGTGCTTT-AAT
* *
379187 TTCTTCTTTTGAGTGCTTCAAT
1 TTCCTCTTTTGAGTGCTTTAAT
379209 TTC
1 TTC
379212 TTTGCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.13, C:0.19, G:0.13, T:0.55
Consensus pattern (22 bp):
TTCCTCTTTTGAGTGCTTTAAT
Found at i:379209 original size:22 final size:23
Alignment explanation
Indices: 379170--379213 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
379160 TTATCTTCCT
379170 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
379193 TTTTGAGTGC-TTCAATTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
379214 TGCTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:381787 original size:5 final size:5
Alignment explanation
Indices: 381764--381800 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
381754 GATGGAATAA
381764 GAAAT G-AAT GAAA- GAAAT GAAAT GAAAAT GAAAT GAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT GAAAT GAA
381801 TTAATAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 16 0.55
6 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:384314 original size:22 final size:23
Alignment explanation
Indices: 384273--384315 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
384263 ATACATCAAA
*
384273 ATGGGTGGCAAATATGAACAAGC
1 ATGGGAGGCAAATATGAACAAGC
384296 ATGGGAGGCAAA-ATGAACAA
1 ATGGGAGGCAAATATGAACAA
384316 ACACTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (23 bp):
ATGGGAGGCAAATATGAACAAGC
Found at i:388745 original size:35 final size:37
Alignment explanation
Indices: 388699--388778 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
388689 GTTGAGAATT
*
388699 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
388734 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
388771 TGGTGATG
1 TGGTGATG
388779 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:389164 original size:19 final size:20
Alignment explanation
Indices: 389117--389167 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
389107 GAAACCCATT
**
389117 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
389137 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
389156 TGAAGATACATG
1 TGAAAATACATG
389168 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:392807 original size:35 final size:37
Alignment explanation
Indices: 392761--392840 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
392751 TTTGAGAATT
*
392761 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
392796 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
392833 TGGTGATG
1 TGGTGATG
392841 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:393226 original size:19 final size:20
Alignment explanation
Indices: 393179--393229 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
393169 GAAACCCCTT
**
393179 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
393199 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
393218 TGAAGATACATG
1 TGAAAATACATG
393230 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:396123 original size:23 final size:25
Alignment explanation
Indices: 396096--396151 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
396086 AAAATCCAGC
396096 AAAGAAAATCAAAGCACTCAAA-AG
1 AAAGAAAATCAAAGCACTCAAAGAG
* *
396120 -AAGAAATTGAAAGCACTCAAAGAG
1 AAAGAAAATCAAAGCACTCAAAGAG
396144 AAAGAAAA
1 AAAGAAAA
396152 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.09
Consensus pattern (25 bp):
AAAGAAAATCAAAGCACTCAAAGAG
Found at i:409392 original size:33 final size:33
Alignment explanation
Indices: 409348--409416 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
409338 CATCACCATA
*
409348 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
409381 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
409414 TTC
1 TTC
409417 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:411512 original size:33 final size:33
Alignment explanation
Indices: 411433--411536 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
411423 ATACAATCTG
* *
411433 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
411469 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
411502 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
411535 TC
1 TC
411537 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:416769 original size:12 final size:11
Alignment explanation
Indices: 416742--416785 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
416732 TGCTACAACA
416742 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
416755 AAAGAAGAAAAG
1 AAA-AAGAAAAG
416767 AAAAGAGAAAAG
1 AAAA-AGAAAAG
416779 AAAAAGA
1 AAAAAGA
416786 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
Done.