Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 23
Found at i:266774 original size:21 final size:21
Alignment explanation
Indices: 266749--266842 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
266739 TGGCATAACT
266749 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* *
266770 TAAACCTTAACACATAAACCA
1 TAAACCCTAACACATAAACCC
* * *
266791 TAAACTCTAA-ACTTTAAACCT
1 TAAACCCTAACAC-ATAAACCC
* * *
266812 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
*
266833 TAAATCCTAA
1 TAAACCCTAA
266843 ACCCTAAACC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:266802 original size:35 final size:35
Alignment explanation
Indices: 266763--266850 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
266753 CCCTAACACA
266763 TAAACCCTAAACCTTAACA-CATAA-ACCATAAACTC
1 TAAACCCTAAACCTTAA-ATCATAACA-CATAAACTC
** * *
266798 TAAACTTTAAACCTTAAATCCTATCACATAAACTC
1 TAAACCCTAAACCTTAAATCATAACACATAAACTC
* *
266833 TAAATCCTAAACCCTAAA
1 TAAACCCTAAACCTTAAA
266851 CCTTATCACA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 1 0.02
35 41 0.95
36 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (35 bp):
TAAACCCTAAACCTTAAATCATAACACATAAACTC
Found at i:266858 original size:35 final size:35
Alignment explanation
Indices: 266789--266863 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
266779 ACACATAAAC
* *
266789 CATAAACTCTAAACTTTAAACCTTAAATCCTATCA
1 CATAAACTCTAAACTCTAAACCCTAAATCCTATCA
266824 CATAAACTCTAAA-TCCTAAACCCTAAA-CCTTATCA
1 CATAAACTCTAAACT-CTAAACCCTAAATCC-TATCA
266859 CATAA
1 CATAA
266864 TTAGTTATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (35 bp):
CATAAACTCTAAACTCTAAACCCTAAATCCTATCA
Found at i:267134 original size:14 final size:14
Alignment explanation
Indices: 267117--267158 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 14
267107 TTTATTCATC
267117 AATAATGTATTTTT
1 AATAATGTATTTTT
267131 AAT-A--TATTTTT
1 AATAATGTATTTTT
267142 AATAATGTAATTTTT
1 AATAATGT-ATTTTT
267157 AA
1 AA
267159 AAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 10 0.42
12 1 0.04
13 1 0.04
14 4 0.17
15 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:268546 original size:16 final size:17
Alignment explanation
Indices: 268524--268567 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 17
268514 ATTGGATGAA
268524 AATATTTTAAATTAATT
1 AATATTTTAAATTAATT
268541 -ATATTTT--ATT--TT
1 AATATTTTAAATTAATT
268553 AATATTTTAAATTAA
1 AATATTTTAAATTAA
268568 ATAGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 10
0.69 0.00 0.31
Matches are distributed among these distances:
12 2 0.09
13 7 0.32
14 3 0.14
15 3 0.14
16 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTTAAATTAATT
Found at i:272757 original size:16 final size:15
Alignment explanation
Indices: 272713--272765 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 15
272703 AATATAAATT
*
272713 AATAAATATTAGAATA
1 AATAAATATTA-TATA
272729 AATAAATAAATTATATA
1 AATAAAT--ATTATATA
272746 ATATAAATATTATATTA
1 A-ATAAATATTATA-TA
272763 AAT
1 AAT
272766 TCTCAGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 15 0.47
17 7 0.22
18 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AATAAATATTATATA
Found at i:273400 original size:21 final size:20
Alignment explanation
Indices: 273314--273471 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
273304 AAATGACCAA
**
273314 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
273333 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
273353 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
273373 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
273394 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
273415 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
273435 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
273456 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
273472 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:273500 original size:20 final size:20
Alignment explanation
Indices: 273438--273707 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
273428 CGATTTTCCA
* ** *
273438 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
273458 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
273478 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
273498 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
273518 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
273538 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
273558 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
273578 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
273598 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
273618 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
273638 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
273658 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
273678 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
273698 AAATCACAAC
1 AAATCGCAAC
273708 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:274429 original size:24 final size:24
Alignment explanation
Indices: 274390--274436 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
274380 AAATTTGGTC
274390 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
274414 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
274437 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:277021 original size:72 final size:72
Alignment explanation
Indices: 276933--277166 Score: 277
Period size: 72 Copynumber: 3.3 Consensus size: 72
276923 GCAACGAGAG
*
276933 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGTAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
276998 AAATGAT
66 AAATGAA
* * *
277005 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
277070 AAATGAA
66 AAATGAA
* * * * * *
277077 AATCGCAACGAGAGAATCG-TAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
277137 CG--A-GAG
64 CGAAATGAA
277143 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
277167 GCAATGCGAA
Statistics
Matches: 139, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.12
72 91 0.65
73 8 0.06
74 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:277047 original size:105 final size:103
Alignment explanation
Indices: 276919--277188 Score: 368
Period size: 105 Copynumber: 2.6 Consensus size: 103
276909 CGGAAATTAC
*
276919 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA-C-AA-GAAAATCGTAATGCGGA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAAATGAAAATCGCAA--C-G-
*
276980 AATGAAAATCGCAATGCGAAATGATAATCGCAATGCGAAATGAA
62 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
277024 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC-AAATGAAAATCGCAACGAG
* *
277089 AGAATCGTAATGCGAAATGAAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
277129 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC-AAATGAAAATCGCA
277189 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
105 123 0.80
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 10 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (103 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAAATGAAAATCGCAACGAGAA
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:277054 original size:53 final size:52
Alignment explanation
Indices: 276919--277188 Score: 388
Period size: 53 Copynumber: 5.1 Consensus size: 52
276909 CGGAAATTAC
*
276919 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
276966 AATCGTAATGCGGAAATGAAAATCGCAATGCGAAATGATAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
277024 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
277077 AATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
277129 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
277182 AATCGCA
1 AATCGCA
277189 TTGCGATTCT
Statistics
Matches: 201, Mismatches: 9, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
47 7 0.03
49 1 0.00
50 1 0.00
52 65 0.32
53 112 0.56
55 2 0.01
56 1 0.00
57 2 0.01
58 10 0.05
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:277194 original size:72 final size:68
Alignment explanation
Indices: 276900--277193 Score: 258
Period size: 72 Copynumber: 4.2 Consensus size: 68
276890 GCATTTGACT
** * * *
276900 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
276964 AAA
66 AAA
* *
276967 ATCGTAATGCGGAAATGAAAATCGCAATGCGAAATGATAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
277032 CG-AGAGA
61 CGAAGAAA
* * * * * *
277039 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGTAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
277101 CGAAATGAAA
61 CG-AA-GAAA
277111 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
277175 AAATGAAA
63 -AA-GAAA
*
277183 ATCGCATTGCG
1 ATCGCAATGCG
277194 ATTCTCTCGT
Statistics
Matches: 185, Mismatches: 23, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 31 0.17
69 4 0.02
70 1 0.01
71 21 0.11
72 106 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:277228 original size:53 final size:52
Alignment explanation
Indices: 277165--277280 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
277155 GAAATGAAAA
*
277165 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
277217 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
277270 TCGCATTGCGA
1 TCGCATTGCGA
277281 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:277243 original size:19 final size:19
Alignment explanation
Indices: 277203--277290 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
277193 GATTCTCTCG
277203 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
277223 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
277242 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
277256 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
277275 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
277291 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:277400 original size:14 final size:14
Alignment explanation
Indices: 277381--277417 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
277371 CATCAATTAC
277381 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
277395 ACAAATCATCTTTT
1 ACAAATCAACTTTT
277409 ACAAATCAA
1 ACAAATCAA
277418 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:279382 original size:19 final size:19
Alignment explanation
Indices: 279342--279462 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
279332 TAGTTTACTT
* *
279342 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
279362 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
279381 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
279400 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
279414 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
279433 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
279452 TCGCAATGCGA
1 TCGCAACGCGA
279463 TTTTGGTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
14 8 0.09
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:279480 original size:19 final size:19
Alignment explanation
Indices: 279458--279586 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
279448 AAAATCGCAA
279458 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
279477 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
279491 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
279510 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
279524 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
279543 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
279562 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
279582 TGCGA
1 TGCGA
279587 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:279500 original size:33 final size:33
Alignment explanation
Indices: 279458--279549 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
279448 AAAATCGCAA
279458 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
279491 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
279524 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
279550 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:279750 original size:93 final size:93
Alignment explanation
Indices: 279634--280288 Score: 1294
Period size: 93 Copynumber: 7.1 Consensus size: 93
279624 ATGGATTGCA
279634 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279698 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
279726 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279791 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
279819 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279884 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
279912 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
279977 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280005 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
280070 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280098 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
280163 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280191 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
280256 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
280284 TTACT
1 TTACT
280289 AAGCAATCTA
Statistics
Matches: 561, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 557 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:282014 original size:14 final size:14
Alignment explanation
Indices: 281995--282084 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
281985 TTGAAATGAA
281995 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
282009 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
282028 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
282042 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
282061 AATCGCAACGAGAG
1 AATCGCAACGAGAG
282075 AATCGCAACG
1 AATCGCAACG
282085 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:282032 original size:33 final size:33
Alignment explanation
Indices: 281987--282101 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
281977 TCTTTTGGTT
281987 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
282020 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
282053 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
282086 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
282102 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:282033 original size:19 final size:19
Alignment explanation
Indices: 282009--282106 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
281999 GCAACGAGAG
*
282009 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
282028 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
282042 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
282061 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
282075 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
282094 AATCGCAATGCGA
1 AATCGCAACGCGA
282107 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:282182 original size:41 final size:41
Alignment explanation
Indices: 282125--282202 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
282115 TCGCGTTGCG
*
282125 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
282166 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
282203 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:282187 original size:20 final size:21
Alignment explanation
Indices: 282126--282201 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
282116 CGCGTTGCGA
282126 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
282147 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
282167 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
282188 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
282202 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:282323 original size:33 final size:33
Alignment explanation
Indices: 282281--282351 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
282271 AATACTAACT
*
282281 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
282314 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
282347 TGAAA
1 TGAAA
282352 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:282585 original size:22 final size:22
Alignment explanation
Indices: 282533--282587 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
282523 TGGTTGTGAG
**
282533 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
282555 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
282577 GGATTTCTTCG
1 GGATTTCTTCG
282588 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:282759 original size:20 final size:20
Alignment explanation
Indices: 282734--282848 Score: 160
Period size: 20 Copynumber: 5.7 Consensus size: 20
282724 CTTTAAATAT
282734 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
282754 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
282776 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
282795 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
282815 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
282835 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
282849 TGTGTTCACG
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:282832 original size:40 final size:40
Alignment explanation
Indices: 282736--282891 Score: 183
Period size: 40 Copynumber: 3.9 Consensus size: 40
282726 TTAAATATCG
* *
282736 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTA-T
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGGA-TACA
* *
282777 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGGATACA
*
282817 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATG-GATACA
* ** *
282857 CGTTGCGATTTTCATATTCGCGTTGCGATTT-TGGA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGGA
282892 AAATCGCAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 67 0.66
41 29 0.29
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGGATACA
Found at i:282860 original size:20 final size:20
Alignment explanation
Indices: 282736--282867 Score: 142
Period size: 20 Copynumber: 6.5 Consensus size: 20
282726 TTAAATATCG
*
282736 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* * *
282756 CGTTGCGATTTTATGTATTA-T
1 CGTTGCGA-TTTACGGA-TACA
*
282777 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
*
282797 CGTTGCGATATACGGATACA
1 CGTTGCGATTTACGGATACA
*
282817 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACA
* *
282837 CGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACG-GATACA
282857 CGTTGCGATTT
1 CGTTGCGATTT
282868 TCATATTCGC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.02
20 76 0.80
21 15 0.16
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACA
Found at i:282880 original size:20 final size:19
Alignment explanation
Indices: 282835--282888 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
282825 TTTACGGATA
* *
282835 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
*
282855 CACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
282875 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
282889 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:282904 original size:21 final size:21
Alignment explanation
Indices: 282874--282956 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
282864 ATTTTCATAT
*
282874 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
282895 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
282916 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
282937 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
282957 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:283327 original size:144 final size:144
Alignment explanation
Indices: 283145--283432 Score: 450
Period size: 144 Copynumber: 2.0 Consensus size: 144
283135 TCTTAAAGTA
* * * *
283145 CATAAAACAACATAATAAAATACATAATTAAAGTCTAGAAACATAAATGACAAACATATAATGTT
1 CATAAAACAACATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
* *
283210 TTTGTTCTTTGGCACAATATTCTAAAATTTAAAGCAATACTTATGACATCTGATACTCCAGTATT
66 TTTGTTCTTTGGCACAACATTCTAAAATTTAAAGCAATACTTATGACATCTAATACTCCAGTATT
283275 ACAATCATCATTCT
131 ACAATCATCATTCT
*
283289 CATAAAACACCATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
1 CATAAAACAACATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
* * * * * *
283354 TTTGTTCTTTGGCACAACATTCTCAAATTTCATGCAATATTTGTGACATCTAATACTCTAGTATT
66 TTTGTTCTTTGGCACAACATTCTAAAATTTAAAGCAATACTTATGACATCTAATACTCCAGTATT
*
283419 ACACTCATCATTCT
131 ACAATCATCATTCT
283433 TTATTTCCTC
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
144 130 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (144 bp):
CATAAAACAACATAATAAAAAACATAATTAAAGCCTAGAAACATAAATGACAAACACATAATATT
TTTGTTCTTTGGCACAACATTCTAAAATTTAAAGCAATACTTATGACATCTAATACTCCAGTATT
ACAATCATCATTCT
Found at i:285748 original size:16 final size:17
Alignment explanation
Indices: 285710--285757 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
285700 TGTTTATGAG
285710 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGT-AA
*
285728 GGAATTGGAATCTGT-A
1 GGAATTGGAATATGTAA
*
285744 GGAATTAGAATATG
1 GGAATTGGAATATG
285758 AATCTGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.31, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATATGTAA
Found at i:286352 original size:33 final size:34
Alignment explanation
Indices: 286300--286402 Score: 165
Period size: 33 Copynumber: 3.1 Consensus size: 34
286290 TTTTCACCCT
286300 AAACCCGAACCCGACCCGAATATCACACTTAAAAA
1 AAACCCGAA-CCGACCCGAATATCACACTTAAAAA
*
286335 AAACCCG-ACCGACCCGAATATCATACTT-AAAA
1 AAACCCGAACCGACCCGAATATCACACTTAAAAA
*
286367 AAATCCGAACCGACCCGAATATCACACTTAAAAA
1 AAACCCGAACCGACCCGAATATCACACTTAAAAA
286401 AA
1 AA
286403 CCCATTCCGA
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
32 10 0.16
33 39 0.62
34 7 0.11
35 7 0.11
ACGTcount: A:0.47, C:0.31, G:0.09, T:0.14
Consensus pattern (34 bp):
AAACCCGAACCGACCCGAATATCACACTTAAAAA
Found at i:286413 original size:33 final size:31
Alignment explanation
Indices: 286310--286417 Score: 144
Period size: 33 Copynumber: 3.3 Consensus size: 31
286300 AAACCCGAAC
286310 CCGACCCGAATATCACACTTAAAAAAAACCCGA
1 CCGACCCGAATATCACACTT-AAAAAAACCC-A
* *
286343 CCGACCCGAATATCATACTTAAAAAAATCCGAA
1 CCGACCCGAATATCACACTTAAAAAAA-CC-CA
286376 CCGACCCGAATATCACACTTAAAAAAACCCA
1 CCGACCCGAATATCACACTTAAAAAAACCCA
286407 TTCCGACCCGA
1 --CCGACCCGA
286418 TCCCAAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
31 1 0.01
32 9 0.13
33 57 0.85
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (31 bp):
CCGACCCGAATATCACACTTAAAAAAACCCA
Found at i:286670 original size:64 final size:63
Alignment explanation
Indices: 286594--286724 Score: 160
Period size: 64 Copynumber: 2.1 Consensus size: 63
286584 AACTTAAACT
* * *
286594 AAACATGGGAAAGTGGTG-GAATTGGATTC-ATATTCCCCCTAATTCCAAAG-GATTCCAGCGAA
1 AAACATGAGAAAGTGATGTG-ATTGAATTCTA-ATT-CCCCTAATT-CAAAGAGATTCCAGCGAA
286656 CC
62 CC
* *
286658 AAACATGAGAAAGTGATGTGATTGAATTCTAATTCCCCTAATTCTAAGAGATTCCAGCGAATC
1 AAACATGAGAAAGTGATGTGATTGAATTCTAATTCCCCTAATTCAAAGAGATTCCAGCGAACC
286721 AAAC
1 AAAC
286725 GTCACCTAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
62 4 0.07
63 26 0.44
64 27 0.46
65 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (63 bp):
AAACATGAGAAAGTGATGTGATTGAATTCTAATTCCCCTAATTCAAAGAGATTCCAGCGAACC
Found at i:286717 original size:63 final size:64
Alignment explanation
Indices: 286594--286724 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 64
286584 AACTTAAACT
* * *
286594 AAACATGGGAAAGTGGTGGAATTGGATTCATATTCCCCCTAATTCCAAAGGATTCCAGCGAACC
1 AAACATGAGAAAGTGATGGAATTGAATTCATATTCCCCCTAATTCCAAAGGATTCCAGCGAACC
*
286658 AAACATGAGAAAGTGATGTG-ATTGAATTC-TAATT-CCCCTAATT-CTAAGAGATTCCAGCGAA
1 AAACATGAGAAAGTGATG-GAATTGAATTCAT-ATTCCCCCTAATTCCAAAG-GATTCCAGCGAA
*
286719 TC
63 CC
286721 AAAC
1 AAAC
286725 GTCACCTAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
62 4 0.07
63 27 0.46
64 27 0.46
65 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (64 bp):
AAACATGAGAAAGTGATGGAATTGAATTCATATTCCCCCTAATTCCAAAGGATTCCAGCGAACC
Found at i:288020 original size:17 final size:17
Alignment explanation
Indices: 287998--288031 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
287988 AATTTTTTAT
*
287998 TTTTATTTTAAATATTA
1 TTTTATATTAAATATTA
288015 TTTTATATTAAATATTA
1 TTTTATATTAAATATTA
288032 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATATTAAATATTA
Found at i:295176 original size:18 final size:18
Alignment explanation
Indices: 295136--295177 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
295126 TATCTCTTTC
*
295136 AATTATTTATTTTTTATT
1 AATTTTTTATTTTTTATT
*
295154 GATTTTTTA-TTTTTATTT
1 AATTTTTTATTTTTTA-TT
295172 AATTTT
1 AATTTT
295178 AGTTTATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
AATTTTTTATTTTTTATT
Found at i:295822 original size:21 final size:23
Alignment explanation
Indices: 295779--295822 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
295769 ATTAGATTAT
*
295779 AACTTTTTAATTATTATAGGTTA
1 AACTTTTTAATTAATATAGGTTA
*
295802 AACTTTTT-A-TAATATATGTTA
1 AACTTTTTAATTAATATAGGTTA
295823 TATTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (23 bp):
AACTTTTTAATTAATATAGGTTA
Found at i:299263 original size:36 final size:36
Alignment explanation
Indices: 299209--299316 Score: 148
Period size: 36 Copynumber: 3.0 Consensus size: 36
299199 AGGCAATATT
* *
299209 GTTGGACTAGCCATAAACTCTG-ACTATAGACAGTAA
1 GTTGGAGTAGCCACAAACTCTGAAC-ATAGACAGTAA
* *
299245 GTTGGAGTAGTCACAAACTCCGAACATAGACAGTAA
1 GTTGGAGTAGCCACAAACTCTGAACATAGACAGTAA
299281 GTTGGAGTAGCCACAAACT-TCGAACATAGACAGTAA
1 GTTGGAGTAGCCACAAACTCT-GAACATAGACAGTAA
299317 AACGGACATG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
36 62 0.97
37 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (36 bp):
GTTGGAGTAGCCACAAACTCTGAACATAGACAGTAA
Found at i:319552 original size:21 final size:21
Alignment explanation
Indices: 319528--319567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
319518 ATCTTATTAA
319528 TTAT-ATTTAATTAATATTTCT
1 TTATAATTT-ATTAATATTTCT
*
319549 TTATAATTTTTTAATATTT
1 TTATAATTTATTAATATTT
319568 TTATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATAATTTATTAATATTTCT
Found at i:335099 original size:3 final size:3
Alignment explanation
Indices: 335091--335137 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
335081 TAGTCATTTA
335091 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
335138 TTTGTAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:340739 original size:208 final size:210
Alignment explanation
Indices: 340379--340796 Score: 822
Period size: 208 Copynumber: 2.0 Consensus size: 210
340369 AGTCGAAGAC
340379 ATTCTAATGGTGACCGGATTCCACAACAAAGCCCCTCAATTCAGATTCGTGCATCGGCGGAATGT
1 ATTCTAATGGTGACCGGATTCCACAACAAAGCCCCTCAATTCAGATTCGTGCATCGGCGGAATGT
340444 TGTTTTAAGCATCGACACAGACAAAACCAACGAGGAGGACCTGTTAAAGGCAGTGACAAAGGCAA
66 TGTTTTAAGCATCGACACAGACAAAACCAACGAGGAGGACCTGTTAAAGGCAGTGACAAAGGCAA
340509 AGGTCATAGTCGAGTCGCTCGGGTTCCTGTTAATCGAGTACACAAGCTATGCCGACACTTCCTTC
131 AGGTCATAGTCGAGTCGCTCGGGTTCCTGTTAATCGAGTACACAAGCTATGCCGACACTTCCTTC
340574 ATACCAGGTCATTAT
196 ATACCAGGTCATTAT
340589 ATTCTAATGGTGACCGGATTCCACAAC-AAG-CCCTCAATTCAGATTCGTGCATCGGCGGAATGT
1 ATTCTAATGGTGACCGGATTCCACAACAAAGCCCCTCAATTCAGATTCGTGCATCGGCGGAATGT
340652 TGTTTTAAGCATCGACACAGACAAAACCAACGAGGAGGACCTGTTAAAGGCAGTGACAAAGGCAA
66 TGTTTTAAGCATCGACACAGACAAAACCAACGAGGAGGACCTGTTAAAGGCAGTGACAAAGGCAA
340717 AGGTCATAGTCGAGTCGCTCGGGTTCCTGTTAATCGAGTACACAAGCTATGCCGACACTTCCTTC
131 AGGTCATAGTCGAGTCGCTCGGGTTCCTGTTAATCGAGTACACAAGCTATGCCGACACTTCCTTC
340782 ATACCAGGTCATTAT
196 ATACCAGGTCATTAT
340797 GTTATATTCT
Statistics
Matches: 208, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
208 178 0.86
209 3 0.01
210 27 0.13
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (210 bp):
ATTCTAATGGTGACCGGATTCCACAACAAAGCCCCTCAATTCAGATTCGTGCATCGGCGGAATGT
TGTTTTAAGCATCGACACAGACAAAACCAACGAGGAGGACCTGTTAAAGGCAGTGACAAAGGCAA
AGGTCATAGTCGAGTCGCTCGGGTTCCTGTTAATCGAGTACACAAGCTATGCCGACACTTCCTTC
ATACCAGGTCATTAT
Found at i:362328 original size:12 final size:12
Alignment explanation
Indices: 362307--362340 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
362297 AATCATTTAA
362307 TTTATTTTAATT
1 TTTATTTTAATT
*
362319 TTTATCTTAATT
1 TTTATTTTAATT
362331 TTTATTTTAA
1 TTTATTTTAA
362341 ATTATGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTTTAATT
Found at i:374136 original size:17 final size:17
Alignment explanation
Indices: 374114--374153 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
374104 GTTTTTTGTA
*
374114 TTTTTTTTCTTCGTCAT
1 TTTTTTTTATTCGTCAT
* *
374131 TTTTTTTTATTTGTTAT
1 TTTTTTTTATTCGTCAT
374148 TTTTTT
1 TTTTTT
374154 ACTAACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (17 bp):
TTTTTTTTATTCGTCAT
Found at i:384390 original size:152 final size:152
Alignment explanation
Indices: 384114--384406 Score: 541
Period size: 152 Copynumber: 1.9 Consensus size: 152
384104 TTTACTGAAG
384114 ATTGGATTTCAACTTTACAGCGAATGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
1 ATTGGATTTCAACTTTACAGCGAATGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
*
384179 CCCAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGA
66 CCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGA
384244 TTTCAACTTCATCACAAACAAC
131 TTTCAACTTCATCACAAACAAC
* * *
384266 ATTGGATTTCAACTTTATAGCGAATGATATCCAATTCAAAGCTCAACTTCACAGCGAATGGGCTT
1 ATTGGATTTCAACTTTACAGCGAATGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
*
384331 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
66 CCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGA
384396 TTTCAACTTCA
131 TTTCAACTTCA
384407 CGACGAAGGA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 136 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (152 bp):
ATTGGATTTCAACTTTACAGCGAATGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
CCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGA
TTTCAACTTCATCACAAACAAC
Found at i:386267 original size:12 final size:13
Alignment explanation
Indices: 386245--386273 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
386235 TGAATCAAAT
386245 TTTTAAATTTTAA
1 TTTTAAATTTTAA
386258 TTTT-AATTTTAA
1 TTTTAAATTTTAA
386270 TTTT
1 TTTT
386274 TGTAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:388064 original size:18 final size:20
Alignment explanation
Indices: 388041--388083 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
388031 ACCGGTCATA
388041 ACCCGACCCGA-CA-CGTTG
1 ACCCGACCCGATCACCGTTG
*
388059 ACCCGACCCGATGACCGTTG
1 ACCCGACCCGATCACCGTTG
388079 ACCCG
1 ACCCG
388084 TTGACCGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.21, C:0.44, G:0.23, T:0.12
Consensus pattern (20 bp):
ACCCGACCCGATCACCGTTG
Found at i:388083 original size:15 final size:15
Alignment explanation
Indices: 388063--388092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
388053 ACGTTGACCC
388063 GACCCGATGACCGTT
1 GACCCGATGACCGTT
*
388078 GACCCGTTGACCGTT
1 GACCCGATGACCGTT
388093 AACCGGCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (15 bp):
GACCCGATGACCGTT
Found at i:390573 original size:24 final size:23
Alignment explanation
Indices: 390520--390591 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
390510 ATACGTTACC
* * *
390520 TGAATTCTATTCTGATTCTGATC
1 TGAATTCTGTTATGATTCTGATA
390543 T-AGATTCTGTTATGATATCTGATA
1 TGA-ATTCTGTTATGAT-TCTGATA
*
390567 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGA-TTCTGATA
390591 T
1 T
390592 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.02
23 12 0.29
24 26 0.63
25 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTATGATTCTGATA
Found at i:395117 original size:12 final size:12
Alignment explanation
Indices: 395079--395170 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
395069 ATTTCCGATT
395079 TGAATTCTGTTC
1 TGAATTCTGTTC
*
395091 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
395103 TGAATTCTGTTC
1 TGAATTCTGTTC
*
395115 TG-ATTCTGATC
1 TGAATTCTGTTC
*
395126 TGGATTCTGTTC
1 TGAATTCTGTTC
* * *
395138 TGAAATCTGATA
1 TGAATTCTGTTC
*
395150 TGAATTCTGTTT
1 TGAATTCTGTTC
*
395162 TGATTTCTG
1 TGAATTCTG
395171 ATATCTTCGT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
10 3 0.05
11 13 0.21
12 41 0.65
13 3 0.05
14 3 0.05
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:395170 original size:24 final size:23
Alignment explanation
Indices: 395065--395174 Score: 96
Period size: 24 Copynumber: 4.6 Consensus size: 23
395055 AAATATTTTA
* *
395065 TCTGATTTCCGATTTGAATTCTGT
1 TCTGA-TTCTGATATGAATTCTGT
* *
395089 TCTGATAC-GTTACCTGAATTCTGT
1 TCTGATTCTGATA--TGAATTCTGT
* *
395113 TCTGATTCTGATCTGGATTCTGT
1 TCTGATTCTGATATGAATTCTGT
*
395136 TCTGAAATCTGATATGAATTCTGT
1 TCTG-ATTCTGATATGAATTCTGT
*
395160 TTTGATTTCTGATAT
1 TCTGA-TTCTGATAT
395175 CTTCGTTTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.03
23 16 0.23
24 49 0.71
25 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (23 bp):
TCTGATTCTGATATGAATTCTGT
Found at i:397599 original size:43 final size:43
Alignment explanation
Indices: 397550--397675 Score: 243
Period size: 43 Copynumber: 2.9 Consensus size: 43
397540 AAAAAAATAA
*
397550 ATATTTATTCGAATTACTTTTATATGTTTCATTCTTTTATCAG
1 ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTATCAG
397593 ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTATCAG
1 ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTATCAG
397636 ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTAT
1 ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTAT
397676 ACTTATTAAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56
Consensus pattern (43 bp):
ATATTTAGTCGAATTACTTTTATATGTTTCATTCTTTTATCAG
Found at i:431431 original size:7 final size:7
Alignment explanation
Indices: 431419--431510 Score: 75
Period size: 7 Copynumber: 13.4 Consensus size: 7
431409 CTAAATTGAT
431419 AACCCTA
1 AACCCTA
431426 AACCCTA
1 AACCCTA
*
431433 AACCAT-
1 AACCCTA
*
431439 AACATCTA
1 AAC-CCTA
431447 AACCCTA
1 AACCCTA
*
431454 AACTCTA
1 AACCCTA
*
431461 AACCAT-
1 AACCCTA
*
431467 AACATCTA
1 AAC-CCTA
431475 AACCCTA
1 AACCCTA
*
431482 TA-CCTA
1 AACCCTA
431488 AA-CCTA
1 AACCCTA
*
431494 AACTCTA
1 AACCCTA
431501 AACCCTA
1 AACCCTA
431508 AAC
1 AAC
431511 TTAAAATGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
6 17 0.26
7 43 0.65
8 6 0.09
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCCTA
Found at i:431436 original size:14 final size:14
Alignment explanation
Indices: 431419--431515 Score: 105
Period size: 14 Copynumber: 7.1 Consensus size: 14
431409 CTAAATTGAT
*
431419 AACCCTAAACCCTA
1 AACCCTAAACTCTA
*
431433 AACCAT-AACATCTA
1 AACCCTAAAC-TCTA
431447 AACCCTAAACTCTA
1 AACCCTAAACTCTA
*
431461 AACCAT-AACATCTA
1 AACCCTAAAC-TCTA
*
431475 AACCCTATAC-CTA
1 AACCCTAAACTCTA
431488 AA-CCTAAACTCTA
1 AACCCTAAACTCTA
431501 AACCCTAAACT-TA
1 AACCCTAAACTCTA
431514 AA
1 AA
431516 ATGATACAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
12 6 0.09
13 20 0.29
14 39 0.56
15 5 0.07
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAACTCTA
Found at i:431450 original size:28 final size:28
Alignment explanation
Indices: 431419--431510 Score: 136
Period size: 28 Copynumber: 3.4 Consensus size: 28
431409 CTAAATTGAT
431419 AACCCTAAACCCTAAACCATAACATCTA
1 AACCCTAAACCCTAAACCATAACATCTA
*
431447 AACCCTAAACTCTAAACCATAACATCTA
1 AACCCTAAACCCTAAACCATAACATCTA
*
431475 AACCCTATA-CCTAAACC-TAA-ACTCTA
1 AACCCTAAACCCTAAACCATAACA-TCTA
431501 AACCCTAAAC
1 AACCCTAAAC
431511 TTAAAATGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
25 1 0.02
26 15 0.26
27 7 0.12
28 35 0.60
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.20
Consensus pattern (28 bp):
AACCCTAAACCCTAAACCATAACATCTA
Found at i:434127 original size:20 final size:20
Alignment explanation
Indices: 434102--434141 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
434092 CAGCAATCAA
434102 ACTTTACTTACAATCTCCAT
1 ACTTTACTTACAATCTCCAT
434122 ACTTTACTTACAATCTCCAT
1 ACTTTACTTACAATCTCCAT
434142 CTGTATTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTTACTTACAATCTCCAT
Found at i:437052 original size:21 final size:20
Alignment explanation
Indices: 437019--437062 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
437009 AAATGTAATT
*
437019 TAATAAATGTTAT-TTCATTA
1 TAATAAATATTATATTCA-TA
437039 TAATAAAATATTATATTCATA
1 TAAT-AAATATTATATTCATA
437060 TAA
1 TAA
437063 GAGTAAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAAATATTATATTCATA
Found at i:440467 original size:26 final size:28
Alignment explanation
Indices: 440437--440498 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
440427 AAAAATTTTT
440437 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
440463 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
440494 AGCTC
1 AGCTC
440499 AGCAATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:443378 original size:24 final size:24
Alignment explanation
Indices: 443341--443392 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
443331 ACAATTAAAG
443341 AAAT-TAAATAATTTTTTATTTTT
1 AAATATAAATAATTTTTTATTTTT
* *
443364 TAATATAAATTATTTTTTATTTTT
1 AAATATAAATAATTTTTTATTTTT
443388 AAATA
1 AAATA
443393 ATACCACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AAATATAAATAATTTTTTATTTTT
Found at i:444394 original size:18 final size:20
Alignment explanation
Indices: 444367--444417 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
444357 ATAAAGTTCT
*
444367 TAAAAATTATTATTAT-C-A
1 TAAAATTTATTATTATACTA
444385 TAAAATTTATTGA-TATACTA
1 TAAAATTTATT-ATTATACTA
*
444405 TAAGATTTATTAT
1 TAAAATTTATTAT
444418 ATTTCTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 13 0.48
19 3 0.11
20 11 0.41
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAAATTTATTATTATACTA
Found at i:448636 original size:2 final size:2
Alignment explanation
Indices: 448629--448656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
448619 ATAATAATGA
448629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
448657 TCTTTACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:448890 original size:14 final size:15
Alignment explanation
Indices: 448871--448901 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
448861 AGTGGTTAAG
448871 TATTTTATAT-TTCA
1 TATTTTATATGTTCA
448885 TATTTTATATGTTCA
1 TATTTTATATGTTCA
448900 TA
1 TA
448902 GTTAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTTTATATGTTCA
Found at i:452341 original size:3 final size:3
Alignment explanation
Indices: 452333--452365 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
452323 ACGGGAAGTC
452333 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
452366 CAAGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:452915 original size:15 final size:15
Alignment explanation
Indices: 452894--452936 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
452884 TGTCGCACCT
452894 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
*
452909 TTGAATGATTCAGTG
1 CTGAATGATTCAGTG
*
452924 CTAAATGATTCAG
1 CTGAATGATTCAG
452937 CATCAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:453013 original size:15 final size:15
Alignment explanation
Indices: 452993--453021 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
452983 GTCACATTCA
452993 GAGCTAATTCATACC
1 GAGCTAATTCATACC
453008 GAGCTAATTCATAC
1 GAGCTAATTCATAC
453022 AGAACCTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (15 bp):
GAGCTAATTCATACC
Found at i:453308 original size:56 final size:55
Alignment explanation
Indices: 453246--453350 Score: 174
Period size: 56 Copynumber: 1.9 Consensus size: 55
453236 TCCGCTACCT
* *
453246 ATATATATGTTTTGATATTATAAGACTAGGGCATGTAAATGTAACCCTAGGTATAC
1 ATATATATGTTTTGATATCATAAGACTAGAGCATGT-AATGTAACCCTAGGTATAC
*
453302 ATATATATGTTTTGGTATCATAAGACTAGAGCATGTAATGTAACCCTAG
1 ATATATATGTTTTGATATCATAAGACTAGAGCATGTAATGTAACCCTAG
453351 CTAGCTAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 13 0.28
56 33 0.72
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (55 bp):
ATATATATGTTTTGATATCATAAGACTAGAGCATGTAATGTAACCCTAGGTATAC
Found at i:461185 original size:60 final size:61
Alignment explanation
Indices: 461112--461229 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 61
461102 AATTCCCCCT
* * *
461112 TACTCGTAATTATTTTGTCATTTTAAGTATA-TTTTTTTATCAAAGTTAAATCACATGTTA
1 TACTCGTAATTATTTTATCATTTGAAGTATATTTTTTTTACCAAAGTTAAATCACATGTTA
461172 TACTCGTAATTATTTTATCATTTGAAGTATATTTTTTTTACCAAAGTTAAATCACATG
1 TACTCGTAATTATTTTATCATTTGAAGTATATTTTTTTTACCAAAGTTAAATCACATG
461230 CTATTGTAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 29 0.54
61 25 0.46
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.48
Consensus pattern (61 bp):
TACTCGTAATTATTTTATCATTTGAAGTATATTTTTTTTACCAAAGTTAAATCACATGTTA
Found at i:465599 original size:21 final size:21
Alignment explanation
Indices: 465570--465614 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
465560 GATTTCTGGG
* *
465570 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
465591 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
465612 CAA
1 CAA
465615 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:467483 original size:103 final size:103
Alignment explanation
Indices: 467291--467606 Score: 542
Period size: 103 Copynumber: 3.1 Consensus size: 103
467281 GGGTCTACGC
*
467291 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
467356 CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
* *
467394 GGTTCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
467459 CCTTGGCATATGTATATGATTCTTAATGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
467497 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * * *
467562 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
*
467600 AGTCCTT
1 GGTCCTT
467607 ATGGACATTA
Statistics
Matches: 201, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 201 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATAT
Found at i:467656 original size:23 final size:23
Alignment explanation
Indices: 467623--467666 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
467613 ATTATTATAT
467623 GGCACTACGGTGCAATTCTACAC
1 GGCACTACGGTGCAATTCTACAC
* *
467646 GGCACTCCGGTGTAATTCTAC
1 GGCACTACGGTGCAATTCTAC
467667 GTAGCACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:467673 original size:23 final size:23
Alignment explanation
Indices: 467624--467685 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
467614 TTATTATATG
*
467624 GCACTACGGTGCAATTCTACACG
1 GCACTACGGTGCAATTCTACACA
* * **
467647 GCACTCCGGTGTAATTCTACGTA
1 GCACTACGGTGCAATTCTACACA
* *
467670 GCACTTCGGTACAATT
1 GCACTACGGTGCAATT
467686 ATACGAGCTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACACA
Found at i:470040 original size:2 final size:2
Alignment explanation
Indices: 470033--470057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
470023 CATGATATGA
470033 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
470058 AAGGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:470954 original size:21 final size:21
Alignment explanation
Indices: 470928--470972 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
470918 GATTTCTGGG
* *
470928 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
470949 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
470970 CAA
1 CAA
470973 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:474258 original size:33 final size:33
Alignment explanation
Indices: 474213--474283 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
474203 ATTCTAGAAA
*
474213 TGAAAATGGATTTTGAA-AATCAAAATGAAATCT
1 TGAAAATGGATTTAGAACAATCAAAATGAAAT-T
**
474246 TGAAGAAT-GATTTAGAACTCTCAAAATGAAATT
1 TGAA-AATGGATTTAGAACAATCAAAATGAAATT
474279 TGAAA
1 TGAAA
474284 GTATTGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
32 1 0.03
33 17 0.52
34 15 0.45
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (33 bp):
TGAAAATGGATTTAGAACAATCAAAATGAAATT
Found at i:478181 original size:20 final size:22
Alignment explanation
Indices: 478144--478204 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
478134 ATTTTGGTGC
* *
478144 AGAGAGAATCGATCCCCCCATG-
1 AGAG-GAACCGATTCCCCCATGA
**
478166 AG-GGAACCGATTCCCCTTTGA
1 AGAGGAACCGATTCCCCCATGA
478187 AGAGGAACCGATTCCCCC
1 AGAGGAACCGATTCCCCC
478205 CAGGGGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 13 0.41
21 3 0.09
22 16 0.50
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (22 bp):
AGAGGAACCGATTCCCCCATGA
Found at i:478217 original size:19 final size:19
Alignment explanation
Indices: 478190--478229 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
478180 CCTTTGAAGA
*
478190 GGAACCGATTCCCCCCAGG
1 GGAACCGATACCCCCCAGG
* *
478209 GGAATCGATACCCCCCTGG
1 GGAACCGATACCCCCCAGG
478228 GG
1 GG
478230 TTCTGTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.38, G:0.30, T:0.12
Consensus pattern (19 bp):
GGAACCGATACCCCCCAGG
Found at i:482053 original size:103 final size:103
Alignment explanation
Indices: 481730--482045 Score: 569
Period size: 103 Copynumber: 3.1 Consensus size: 103
481720 GGGTCTACGC
* *
481730 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAACTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
481795 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
481833 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
481898 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
481936 GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
482001 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
482039 AGTCCTT
1 GGTCCTT
482046 ATGGACATTA
Statistics
Matches: 205, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:482095 original size:23 final size:23
Alignment explanation
Indices: 482062--482129 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
482052 ATTATTATAT
482062 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
482085 GGCACTCCGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
* *
482108 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
482130 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:487680 original size:81 final size:81
Alignment explanation
Indices: 487450--487685 Score: 235
Period size: 81 Copynumber: 2.9 Consensus size: 81
487440 TCATTTTTGG
* * * * **
487450 GAAAACGCCGCTAAACCT-CGTACTTTAGAGGTGTTTATGTAAACAATTCTGTGATAGCCAGATA
1 GAAAACGCCGCTAAA-ATGCGTACTTTAGTGGTGTTTATGTAAAAAATACTGCAATAGCCAGATA
487514 TATAGTGGTGTTTTCGT
65 TATAGTGGTGTTTTCGT
* * * * * * * *
487531 GAAAATGCCGTTAAAAATGCGGACTTTAGTAGCGTTTATGTAAAAAATAATGCTATAGCCAGAGA
1 GAAAACGCCGCT-AAAATGCGTACTTTAGTGGTGTTTATGTAAAAAATACTGCAATAGCCAGATA
487596 TATAGTGGCT-TTTT-GT
65 TATAGTGG-TGTTTTCGT
** * * **
487612 TTAAACGCCGCTACAAATGCGTACTTTAGTGGTGTTTATGTAAAAAATACGGCAATATCTTGATA
1 GAAAACGCCGCTA-AAATGCGTACTTTAGTGGTGTTTATGTAAAAAATACTGCAATAGCCAGATA
487677 TATAGTGGT
65 TATAGTGGT
487686 CATTGTTTTG
Statistics
Matches: 124, Mismatches: 27, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
80 2 0.02
81 70 0.56
82 51 0.41
83 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Consensus pattern (81 bp):
GAAAACGCCGCTAAAATGCGTACTTTAGTGGTGTTTATGTAAAAAATACTGCAATAGCCAGATAT
ATAGTGGTGTTTTCGT
Found at i:488534 original size:22 final size:21
Alignment explanation
Indices: 488509--488549 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
488499 TATACAAAAT
488509 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
488531 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
488550 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:488862 original size:19 final size:17
Alignment explanation
Indices: 488824--488857 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
488814 TCTCAAAACG
488824 CCGCCAAAGTATAAATA
1 CCGCCAAAGTATAAATA
488841 CCGCCAAAGTATAAATA
1 CCGCCAAAGTATAAATA
488858 TACCGATCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
CCGCCAAAGTATAAATA
Found at i:491016 original size:22 final size:22
Alignment explanation
Indices: 490991--491055 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
490981 TGTTCCCTTA
490991 GAATGTGTATGAGTCAGCTTTG
1 GAATGTGTATGAGTCAGCTTTG
* * **
491013 GAATGCGCA-GAGCTTTTGC-TTG
1 GAATGTGTATGAG--TCAGCTTTG
491035 GAATGTGTATGAGTCAGCTTT
1 GAATGTGTATGAGTCAGCTTT
491056 ATAAACCTCC
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
21 6 0.19
22 19 0.61
23 6 0.19
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (22 bp):
GAATGTGTATGAGTCAGCTTTG
Found at i:496036 original size:21 final size:20
Alignment explanation
Indices: 496010--496052 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
496000 TTTAACTTTT
496010 GCAACGCGAAAAATCAAATTC
1 GCAACGCG-AAAATCAAATTC
* *
496031 GCAACGTGAAAGTCAAATTC
1 GCAACGCGAAAATCAAATTC
496051 GC
1 GC
496053 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAATCAAATTC
Found at i:498580 original size:24 final size:24
Alignment explanation
Indices: 498546--498599 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
498536 ATGAAACATC
498546 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
498570 ATCAAAGTCCGGGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
498594 ATCAAA
1 ATCAAA
498600 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:499516 original size:20 final size:21
Alignment explanation
Indices: 499493--499580 Score: 94
Period size: 20 Copynumber: 4.4 Consensus size: 21
499483 AAACATTTGT
*
499493 GTTGCGAAATT-AAAATTCGT
1 GTTGCGAAATTCAAAATTCGA
* *
499513 GTTGCGAATTTGAAAA-TCGA
1 GTTGCGAAATTCAAAATTCGA
* *
499533 GTTGCGAAA-ACAAAATTCGC
1 GTTGCGAAATTCAAAATTCGA
*
499553 GTTGCG-AATTCAAAAATCGA
1 GTTGCGAAATTCAAAATTCGA
499573 GTTGCGAA
1 GTTGCGAA
499581 TTTGGAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.11
20 44 0.80
21 5 0.09
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (21 bp):
GTTGCGAAATTCAAAATTCGA
Found at i:499548 original size:40 final size:40
Alignment explanation
Indices: 499493--499580 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
499483 AAACATTTGT
** * **
499493 GTTGCGAAATTAAAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAAAAATCGA
499533 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAAAAATCGA
1 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAAAAATCGA
499573 GTTGCGAA
1 GTTGCGAA
499581 TTTGGAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGCGTTGCGAATTCAAAAATCGA
Found at i:500229 original size:20 final size:19
Alignment explanation
Indices: 500176--500244 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
500166 ATTATTTTGA
* *
500176 TATTAATTAAATTAGATAT
1 TATTATTTAAATTATATAT
* *
500195 TTTTATATAATATTATATAT
1 TATTATTTAA-ATTATATAT
*
500215 TATTACTTTAAATTATGTAT
1 TATTA-TTTAAATTATATAT
*
500235 TATTTTTTAA
1 TATTATTTAA
500245 GAATATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 12 0.30
20 24 0.60
21 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTATTTAAATTATATAT
Found at i:501993 original size:2 final size:2
Alignment explanation
Indices: 501986--502022 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
501976 ATTTGGAAAT
501986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
502023 CAATTGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:502091 original size:2 final size:2
Alignment explanation
Indices: 502084--502133 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
502074 GTGATCCAAC
502084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
502126 AT AT AT AT
1 AT AT AT AT
502134 CATTTAACCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505360 original size:36 final size:36
Alignment explanation
Indices: 505310--505533 Score: 331
Period size: 36 Copynumber: 6.2 Consensus size: 36
505300 TGAATAAGAA
* * * *
505310 GAACGAAAGAAAGCATCGGTACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* *
505346 GAACGGAATGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
505382 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* *
505418 GAACGGAAGGAGGCATCGGCACTTCCAATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* * *
505454 GAACGGAAGGAAACATCGACACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
505490 GAACGGAATGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
505526 GAACGGAA
1 GAACGGAA
505534 AGATGTATTA
Statistics
Matches: 167, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 167 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
Found at i:505406 original size:72 final size:72
Alignment explanation
Indices: 505310--505533 Score: 367
Period size: 72 Copynumber: 3.1 Consensus size: 72
505300 TGAATAAGAA
* * * *
505310 GAACGAAAGAAAGCATCGGTACTTCCGATTCAAGTTGAACGGAATGAAGCATCGACACTTCCGAT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTTGAACGGAATGAAGCATCGGCACTTCCGAT
505375 TCAAGTC
66 TCAAGTC
* * *
505382 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTTGAACGGAAGGAGGCATCGGCACTTCCAAT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTTGAACGGAATGAAGCATCGGCACTTCCGAT
505447 TCAAGTC
66 TCAAGTC
* *
505454 GAACGGAAGGAAACATCGACACTTCCGATTCAAGTTGAACGGAATGAAGCATCGGCACTTCCGAT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTTGAACGGAATGAAGCATCGGCACTTCCGAT
505519 TCAAGTC
66 TCAAGTC
505526 GAACGGAA
1 GAACGGAA
505534 AGATGTATTA
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 140 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (72 bp):
GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTTGAACGGAATGAAGCATCGGCACTTCCGAT
TCAAGTC
Found at i:506525 original size:14 final size:14
Alignment explanation
Indices: 506503--506532 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
506493 TTTGTTAAGC
506503 CTAACAGACTCTAA
1 CTAACAGACTCTAA
*
506517 CTAATAGACTCTAA
1 CTAACAGACTCTAA
506531 CT
1 CT
506533 GAATCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (14 bp):
CTAACAGACTCTAA
Found at i:510000 original size:18 final size:18
Alignment explanation
Indices: 509979--510067 Score: 97
Period size: 18 Copynumber: 4.9 Consensus size: 18
509969 ATTATCGTAA
*
509979 GAAGCACGATGATCATTG
1 GAAGCACGATTATCATTG
* *
509997 GAAGCACGATTATCGTAG
1 GAAGCACGATTATCATTG
* ** * *
510015 GAAGGACGACGACCATTA
1 GAAGCACGATTATCATTG
*
510033 GAAACACGATTATCATTG
1 GAAGCACGATTATCATTG
510051 GAAGCACGATTATCATT
1 GAAGCACGATTATCATT
510068 TGTGACACAG
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (18 bp):
GAAGCACGATTATCATTG
Found at i:510008 original size:36 final size:36
Alignment explanation
Indices: 509968--510067 Score: 119
Period size: 36 Copynumber: 2.8 Consensus size: 36
509958 TAGGAAGTCT
* * *
509968 GATTATCGTAAGAAGCACGATGATCATTGGAAGCAC
1 GATTATCGTAGGAAGCACGATGATCATTAGAAACAC
* * *
510004 GATTATCGTAGGAAGGACGACGACCATTAGAAACAC
1 GATTATCGTAGGAAGCACGATGATCATTAGAAACAC
* * *
510040 GATTATCATTGGAAGCACGATTATCATT
1 GATTATCGTAGGAAGCACGATGATCATT
510068 TGTGACACAG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (36 bp):
GATTATCGTAGGAAGCACGATGATCATTAGAAACAC
Found at i:511137 original size:14 final size:14
Alignment explanation
Indices: 511118--511147 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
511108 TTTGTTAAGC
511118 CTAACAGACTCTAA
1 CTAACAGACTCTAA
511132 CTAACAGACTCTAA
1 CTAACAGACTCTAA
511146 CT
1 CT
511148 GAATCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (14 bp):
CTAACAGACTCTAA
Found at i:514047 original size:31 final size:31
Alignment explanation
Indices: 514012--514080 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
514002 TATAACTATG
* * *
514012 ATTTGATCCTTTCAAAAATTATAAAATTACA
1 ATTTGATCCATCCAAAAAATATAAAATTACA
514043 ATTTGAT-CATCCAAAAAATATAAAATTACA
1 ATTTGATCCATCCAAAAAATATAAAATTACA
*
514073 AATTGATC
1 ATTTGATC
514081 AGACCATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (31 bp):
ATTTGATCCATCCAAAAAATATAAAATTACA
Found at i:514065 original size:30 final size:30
Alignment explanation
Indices: 514024--514081 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
514014 TTGATCCTTT
* *
514024 CAAAAATTATAAAATTACAATTTGATCATC
1 CAAAAAATATAAAATTACAAATTGATCATC
514054 CAAAAAATATAAAATTACAAATTGATCA
1 CAAAAAATATAAAATTACAAATTGATCA
514082 GACCATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAAAAATATAAAATTACAAATTGATCATC
Found at i:514638 original size:23 final size:23
Alignment explanation
Indices: 514612--514659 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
514602 ATAAAGTACA
*
514612 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
514635 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
514658 AT
1 AT
514660 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:515072 original size:20 final size:21
Alignment explanation
Indices: 515034--515073 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
515024 TCCACAGTGA
* *
515034 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
515055 AAAAAGGATAGACA-TTTTA
1 AAAAAGGATAGACACTTTTA
515074 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:515111 original size:23 final size:23
Alignment explanation
Indices: 515076--515125 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
515066 ACATTTTACA
*
515076 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATC
* *
515099 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATC
515122 ATAT
1 ATAT
515126 GTTTACCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATC
Found at i:515522 original size:25 final size:25
Alignment explanation
Indices: 515465--515530 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
515455 TCACTCAAAG
*
515465 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
515490 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
515515 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
515531 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:518519 original size:183 final size:182
Alignment explanation
Indices: 517995--518486 Score: 878
Period size: 183 Copynumber: 2.7 Consensus size: 182
517985 TTAAAATTAC
*
517995 CGACACTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 CGACACTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
* *
518060 TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
* *
518125 TATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 TATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
518177 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
518242 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
518307 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
518360 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTT-A-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
518424 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
64 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
518487 ATAGCATTGC
Statistics
Matches: 297, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
182 10 0.03
183 284 0.96
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (182 bp):
CGACACTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:518554 original size:25 final size:25
Alignment explanation
Indices: 518526--518617 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
518516 TAATATGTTG
518526 AAAGGATCGATACTTTTTTTGTTAA
1 AAAGGATCGATACTTTTTTTGTTAA
** *
518551 AAAGTTTCCATACTTTTTTTGTTAA
1 AAAGGATCGATACTTTTTTTGTTAA
** * *
518576 AAAGTTTCTATAC--TTTTT-ATAA
1 AAAGGATCGATACTTTTTTTGTTAA
518598 AAAGGATCGATACTTTTTTT
1 AAAGGATCGATACTTTTTTT
518618 AAAGATATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.23
23 5 0.09
24 5 0.09
25 34 0.60
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (25 bp):
AAAGGATCGATACTTTTTTTGTTAA
Found at i:518567 original size:24 final size:25
Alignment explanation
Indices: 518535--518593 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
518525 GAAAGGATCG
518535 ATACTTTTTTTGTTAAAAAGTTTCC
1 ATACTTTTTTTGTTAAAAAGTTTCC
*
518560 ATACTTTTTTTGTTAAAAAGTTTCT
1 ATACTTTTTTTGTTAAAAAGTTTCC
518585 ATACTTTTT
1 ATACTTTTT
518594 ATAAAAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (25 bp):
ATACTTTTTTTGTTAAAAAGTTTCC
Found at i:518598 original size:22 final size:22
Alignment explanation
Indices: 518541--518620 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
518531 ATCGATACTT
518541 TTTTTGTTAAAAAGTTTCCATAC
1 TTTTT-TTAAAAAGTTTCCATAC
*
518564 TTTTTTTGTTAAAAAGTTTCTATAC
1 --TTTTT-TTAAAAAGTTTCCATAC
* ** *
518589 TTTTTATAAAAAGGATCGATAC
1 TTTTTTTAAAAAGTTTCCATAC
518611 TTTTTTTAAA
1 TTTTTTTAAA
518621 GATATGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 22 0.45
23 5 0.10
25 22 0.45
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTTTTAAAAAGTTTCCATAC
Found at i:520044 original size:3 final size:3
Alignment explanation
Indices: 520036--520116 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
520026 ACTTGTTTGG
* * * * **
520036 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATT GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
520084 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
520117 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:520053 original size:12 final size:12
Alignment explanation
Indices: 520040--520128 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
520030 GTTTGGATCA
* *
520040 TCATCTTCATCA
1 TCATCGTCATCT
* *
520052 TCATCATCATCA
1 TCATCGTCATCT
* *
520064 TCGTCATCATCT
1 TCATCGTCATCT
* * *
520076 TCATTGCCAGCT
1 TCATCGTCATCT
*
520088 TCATCGTCATCA
1 TCATCGTCATCT
520100 TCATCGTCATCT
1 TCATCGTCATCT
*
520112 TCATCGTCAGCT
1 TCATCGTCATCT
520124 TCATC
1 TCATC
520129 TTCTGCGATC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:520059 original size:18 final size:18
Alignment explanation
Indices: 520036--520116 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 18
520026 ACTTGTTTGG
* *
520036 ATCATCATCTTCATCATC
1 ATCATCATCATCGTCATC
520054 ATCATCATCATCGTCATC
1 ATCATCATCATCGTCATC
* * *
520072 ATCTTCATTGCCAGCTTCATC
1 ATCATCA-T--CATCGTCATC
*
520093 GTCATCATCATCGTCATC
1 ATCATCATCATCGTCATC
*
520111 TTCATC
1 ATCATC
520117 GTCAGCTTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 35 0.70
19 1 0.02
20 1 0.02
21 13 0.26
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (18 bp):
ATCATCATCATCGTCATC
Found at i:520099 original size:36 final size:36
Alignment explanation
Indices: 520052--520128 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
520042 ATCTTCATCA
* *
520052 TCATCATCATCATCGTCATCATCTTCATTGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
520088 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
520124 TCATC
1 TCATC
520129 TTCTGCGATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:520127 original size:18 final size:18
Alignment explanation
Indices: 520070--520131 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
520060 ATCATCGTCA
* *
520070 TCATCTTCATTGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
520088 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
520106 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
520124 TCATCTTC
1 TCATCTTC
520132 TGCGATCGCT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:520131 original size:6 final size:6
Alignment explanation
Indices: 520040--520131 Score: 60
Period size: 6 Copynumber: 15.3 Consensus size: 6
520030 GTTTGGATCA
* * * * * * *
520040 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCAT-T GCCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT -TCATCT
* * * * *
520088 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
520132 TGCGATCGCT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
5 1 0.01
6 66 0.97
7 1 0.01
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:522042 original size:185 final size:184
Alignment explanation
Indices: 521711--522289 Score: 769
Period size: 185 Copynumber: 3.1 Consensus size: 184
521701 GGTTCGATGA
* *
521711 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
1 TTTTGGGTTCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCAT
521776 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
66 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
521841 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
131 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
521895 TTTTGGGTTCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCAT
1 TTTTGGGTTCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCAT
*
521960 TCTGGAAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTC
66 TCTGG-AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTC
522025 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
130 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
** * ***
522080 TTTTGGGTTCG--A-TGATT-T-T-GGGATCGACACTTTTTATATATG-ATCGACACT-TTATGG
1 TTTTGGGTTCGACACTTTTTATATATGGATCGACAC--TTTATGGGTGCAT---C-CTGTT-T--
* ****
522137 GTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACAC
57 -T----CC---ATT-CATTC--TGGAAAAAAAA--TATCGACACAAACTATATTAGTGTCGACAC
522202 ATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATA
109 ATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATA
522267 TTACATTATAC
174 TTACATTATAC
522278 TTTTGGGTTCGA
1 TTTTGGGTTCGA
522290 TGATTTGGGA
Statistics
Matches: 356, Mismatches: 15, Indels: 33
0.88 0.04 0.08
Matches are distributed among these distances:
179 10 0.03
180 3 0.01
181 8 0.02
182 3 0.01
183 4 0.01
184 71 0.20
185 124 0.35
187 1 0.00
191 2 0.01
194 2 0.01
195 5 0.01
196 6 0.02
197 1 0.00
198 116 0.33
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (184 bp):
TTTTGGGTTCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCAT
TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC
Found at i:522235 original size:198 final size:199
Alignment explanation
Indices: 521895--522546 Score: 1173
Period size: 198 Copynumber: 3.3 Consensus size: 199
521885 TACATTATAC
* *
521895 TTTTGGGTTCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
*
521960 TCTGGAAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTC
66 TCTGG-AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTC
522025 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
130 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
522090 GATGA
195 GATGA
522095 TTTTGGGATCGACACTTTTTATATAT-GATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
522159 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
66 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
522224 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
131 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
522289 ATGA
196 ATGA
522293 -TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
* *
522357 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCA
66 TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
* * *
522422 TAAAACCGGTAGACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTC
131 TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTC
*
522487 GATGT
195 GATGA
* *
522492 TTTTGGGATTGACACTTTTTATATATGTATCGACACTTTATGGGTGCACCCTGTT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
522547 GGCCATATTG
Statistics
Matches: 438, Mismatches: 11, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
197 25 0.06
198 287 0.66
199 49 0.11
200 77 0.18
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (199 bp):
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCAT
TCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCA
TAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCG
ATGA
Found at i:522696 original size:19 final size:19
Alignment explanation
Indices: 522665--522713 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
522655 TTATATTCAC
*
522665 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
* *
522684 ATGCAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
522703 ATACAAAATTA
1 ATACAAAATTA
522714 ACCCTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:524472 original size:23 final size:23
Alignment explanation
Indices: 524445--524491 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
524435 GTTCACTCCT
524445 CAAATCCACAACCTCCTTCACCA
1 CAAATCCACAACCTCCTTCACCA
524468 CAAATCCACAACCTCCTTCACCA
1 CAAATCCACAACCTCCTTCACCA
524491 C
1 C
524492 TCCCTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (23 bp):
CAAATCCACAACCTCCTTCACCA
Found at i:524562 original size:33 final size:33
Alignment explanation
Indices: 524525--524590 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
524515 CATCTTAATA
*
524525 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
524558 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
524591 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:524649 original size:21 final size:21
Alignment explanation
Indices: 524624--524688 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
524614 CCCCTTATGC
* *
524624 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
524645 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
524666 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
524687 CT
1 CT
524689 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Done.