Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008705.1 Hibiscus syriacus cultivar Beakdansim tig00111745_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: 1220187
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:236 original size:22 final size:20
Alignment explanation
Indices: 187--237 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
177 TAACACCTTG
*
187 TATAACAACCTTAACCAACT
1 TATAACAACCTTAACCAACC
207 TAGTTAACAACCTCATAACCAACC
1 TA--TAACAACCT--TAACCAACC
231 TATAACA
1 TATAACA
238 GACACAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
22 14 0.54
24 10 0.38
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TATAACAACCTTAACCAACC
Found at i:3534 original size:46 final size:46
Alignment explanation
Indices: 3462--3558 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
3452 TCAAGATCAG
*
3462 GTTCGATTCTCATCGAGATACCATAATTCGAGTGCGAGCTTATTTA
1 GTTCCATTCTCATCGAGATACCATAATTCGAGTGCGAGCTTATTTA
* *
3508 GTTCCATTCTCATTGAGATACCATAATTCGAGTGCGAGCTTTTTTA
1 GTTCCATTCTCATCGAGATACCATAATTCGAGTGCGAGCTTATTTA
3554 GTTCC
1 GTTCC
3559 TAAACTAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (46 bp):
GTTCCATTCTCATCGAGATACCATAATTCGAGTGCGAGCTTATTTA
Found at i:5842 original size:11 final size:11
Alignment explanation
Indices: 5826--5887 Score: 81
Period size: 11 Copynumber: 5.7 Consensus size: 11
5816 TTAGTTAGTA
5826 TTTGTTATTAG
1 TTTGTTATTAG
*
5837 TTTGTTATCAG
1 TTTGTTATTAG
*
5848 TTTGTTA-TGG
1 TTTGTTATTAG
*
5858 TTTGTTATCAG
1 TTTGTTATTAG
*
5869 CTTGTTATTAG
1 TTTGTTATTAG
5880 TTTGTTAT
1 TTTGTTAT
5888 GGTTGTTGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 8 0.19
11 34 0.81
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.60
Consensus pattern (11 bp):
TTTGTTATTAG
Found at i:5874 original size:32 final size:32
Alignment explanation
Indices: 5826--5891 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
5816 TTAGTTAGTA
* *
5826 TTTGTTATTAGTTTGTTATCAGTTTGTTATGG
1 TTTGTTATCAGCTTGTTATCAGTTTGTTATGG
*
5858 TTTGTTATCAGCTTGTTATTAGTTTGTTATGG
1 TTTGTTATCAGCTTGTTATCAGTTTGTTATGG
5890 TT
1 TT
5892 GTTGCTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.15, C:0.05, G:0.21, T:0.59
Consensus pattern (32 bp):
TTTGTTATCAGCTTGTTATCAGTTTGTTATGG
Found at i:5906 original size:20 final size:22
Alignment explanation
Indices: 5883--5925 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5873 TTATTAGTTT
5883 GTTATGGT-TGTTGCTTA-TTA
1 GTTATGGTGTGTTGCTTACTTA
5903 GTTATGGTGTGTTGCTTACTTA
1 GTTATGGTGTGTTGCTTACTTA
5925 G
1 G
5926 ACTATAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.51
Consensus pattern (22 bp):
GTTATGGTGTGTTGCTTACTTA
Found at i:7279 original size:36 final size:36
Alignment explanation
Indices: 7232--7696 Score: 573
Period size: 36 Copynumber: 12.9 Consensus size: 36
7222 TGGTAAAGTT
* *
7232 AGCATCGGCACTTTCGATTCAAGTCGAACGGAAGGA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
7268 AGCATC-AGCACTTCCGATTCAAGTCGAACGGAAGGA
1 AGCATCGA-CACTTCCGATTCAAGTCGAACGGAAGGA
*
7304 GGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* * * * *
7340 GGCATTGGCACTTTCGATTCAAGTCGAATGGAA-GA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
*
7375 AGGCATCGACACTTCCGATTCAAGTCGAACGAAAGGA
1 A-GCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* * * *
7412 GGGATCGACACTTCCGATTCAAGTCGAA-AGAAAGA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* *
7447 AGGCATCGACACTTCCGATTCAAGTAGAACGGAA-TA
1 A-GCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
*
7483 AGGCATCGACACTTCCGATTCAAGTCGAACGGAA-TA
1 A-GCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* * *
7519 AGGCATCGGCACTTCCAATTCAAGTCGAAAGGAAGGA
1 A-GCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* * *
7556 GGCATCGACACTTTCGATTCAAGTCGAACAGAAGGA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
* * *
7592 GGCATC-AGCACTTCAGATTCAAATCGAACGGAAGGA
1 AGCATCGA-CACTTCCGATTCAAGTCGAACGGAAGGA
* * *
7628 AGCATCGACACTTTCGATTCAAATCAAACGGAAGGA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
*
7664 AGCATCGCCACTTCCGATTCAAGTCGAACGGAA
1 AGCATCGACACTTCCGATTCAAGTCGAACGGAA
7697 AGATGTATCA
Statistics
Matches: 374, Mismatches: 46, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
35 7 0.02
36 359 0.96
37 8 0.02
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (36 bp):
AGCATCGACACTTCCGATTCAAGTCGAACGGAAGGA
Found at i:7816 original size:11 final size:11
Alignment explanation
Indices: 7800--7881 Score: 89
Period size: 11 Copynumber: 7.7 Consensus size: 11
7790 TTAGTTAGTA
7800 TTTGTTATTAG
1 TTTGTTATTAG
*
7811 TTTGTTATCAG
1 TTTGTTATTAG
*
7822 TTTGTTA-TGG
1 TTTGTTATTAG
*
7832 TTTGTTATCAG
1 TTTGTTATTAG
*
7843 CTTGTTATTAG
1 TTTGTTATTAG
*
7854 -TTGTTA-TGG
1 TTTGTTATTAG
7863 TTTGTTATTAG
1 TTTGTTATTAG
*
7874 CTTGTTAT
1 TTTGTTAT
7882 GGTGTGTTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
9 2 0.03
10 20 0.34
11 36 0.62
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.59
Consensus pattern (11 bp):
TTTGTTATTAG
Found at i:7861 original size:31 final size:32
Alignment explanation
Indices: 7800--7881 Score: 130
Period size: 31 Copynumber: 2.6 Consensus size: 32
7790 TTAGTTAGTA
*
7800 TTTGTTATTAGTTTGTTATCAGTTTGTTATGG
1 TTTGTTATTAGCTTGTTATCAGTTTGTTATGG
* *
7832 TTTGTTATCAGCTTGTTATTAG-TTGTTATGG
1 TTTGTTATTAGCTTGTTATCAGTTTGTTATGG
7863 TTTGTTATTAGCTTGTTAT
1 TTTGTTATTAGCTTGTTAT
7882 GGTGTGTTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 27 0.59
32 19 0.41
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.59
Consensus pattern (32 bp):
TTTGTTATTAGCTTGTTATCAGTTTGTTATGG
Found at i:7884 original size:21 final size:22
Alignment explanation
Indices: 7800--7881 Score: 107
Period size: 21 Copynumber: 3.9 Consensus size: 22
7790 TTAGTTAGTA
7800 TTTGTTATTAGTTTGTTATCAG
1 TTTGTTATTAGTTTGTTATCAG
*
7822 TTTGTTA-TGGTTTGTTATCAG
1 TTTGTTATTAGTTTGTTATCAG
* *
7843 CTTGTTATTAG-TTGTTAT-GG
1 TTTGTTATTAGTTTGTTATCAG
*
7863 TTTGTTATTAGCTTGTTAT
1 TTTGTTATTAGTTTGTTAT
7882 GGTGTGTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.21
21 33 0.62
22 9 0.17
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.59
Consensus pattern (22 bp):
TTTGTTATTAGTTTGTTATCAG
Found at i:7889 original size:21 final size:20
Alignment explanation
Indices: 7845--7889 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
7835 GTTATCAGCT
*
7845 TGTTATTAGTTGTTATGGTT
1 TGTTATTAGTTGTTATGGTG
7865 TGTTATTAGCTTGTTATGGTG
1 TGTTATTAG-TTGTTATGGTG
7886 TGTT
1 TGTT
7890 GCTTACTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.13, C:0.02, G:0.27, T:0.58
Consensus pattern (20 bp):
TGTTATTAGTTGTTATGGTG
Found at i:8294 original size:58 final size:57
Alignment explanation
Indices: 8223--8345 Score: 135
Period size: 57 Copynumber: 2.1 Consensus size: 57
8213 AGTTTGGGGT
* *
8223 TTAATTTAGAATGA-TGTCATAGTTTAAAG-ATTAAATTAAAATGTTCAAAATTTAGAA-A
1 TTAATTTAAAATGAGAGTCATAG-TT-AAGTA-TAAATTAAAATGTTCAAAATTTA-AATA
* * * *
8281 TTAATTTAAAATGAGAGTTATAGTTGAGTATGAATTGAAATGTTCAAAATTTAAATA
1 TTAATTTAAAATGAGAGTCATAGTTAAGTATAAATTAAAATGTTCAAAATTTAAATA
8338 TTAATTTA
1 TTAATTTA
8346 GAATAAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 2 0.04
57 32 0.57
58 16 0.29
59 6 0.11
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (57 bp):
TTAATTTAAAATGAGAGTCATAGTTAAGTATAAATTAAAATGTTCAAAATTTAAATA
Found at i:18249 original size:13 final size:13
Alignment explanation
Indices: 18231--18256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18221 TAGTTTTTAA
18231 ATTTTTTTAATTT
1 ATTTTTTTAATTT
18244 ATTTTTTTAATTT
1 ATTTTTTTAATTT
18257 GAGTGAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:20766 original size:32 final size:31
Alignment explanation
Indices: 20730--20812 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 31
20720 TTTAGGTAAA
*
20730 AAAATGAAACAAAAAGTTAACAA-TGTG-GTACT
1 AAAATGAAACAAAAA-ATAA-AAGT-TGAGTACT
*
20762 AAAATAAAACAAAAAATAAAAGTTGAGTACT
1 AAAATGAAACAAAAAATAAAAGTTGAGTACT
*
20793 AAAATGAACCAAAAAATAAA
1 AAAATGAAACAAAAAATAAA
20813 TATTAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
30 4 0.09
31 27 0.60
32 14 0.31
ACGTcount: A:0.63, C:0.08, G:0.11, T:0.18
Consensus pattern (31 bp):
AAAATGAAACAAAAAATAAAAGTTGAGTACT
Found at i:21478 original size:13 final size:12
Alignment explanation
Indices: 21457--21488 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
21447 GAGAATGATC
21457 AAAATAAAATTA
1 AAAATAAAATTA
21469 AAACATAAAATTA
1 AAA-ATAAAATTA
21482 AAAATAA
1 AAAATAA
21489 TTTTTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:23714 original size:13 final size:14
Alignment explanation
Indices: 23691--23720 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
23681 TTTCCACTAC
23691 AGACGTGCATATGA
1 AGACGTGCATATGA
23705 AGAC-TGCATATGA
1 AGACGTGCATATGA
23718 AGA
1 AGA
23721 ATGTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:23739 original size:4 final size:4
Alignment explanation
Indices: 23730--23756 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23720 AATGTTCAAC
23730 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
23757 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:24669 original size:17 final size:17
Alignment explanation
Indices: 24647--24690 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
24637 ATGTAAAAAT
24647 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
24664 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
24681 AAATATTTAA
1 AAATATTTAA
24691 TCAATTAAGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:40292 original size:35 final size:35
Alignment explanation
Indices: 40244--40311 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
40234 TATTATTTTG
* *
40244 ATTATTTTTGAATTTGGGGTTTAGAATGTAATTGA
1 ATTATTTTGGAATTTGGGGTTTAGAATGAAATTGA
40279 ATTATTTTGGAATTTGGGGTTTAGAATGAAATT
1 ATTATTTTGGAATTTGGGGTTTAGAATGAAATT
40312 AAGGACTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (35 bp):
ATTATTTTGGAATTTGGGGTTTAGAATGAAATTGA
Found at i:41516 original size:50 final size:51
Alignment explanation
Indices: 41393--41580 Score: 272
Period size: 51 Copynumber: 3.7 Consensus size: 51
41383 ATACTTATAT
* *
41393 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTTACTTACAA
1 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
* * * * *
41444 AGTTGTAAGTATTTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACGC
1 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
41495 CGGTGT-AGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
1 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
* *
41545 CGGTGTAA-ATATGTGTTAAGTACTACATTTTTTTAT
1 CGGTGTAAGA-ATGTGTTAAGTGCTACACTTTTTTAT
41581 AGTATGAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
50 48 0.40
51 73 0.60
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (51 bp):
CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAC
Found at i:41562 original size:101 final size:102
Alignment explanation
Indices: 41393--41580 Score: 297
Period size: 101 Copynumber: 1.9 Consensus size: 102
41383 ATACTTATAT
* * * *
41393 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTTACTTACAAAGTTGTAAGTATTT
1 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAAAGGTGTAAATATGT
*
41458 GTTAAGTGCTACACTTTTTTATTTTATTCACTTACGC
66 GTTAAGTACTACACTTTTTTATTTTATTCACTTACGC
**
41495 CGGTGT-AGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTGTAAATATGT
1 CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAAAGGTGTAAATATGT
*
41559 GTTAAGTACTACATTTTTTTAT
66 GTTAAGTACTACACTTTTTTAT
41581 AGTATGAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 72 0.92
102 6 0.08
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (102 bp):
CGGTGTAAGAATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACAAAGGTGTAAATATGT
GTTAAGTACTACACTTTTTTATTTTATTCACTTACGC
Found at i:47174 original size:20 final size:20
Alignment explanation
Indices: 47122--47175 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
47112 AAACACTGGT
*
47122 AGTATCGATACTACCTAGAG
1 AGTATCGATACTTCCTAGAG
47142 AGTATCGATACTTCCTAGAG
1 AGTATCGATACTTCCTAGAG
47162 AGTATCGATACTTC
1 AGTATCGATACTTC
47176 TCTTACATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTTCCTAGAG
Found at i:52554 original size:20 final size:23
Alignment explanation
Indices: 52525--52577 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 23
52515 AAATGTCAAA
52525 ATATAT-ATATT-CAT-TAATAA-
1 ATATATAATATTACATAT-ATAAT
52545 ATA-ATAATATTACATATATAAT
1 ATATATAATATTACATATATAAT
52567 ATATATAATAT
1 ATATATAATAT
52578 GTATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.07
20 8 0.29
21 7 0.25
22 4 0.14
23 7 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATAATATTACATATATAAT
Found at i:53360 original size:211 final size:211
Alignment explanation
Indices: 53066--53528 Score: 802
Period size: 211 Copynumber: 2.2 Consensus size: 211
53056 GTATTGTTCC
* * * * * *
53066 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAA
53131 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
53196 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
53261 TGAACTTGCGTTGTCTG
195 TGAACTTACGTTGTCTG
*
53278 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAA
*
53342 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
53407 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
53472 GAACTTACGTTGTCTG
196 GAACTTACGTTGTCTG
*
53488 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAATTGGCTCTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTG-AAATTGGCTCTG
53529 GGTAAAACCT
Statistics
Matches: 239, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
210 80 0.33
211 114 0.48
212 45 0.19
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (211 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTACGTTGTCTG
Found at i:53408 original size:105 final size:105
Alignment explanation
Indices: 53066--53528 Score: 800
Period size: 105 Copynumber: 4.4 Consensus size: 105
53056 GTATTGTTCC
* * * * * *
53066 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
53131 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53172 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
53237 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53278 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
53343 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53383 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
53448 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
53488 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAATTGGCTCTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTG-AAATTGGCTCTG
53529 GGTAAAACCT
Statistics
Matches: 343, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
105 183 0.53
106 160 0.47
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:63775 original size:10 final size:10
Alignment explanation
Indices: 63750--63783 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
63740 AACGTTAGTA
*
63750 AAATAGAAAT
1 AAATAAAAAT
*
63760 AGATAAAAAT
1 AAATAAAAAT
63770 AAATAAAAAT
1 AAATAAAAAT
63780 AAAT
1 AAAT
63784 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:65171 original size:2 final size:2
Alignment explanation
Indices: 65160--65219 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
65150 AAATGTGTAC
*
65160 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65201 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
65220 ACATATAAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66867 original size:24 final size:25
Alignment explanation
Indices: 66834--66880 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
66824 TCGATCGCGA
66834 GTTAGAAAATATTTGATT-CTTGATC
1 GTTAGAAAATATTTG-TTGCTTGATC
*
66859 GTTA-AAAATTTTTGTTGCTTGA
1 GTTAGAAAATATTTGTTGCTTGA
66881 CTCGACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.70
25 4 0.20
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (25 bp):
GTTAGAAAATATTTGTTGCTTGATC
Found at i:67226 original size:22 final size:23
Alignment explanation
Indices: 67200--67254 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
67190 ATAAATCTAC
67200 TAATATGAAA-A-TATGAATTAA
1 TAATATGAAATATTATGAATTAA
67221 TAAATAT-ACTAATATTATGAATTAA
1 T-AATATGA--AATATTATGAATTAA
67246 TAATATGAA
1 TAATATGAA
67255 TAAAATATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
21 2 0.07
22 5 0.18
23 3 0.11
24 6 0.21
25 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
TAATATGAAATATTATGAATTAA
Found at i:67245 original size:25 final size:25
Alignment explanation
Indices: 67211--67287 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
67201 AATATGAAAA
67211 TATGAATTAATAAATATACTAATAT
1 TATGAATTAATAAATATACTAATAT
* *
67236 TATGAATTAAT-AATATGAATAA-AA
1 TATGAATTAATAAATAT-ACTAATAT
** *
67260 TATGAATCGATAAATCTACTAATAT
1 TATGAATTAATAAATATACTAATAT
67285 TAT
1 TAT
67288 ATAAAGCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (25 bp):
TATGAATTAATAAATATACTAATAT
Found at i:67252 original size:13 final size:13
Alignment explanation
Indices: 67209--67266 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
67199 CTAATATGAA
67209 AATATGAATTAAT
1 AATATGAATTAAT
*
67222 AA-AT-ATACTAAT
1 AATATGA-ATTAAT
*
67234 ATTATGAATTAAT
1 AATATGAATTAAT
67247 AATATGAA-TAA-
1 AATATGAATTAAT
67258 AATATGAAT
1 AATATGAAT
67267 CGATAAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 9 0.24
12 11 0.30
13 16 0.43
14 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (13 bp):
AATATGAATTAAT
Found at i:67256 original size:22 final size:22
Alignment explanation
Indices: 67200--67266 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
67190 ATAAATCTAC
67200 TAATATGAA-AATATGAATTAA
1 TAATATGAATAATATGAATTAA
* *
67221 TAAATATACTAATATTATGAATTAA
1 T-AATAT--GAATAATATGAATTAA
67246 TAATATGAATAAAATATGAAT
1 TAATATGAAT--AATATGAAT
67267 CGATAAATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
21 1 0.03
22 8 0.22
24 15 0.42
25 12 0.33
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (22 bp):
TAATATGAATAATATGAATTAA
Found at i:67263 original size:11 final size:12
Alignment explanation
Indices: 67209--67266 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
67199 CTAATATGAA
67209 AATATGAATTAAT
1 AATATGAA-TAAT
*
67222 AAATAT-ACTAAT
1 -AATATGAATAAT
*
67234 ATTATGAATTAAT
1 AATATGAA-TAAT
67247 AATATGAATAA-
1 AATATGAATAAT
67258 AATATGAAT
1 AATATGAAT
67267 CGATAAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 13 0.34
12 8 0.21
13 12 0.32
14 5 0.13
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (12 bp):
AATATGAATAAT
Found at i:74504 original size:21 final size:20
Alignment explanation
Indices: 74446--74697 Score: 131
Period size: 20 Copynumber: 12.6 Consensus size: 20
74436 AAATGACCAA
* * *
74446 CAAATTCGCAACGAGAACTC
1 CAAATTCGCAACGCGAATTT
* *
74466 CAATTTCGCAAC-CCAATTT
1 CAAATTCGCAACGCGAATTT
74485 CCAAATTCGCAACGCGAATTT
1 -CAAATTCGCAACGCGAATTT
* *
74506 GTAAA-TCGCAAGGCGAATTT
1 -CAAATTCGCAACGCGAATTT
* * *
74526 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACGC-GAATTT
* * *
74546 CAAATTCGCAATGTG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
* * * **
74566 CAAATTTTGCAACACAAAAGT
1 CAAA-TTCGCAACGCGAATTT
* *
74587 CAAATTCGCAAAGCGGAATTG
1 CAAATTCGCAACGC-GAATTT
*
74608 CAAATTCGCAAAGCAGAATTT
1 CAAATTCGCAACGC-GAATTT
*
74629 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
** *
74648 CAAATTCGCAACTAGATTTT
1 CAAATTCGCAACGCGAATTT
* *
74668 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGAATTT
*
74688 -AATTTCGCAA
1 CAAATTCGCAA
74698 AAGGTTTTAG
Statistics
Matches: 180, Mismatches: 42, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.01
19 33 0.18
20 89 0.49
21 56 0.31
22 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:74673 original size:20 final size:19
Alignment explanation
Indices: 74586--74697 Score: 100
Period size: 19 Copynumber: 5.6 Consensus size: 19
74576 AACACAAAAG
*
74586 TCAAATTCGCAAAGCGGAATT
1 TCAAATTCGC-AA-CTGAATT
* *
74607 GCAAATTCGCAAAGCAGAATT
1 TCAAATTCGC-AA-CTGAATT
74628 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
74647 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
74667 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
74687 T-AATTTCGCAA
1 TCAAATTCGCAA
74698 AAGGTTTTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.35
20 23 0.29
21 28 0.35
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:74881 original size:16 final size:16
Alignment explanation
Indices: 74860--74890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
74850 TCTCTAATTT
74860 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
74876 TTTTTATATAATTTT
1 TTTTTACATAATTTT
74891 TCAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:75507 original size:12 final size:12
Alignment explanation
Indices: 75486--75519 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
75476 ACCACATTTC
*
75486 CAATACCAAACA
1 CAATATCAAACA
75498 CAATATCAAACA
1 CAATATCAAACA
*
75510 CAATCTCAAA
1 CAATATCAAA
75520 ACCCACAACC
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:75672 original size:24 final size:24
Alignment explanation
Indices: 75645--75698 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
75635 GTATTCAAAA
*
75645 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTAAATACCCGGAC
* *
75669 TTTGATCTTGGTAAATACTCGGAT
1 TTTGATCTTGGTAAATACCCGGAC
75693 TTTGAT
1 TTTGAT
75699 GATGTGATGG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCGGAC
Found at i:75890 original size:12 final size:12
Alignment explanation
Indices: 75873--75897 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75863 ATATAACCCT
75873 GAAGAAGAAAAA
1 GAAGAAGAAAAA
75885 GAAGAAGAAAAA
1 GAAGAAGAAAAA
75897 G
1 G
75898 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:77984 original size:18 final size:18
Alignment explanation
Indices: 77961--77996 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
77951 AAGCAAAAGG
*
77961 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
77979 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
77997 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:78861 original size:18 final size:18
Alignment explanation
Indices: 78840--78876 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
78830 GTAATTGGAG
78840 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
78858 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
78876 T
1 T
78877 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:78883 original size:24 final size:24
Alignment explanation
Indices: 78832--78884 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
78822 TTTCATATGT
* * *
78832 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
78856 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
78880 AATTT
1 AATTT
78885 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:79862 original size:18 final size:18
Alignment explanation
Indices: 79829--79864 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
79819 AAGCAAAAGG
**
79829 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
79847 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
79865 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:80132 original size:14 final size:14
Alignment explanation
Indices: 80113--80139 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80103 TGGAATGTGT
80113 TTGATGTTGTATAC
1 TTGATGTTGTATAC
80127 TTGATGTTGTATA
1 TTGATGTTGTATA
80140 TTGCGATCAA
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:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (14 bp):
TTGATGTTGTATAC
Found at i:80172 original size:20 final size:20
Alignment explanation
Indices: 80147--80216 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
80137 ATATTGCGAT
* *
80147 CAACGCGAAATTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
80167 CAACGCGAAAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCG
80187 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
80207 CAACGCGAAA
1 CAACGCGAAA
80217 TCGTAAACCG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:80263 original size:20 final size:20
Alignment explanation
Indices: 80238--80312 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
80228 AAATCGTGAC
80238 GCGAATTTAACTTTCGCGTT
1 GCGAATTTAACTTTCGCGTT
* ** ** *
80258 GCGAATGTAAAATAAGCATT
1 GCGAATTTAACTTTCGCGTT
* *
80278 GCGAATTTGACTTTCACGTT
1 GCGAATTTAACTTTCGCGTT
*
80298 GCGAATTTACCTTTC
1 GCGAATTTAACTTTC
80313 AAATCAATTA
Statistics
Matches: 39, Mismatches: 16, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
GCGAATTTAACTTTCGCGTT
Found at i:80385 original size:67 final size:64
Alignment explanation
Indices: 80312--80440 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 64
80302 ATTTACCTTT
*
80312 CAAATCAATTAAACAAGTAAAAATAATAATTCTTATTTACACATCAAATTAAATAAATCAACTTT
1 CAAATCAATTAAACAAG-AAAAA-AATAATTCTTATTTACACATC-AATTAAACAAATCAACTTT
80377 TA
63 TA
* * *
80379 CAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAACAAATCAACTTT
1 CAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTAAACAAATCAACTTT
80441 CAATGTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 18 0.31
65 19 0.33
66 4 0.07
67 17 0.29
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (64 bp):
CAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTAAACAAATCAACTTTTA
Found at i:81797 original size:21 final size:21
Alignment explanation
Indices: 81773--81875 Score: 93
Period size: 21 Copynumber: 4.9 Consensus size: 21
81763 GCGGGCGGGA
81773 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
* **
81794 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGATAGGGG
* * *
81815 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGATAGGGG
**
81836 CCTCTTGAACGAT-ATGAGGCA
1 CCTCTTGAACGATGAT-AGGGG
*
81857 CCTCTTGAATGATGATAGG
1 CCTCTTGAACGATGATAGG
81876 TGCATCGGGC
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 60 0.92
22 3 0.05
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATGATAGGGG
Found at i:81869 original size:42 final size:42
Alignment explanation
Indices: 81772--81871 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
81762 GGCGGGCGGG
* * * * *
81772 ACCTCTTGAACGATGATAGGGGCCTCTTGAACGGTGGGAGGG
1 ACCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGGC
* * *
81814 GCTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATATGAGGC
1 ACCTCTT-GAATGATGAGAGGGGCCTCTTGAACGATAGGAGGC
81856 ACCTCTTGAATGATGA
1 ACCTCTTGAATGATGA
81872 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (42 bp):
ACCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGGC
Found at i:84092 original size:20 final size:20
Alignment explanation
Indices: 84053--84092 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
84043 TGCGATTTTG
* * *
84053 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
84073 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
84093 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:84448 original size:21 final size:21
Alignment explanation
Indices: 84422--84461 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
84412 GGAGATAGAC
84422 GGATTTCGTCGGAGATGGGAT
1 GGATTTCGTCGGAGATGGGAT
84443 GGATTTCGTCGGAGATGGG
1 GGATTTCGTCGGAGATGGG
84462 GACAGATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.45, T:0.28
Consensus pattern (21 bp):
GGATTTCGTCGGAGATGGGAT
Found at i:84473 original size:22 final size:21
Alignment explanation
Indices: 84427--84475 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
84417 TAGACGGATT
** *
84427 TCGTCGGAGATGGGATGGATT
1 TCGTCGGAGATGGGACAGATG
84448 TCGTCGGAGATGGGGACAGATG
1 TCGTCGGAGAT-GGGACAGATG
84470 TCGTCG
1 TCGTCG
84476 TAGAGAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.18, C:0.14, G:0.43, T:0.24
Consensus pattern (21 bp):
TCGTCGGAGATGGGACAGATG
Found at i:84612 original size:20 final size:20
Alignment explanation
Indices: 84584--84650 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
84574 TGTGTTTCGC
84584 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
84604 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
84624 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
84644 GTTGCGA
1 GTTGCGA
84651 TTTACAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:84667 original size:20 final size:20
Alignment explanation
Indices: 84644--84690 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
84634 TGACTTATGT
84644 GTTGCGATTTACAAATTCGA
1 GTTGCGATTTACAAATTCGA
** *
84664 GTTGCGATTTACATTTTCGC
1 GTTGCGATTTACAAATTCGA
84684 GTTGCGA
1 GTTGCGA
84691 AATTGGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGA
Found at i:84668 original size:40 final size:41
Alignment explanation
Indices: 84579--84670 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
84569 AATATTGTGT
* * *
84579 TTCGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTA
1 TTCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACAA
84620 -TCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAA
1 TTCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGAC-AA
*
84659 TTCGAGTTGCGA
1 TTCGCGTTGCGA
84671 TTTACATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
38 2 0.04
39 5 0.11
40 38 0.84
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (41 bp):
TTCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACAA
Found at i:87979 original size:6 final size:6
Alignment explanation
Indices: 87968--87993 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
87958 AGCCTTGAAA
87968 AAGGGG AAGGGG AAGGGG AAGGGG AA
1 AAGGGG AAGGGG AAGGGG AAGGGG AA
87994 AGAGAAAGGG
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:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:88056 original size:14 final size:15
Alignment explanation
Indices: 88033--88061 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
88023 TATTAAAATT
88033 TTAATCTTTTTTAAA
1 TTAATCTTTTTTAAA
88048 TTAAT-TTTTTTAAA
1 TTAATCTTTTTTAAA
88062 ATATGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATCTTTTTTAAA
Found at i:92477 original size:12 final size:12
Alignment explanation
Indices: 92446--92487 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
92436 ATTTTATGTT
92446 TTAATTATTAATTA
1 TTAATTA-TAA-TA
92460 TT-ATTATAATA
1 TTAATTATAATA
92471 TTAATTATAATA
1 TTAATTATAATA
92483 TTAAT
1 TTAAT
92488 ATATTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 17 0.63
13 4 0.15
14 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTATAATA
Found at i:92487 original size:18 final size:17
Alignment explanation
Indices: 92445--92489 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
92435 TATTTTATGT
*
92445 TTTAATTATTAATTATTA
1 TTTAA-TATTAATTATAA
92463 TTATAATATTAATTATAA
1 TT-TAATATTAATTATAA
92481 TATTAATAT
1 T-TTAATAT
92490 ATTTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATATTAATTATAA
Found at i:95504 original size:19 final size:19
Alignment explanation
Indices: 95480--95517 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
95470 GCATTAAGCC
*
95480 TTTAAAATAATAATTTAAA
1 TTTAAAATAATAATATAAA
95499 TTTAAAATAATAATATAAA
1 TTTAAAATAATAATATAAA
95518 AGAAGACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAAAATAATAATATAAA
Found at i:97865 original size:20 final size:20
Alignment explanation
Indices: 97840--97892 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
97830 TTAAGTTGTT
97840 GGTATCGATACTCAGATAAG
1 GGTATCGATACTCAGATAAG
*
97860 GGTATCGATACTCAGATAGG
1 GGTATCGATACTCAGATAAG
97880 GGTATCGATACTC
1 GGTATCGATACTC
97893 CTGAGCTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (20 bp):
GGTATCGATACTCAGATAAG
Found at i:97917 original size:20 final size:20
Alignment explanation
Indices: 97880--97931 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
97870 CTCAGATAGG
*
97880 GGTATCGATACTCCTGAG-C
1 GGTATCGATACTCATGAGTC
*
97899 TGGTATCGATACTGATGAGTC
1 -GGTATCGATACTCATGAGTC
*
97920 AGTATCGATACT
1 GGTATCGATACT
97932 ACTTCAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTCATGAGTC
Found at i:100505 original size:24 final size:23
Alignment explanation
Indices: 100478--100522 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
100468 AAGATATATG
100478 ATATG-ATATACATGATTATATGCA
1 ATATGTAT-TACATG-TTATATGCA
100502 ATATGTATTACATGTTATATG
1 ATATGTATTACATGTTATATG
100523 AAATGACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 11 0.55
25 2 0.10
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATGTATTACATGTTATATGCA
Found at i:101424 original size:21 final size:21
Alignment explanation
Indices: 101398--101437 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
101388 TTACGAAAGT
101398 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
101419 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
101438 ACATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:101989 original size:18 final size:19
Alignment explanation
Indices: 101966--102016 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
101956 TAAAAATATT
101966 TTTATTATATTATATTT-A
1 TTTATTATATTATATTTGA
*
101984 TTTATTATTTTATTATTTGA
1 TTTATTATATTA-TATTTGA
102004 TTGTATTA-ATTAT
1 TT-TATTATATTAT
102017 CTTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 6 0.21
21 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTATTATATTATATTTGA
Found at i:102596 original size:19 final size:19
Alignment explanation
Indices: 102572--102618 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
102562 GGTGGTTGCG
*
102572 AGAGAAATTTCGACAGTTA
1 AGAGAAATTTCCACAGTTA
*
102591 AGAGAAATTTCCACAGTTG
1 AGAGAAATTTCCACAGTTA
*
102610 AGTGAAATT
1 AGAGAAATT
102619 GTTCCATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (19 bp):
AGAGAAATTTCCACAGTTA
Found at i:103179 original size:2 final size:2
Alignment explanation
Indices: 103174--103200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103164 AATATATATA
103174 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
103201 TTTACTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:103731 original size:101 final size:102
Alignment explanation
Indices: 103556--103744 Score: 247
Period size: 101 Copynumber: 1.9 Consensus size: 102
103546 AAGCTGGTAG
* * * * *
103556 TTGAATGTCTTCCCCTTGAACTTGAAGGCATCGTGTCATATGGGTTTTGAACTGAGTGTTGTATC
1 TTGAATGTCCTCCCCTGGAACTTGAAGGCATCGTGTCAAATGGGTATTGAACAGAGTGTTGTATC
*
103621 ACAGGCATCTCCATATTGAGGTCGAAAAAGCTCTCAC
66 ACAGGCATCTCCATATTCAGGTCGAAAAAGCTCTCAC
* * *
103658 TTGAATG-CCTCCCCTGGAACTTTAAGGCATCGTGTCAAATGGGTATTGAACAGATTGTTGTGTC
1 TTGAATGTCCTCCCCTGGAACTTGAAGGCATCGTGTCAAATGGGTATTGAACAGAGTGTTGTATC
* * *
103722 GA-TGTCATCTCTATATTCAGGTC
66 -ACAGGCATCTCCATATTCAGGTC
103745 AAAGAAATAG
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
101 66 0.89
102 8 0.11
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (102 bp):
TTGAATGTCCTCCCCTGGAACTTGAAGGCATCGTGTCAAATGGGTATTGAACAGAGTGTTGTATC
ACAGGCATCTCCATATTCAGGTCGAAAAAGCTCTCAC
Found at i:119676 original size:30 final size:30
Alignment explanation
Indices: 119642--119708 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
119632 AGTTTTAAAC
119642 AAAATACTAATTTTAACTTA-AAT-TTTAGAT
1 AAAATACTAA-TTTAA-TTATAATCTTTAGAT
*
119672 AAAATATTAATTTAATTATTAATCTTTAGAT
1 AAAATACTAATTTAATTA-TAATCTTTAGAT
119703 AAAATA
1 AAAATA
119709 TATATTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 3 0.09
29 5 0.15
30 12 0.36
31 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (30 bp):
AAAATACTAATTTAATTATAATCTTTAGAT
Found at i:126397 original size:21 final size:21
Alignment explanation
Indices: 126372--126411 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
126362 TTGAGACACT
126372 CTTTCTTTAAAATTTTAAACA
1 CTTTCTTTAAAATTTTAAACA
126393 CTTTCTTTAAAATTTTAAA
1 CTTTCTTTAAAATTTTAAA
126412 TCATCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTTCTTTAAAATTTTAAACA
Found at i:127820 original size:17 final size:15
Alignment explanation
Indices: 127779--127818 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
127769 TTATATTATC
127779 TATTT-TATATCCTA
1 TATTTATATATCCTA
127793 TATTTATATATCCTA
1 TATTTATATATCCTA
127808 TATTTATATAT
1 TATTTATATAT
127819 ATACATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATATATCCTA
Found at i:127821 original size:27 final size:26
Alignment explanation
Indices: 127758--127828 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
127748 GTATTGTATA
127758 TATATATATACTTATATTATCTATTT
1 TATATATATACTTATATTATCTATTT
* *
127784 TATATCCTATATTTATA-TATCCTATATT
1 TATAT-ATATACTTATATTAT-CTAT-TT
*
127812 TATATATATACATATAT
1 TATATATATACTTATAT
127829 GTTTTTCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 8 0.22
27 21 0.58
28 7 0.19
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATATATACTTATATTATCTATTT
Found at i:127862 original size:17 final size:19
Alignment explanation
Indices: 127830--127873 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
127820 TACATATATG
*
127830 TTTTTCTACTATTTTTC-T
1 TTTTTATACTATTTTTCAT
127848 TTTTTATACTA-TTTTCAT
1 TTTTTATACTATTTTTCAT
127866 TTTCTTAT
1 TTT-TTAT
127874 TATTCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTATACTATTTTTCAT
Found at i:130091 original size:229 final size:227
Alignment explanation
Indices: 129659--130144 Score: 882
Period size: 229 Copynumber: 2.1 Consensus size: 227
129649 GTAAATTATC
* *
129659 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
129724 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
129789 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
*
129854 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTTAAAAAAAGTATA
* *
129886 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
129951 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-TT
* *
130016 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
130081 GAAACATAAATTACATAACTTTAAAAAAAGTATA
194 GAAACATAAATTACATAACTTTAAAAAAAGTATA
130115 TATCATTTTTATAAAAGTGTTCATACTTAT
1 TATCATTTTTATAAAAGTGTTCATACTTAT
130145 AAAAGTAGGT
Statistics
Matches: 248, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
227 36 0.15
228 85 0.34
229 127 0.51
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:130446 original size:20 final size:20
Alignment explanation
Indices: 130423--130469 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
130413 CGATATACCA
130423 GGTAAAA-ATATGATAAAACC
1 GGTAAAAGA-ATGATAAAACC
130443 GGTAAAAGAATGATAAAACC
1 GGTAAAAGAATGATAAAACC
130463 GGTAAAA
1 GGTAAAA
130470 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (20 bp):
GGTAAAAGAATGATAAAACC
Found at i:130557 original size:181 final size:182
Alignment explanation
Indices: 130211--130683 Score: 673
Period size: 181 Copynumber: 2.6 Consensus size: 182
130201 GATCCAAATT
* * * *
130211 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGT-ATAGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAG-AATGAT
* * * * * * *
130275 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTATCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
130340 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
130393 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAAAAGAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAGAATGATA
* *
130458 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
130522 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * * *
130574 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAGCCGGTATCAA-AATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-AAAGAATGAT
* *
130638 AAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
130684 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 163 0.62
182 96 0.37
183 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAGAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:130627 original size:20 final size:19
Alignment explanation
Indices: 130604--130650 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
130594 CGATATAACA
*
130604 GGTAAAAATATGATAAAGCC
1 GGTAAAAA-ATGATAAAACC
*
130624 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
130644 GGTAAAA
1 GGTAAAA
130651 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:132047 original size:23 final size:23
Alignment explanation
Indices: 132016--132088 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
132006 ATAGGTAAAA
*
132016 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
132039 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
132062 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
132085 ATAT
1 ATAT
132089 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:133237 original size:28 final size:28
Alignment explanation
Indices: 133188--133262 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
133178 TTTATGTGTA
* **
133188 AATTAAATATTAAGACCATTTTTTGAAT-
1 AATTAAATATTAGGACTTTTTTTTG-ATG
133216 AATTAAATATTAGGACTTTTTTTTTGATG
1 AATTAAATATTAGGAC-TTTTTTTTGATG
*
133245 CATTAAATATTAGGACTT
1 AATTAAATATTAGGACTT
133263 GTGAAAGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (28 bp):
AATTAAATATTAGGACTTTTTTTTGATG
Found at i:134723 original size:44 final size:39
Alignment explanation
Indices: 134653--134740 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 39
134643 ACTATCGCAA
134653 TGCGA-TTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTT--CGT
134693 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
1 TGCGATTT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCGT
134735 TGCGAT
1 TGCGAT
134741 AGTCGAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
40 5 0.11
41 2 0.05
42 18 0.41
44 19 0.43
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (39 bp):
TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGT
Found at i:134734 original size:63 final size:61
Alignment explanation
Indices: 134661--134929 Score: 258
Period size: 63 Copynumber: 4.3 Consensus size: 61
134651 AATGCGATTT
*
134661 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAG
* * * *
134724 TCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATGG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* * * * * *
134785 TCAAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTACGAT
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA-
*
134846 TTAT
59 -TAG
* * *
134850 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATGTATTCCAAATTCGTTCCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
*
134911 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTT--CGTTGCGAT
134930 TTATTCTAAG
Statistics
Matches: 170, Mismatches: 22, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
61 44 0.26
63 101 0.59
65 25 0.15
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:134761 original size:84 final size:82
Alignment explanation
Indices: 134669--134963 Score: 371
Period size: 84 Copynumber: 3.5 Consensus size: 82
134659 TTTCCAAATT
* * *
134669 CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGCGTTGCGATTATTCCAAGTT
*
134732 CGTTGCGATAGTCGAAGTTTG
62 CGTTGCGATAGTCGAAGTTCG
*
134753 CGTTGCGATTTATTCCAAGTTCGTTGCGATGGT-CAAAGTTCGCGTTGCGATTTATTCCAAGTTC
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAA-TTCGCGTTGCGA-TTATTCCAAGTTC
134817 GTTGCGATAGTCGAAGTTCG
63 GTTGCGATAGTCGAAGTTCG
* * * *
134837 CGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATGTATTCCAAATTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATTCGCGTTGCGAT-TATTCCAAGTTCG
*
134902 TTCCGATAGTCGAAGTTCG
64 TTGCGATAGTCGAAGTTCG
* *
134921 CGTTGCGATTTATTCTAAGTTCGTTGCGATAGTCCAAAATCGC
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATTCGC
134964 AACGACTAGT
Statistics
Matches: 188, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
81 4 0.02
82 14 0.07
83 1 0.01
84 157 0.84
85 2 0.01
86 10 0.05
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (82 bp):
CGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAATTCGCGTTGCGATTATTCCAAGTTCGTT
GCGATAGTCGAAGTTCG
Found at i:134770 original size:42 final size:42
Alignment explanation
Indices: 134709--134954 Score: 397
Period size: 42 Copynumber: 5.9 Consensus size: 42
134699 TTATTCCAAA
*
134709 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
134749 TTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATGGTCAAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
134791 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
134833 TTCGCGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
134875 TTCGCGTTGCGATGTATTCCAAATTCGTTCCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
134917 TTCGCGTTGCGATTTATTCTAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
134955 CAAAATCGCA
Statistics
Matches: 188, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 11 0.06
42 177 0.94
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:135742 original size:6 final size:6
Alignment explanation
Indices: 135726--135757 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
135716 TCTCGTCTCG
135726 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
135758 AGTTGCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:137056 original size:2 final size:2
Alignment explanation
Indices: 137051--137076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
137041 ATATTTTACA
137051 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
137077 CACAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137688 original size:19 final size:19
Alignment explanation
Indices: 137664--137701 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
137654 CTTTAATTGA
137664 GAATTTATAATTAATATAG
1 GAATTTATAATTAATATAG
*
137683 GAATTTATAATTAGTATAG
1 GAATTTATAATTAATATAG
137702 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
GAATTTATAATTAATATAG
Found at i:145846 original size:31 final size:31
Alignment explanation
Indices: 145808--145882 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
145798 ATTCACCGGG
145808 TTTGTCCGCTGTATTTTCGTTTTTCTGAGAA
1 TTTGTCCGCTGTATTTTCGTTTTTCTGAGAA
145839 TTTGTCCGCTGTATTTTCGTTTTTCTGAGAA
1 TTTGTCCGCTGTATTTTCGTTTTTCTGAGAA
145870 TTTGTCCGCTGTA
1 TTTGTCCGCTGTA
145883 AAATAAGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (31 bp):
TTTGTCCGCTGTATTTTCGTTTTTCTGAGAA
Found at i:155130 original size:24 final size:24
Alignment explanation
Indices: 155085--155130 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
155075 TTCGAACTTA
*
155085 ATATTAAACCCTTTCAATTCAAAT
1 ATATTAAACCCTTTCAACTCAAAT
155109 ATATTAAA-CCTTTCAAACTCAA
1 ATATTAAACCCTTTC-AACTCAA
155131 CTCATTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATTAAACCCTTTCAACTCAAAT
Found at i:155591 original size:21 final size:21
Alignment explanation
Indices: 155567--155606 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
155557 AACTACTATT
*
155567 TTTAATTTTTAATTTTTTAAA
1 TTTAATTTTGAATTTTTTAAA
*
155588 TTTAATTTTGATTTTTTTA
1 TTTAATTTTGAATTTTTTA
155607 TTAAACTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTAATTTTGAATTTTTTAAA
Found at i:164731 original size:21 final size:21
Alignment explanation
Indices: 164707--164759 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
164697 TTACTTAGGG
164707 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
164728 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
164749 TACCGATTCCC
1 AACCGATTCCC
164760 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:164968 original size:13 final size:13
Alignment explanation
Indices: 164950--164981 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
164940 CTCAAGTTCG
164950 TTAATTCAAATAC
1 TTAATTCAAATAC
*
164963 TTAATTGAAATAC
1 TTAATTCAAATAC
164976 TTAATT
1 TTAATT
164982 ACTCAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (13 bp):
TTAATTCAAATAC
Found at i:165045 original size:31 final size:32
Alignment explanation
Indices: 164995--165085 Score: 134
Period size: 31 Copynumber: 2.9 Consensus size: 32
164985 CAACATAATG
*
164995 AAATACTTAAATACTTCCAAGTTTGATAAATTC
1 AAATACTTAAA-ACTTCCAAGTTCGATAAATTC
165028 AAATACTT-AAACTTCCAAGTTCGATAAATTC
1 AAATACTTAAAACTTCCAAGTTCGATAAATTC
165059 -AATACTTAAAAACTT-CAAGTTCGATAA
1 AAATACTT-AAAACTTCCAAGTTCGATAA
165086 TTGAAACAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
30 7 0.13
31 32 0.58
32 8 0.15
33 8 0.15
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (32 bp):
AAATACTTAAAACTTCCAAGTTCGATAAATTC
Found at i:175470 original size:78 final size:77
Alignment explanation
Indices: 175315--175474 Score: 196
Period size: 78 Copynumber: 2.1 Consensus size: 77
175305 AGTGCTGCCA
* *
175315 CTTTTCTTGCAATGCTGTGCAAAGGCATCTGAGGCATCACCTTTAGTCTCAACAGTATTTAAATC
1 CTTTTCTTGCAATGCTGTGCAAAGGCATCTGAGGCATAACCTTTAGTCTCAACAGTATTTAAATA
*
175380 CAGCATACCCCT
66 CAGCAAACCCCT
* * * * * *
175392 CTTTTCTTGCAATGCCTTTGCAAGGGCTTCTGAGGCATTAAGC-TTAGTCTCAGCAGTATTTGAA
1 CTTTTCTTGCAATG-CTGTGCAAAGGCATCTGAGGCA-TAACCTTTAGTCTCAACAGTATTTAAA
* *
175456 TAGAGCAAATCCCT
64 TACAGCAAACCCCT
175470 CTTTT
1 CTTTT
175475 ACCTCATCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
77 14 0.20
78 53 0.76
79 3 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (77 bp):
CTTTTCTTGCAATGCTGTGCAAAGGCATCTGAGGCATAACCTTTAGTCTCAACAGTATTTAAATA
CAGCAAACCCCT
Found at i:179479 original size:21 final size:21
Alignment explanation
Indices: 179437--179480 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
179427 AGTGACTAAC
* *
179437 CGATTAAACAAGTTAATAAAA
1 CGATTAAACAAATAAATAAAA
* *
179458 CGATTAATCAAATAAATTAAA
1 CGATTAAACAAATAAATAAAA
179479 CG
1 CG
179481 TAAAACTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (21 bp):
CGATTAAACAAATAAATAAAA
Found at i:184474 original size:18 final size:18
Alignment explanation
Indices: 184449--184491 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
184439 CACGGAATGC
184449 AAGATTACCGATAGGAAT
1 AAGATTACCGATAGGAAT
* * *
184467 AGGATTACCGGTGGGAAT
1 AAGATTACCGATAGGAAT
184485 AAGATTA
1 AAGATTA
184492 ATGGGAATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (18 bp):
AAGATTACCGATAGGAAT
Found at i:184662 original size:14 final size:11
Alignment explanation
Indices: 184630--184655 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
184620 TAACAAGTTA
184630 AATTTTATTAT
1 AATTTTATTAT
184641 AATTTTATTAT
1 AATTTTATTAT
184652 AATT
1 AATT
184656 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTATTAT
Found at i:188695 original size:15 final size:15
Alignment explanation
Indices: 188678--188707 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
188668 ATCTTTCTTT
188678 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
188694 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
188708 GATCTGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:189302 original size:13 final size:14
Alignment explanation
Indices: 189271--189304 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
189261 TAGTTTTAAA
189271 TATAAAAAATAATT
1 TATAAAAAATAATT
*
189285 AATAAAAAAT-ATT
1 TATAAAAAATAATT
189298 TATAAAA
1 TATAAAA
189305 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TATAAAAAATAATT
Found at i:196428 original size:22 final size:22
Alignment explanation
Indices: 196400--196442 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
196390 TACATGCAGG
*
196400 CGACCTCTTCCGACGTGCATGA
1 CGACCTCTTCAGACGTGCATGA
196422 CGACCTCTTCAGACGTGCATG
1 CGACCTCTTCAGACGTGCATG
196443 GCGCATGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (22 bp):
CGACCTCTTCAGACGTGCATGA
Found at i:196484 original size:31 final size:31
Alignment explanation
Indices: 196449--196541 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
196439 CATGGCGCAT
196449 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
*
196480 GCAAAGTTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
*
196511 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
196542 TAGAACACTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:207264 original size:22 final size:22
Alignment explanation
Indices: 207222--207264 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
207212 ACTTCTTTAA
*
207222 AACCTTAAACCACTAAGAAAAT
1 AACCTTAAACCACTAACAAAAT
207244 AACC-TAAACCACTAATCAAAA
1 AACCTTAAACCACTAA-CAAAA
207265 CCCTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (22 bp):
AACCTTAAACCACTAACAAAAT
Found at i:210058 original size:3 final size:3
Alignment explanation
Indices: 210050--210085 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
210040 AATATTATAC
*
210050 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
210086 ATTTTTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:210065 original size:12 final size:12
Alignment explanation
Indices: 210022--210084 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
210012 AATTTTATTT
210022 ATAA-ATTAA-A
1 ATAATATTAATA
210032 AT-ATATTAA-A
1 ATAATATTAATA
* *
210042 TATTATACTAATA
1 -ATAATATTAATA
210055 ATAATATTAATA
1 ATAATATTAATA
*
210067 ATAATAATAATA
1 ATAATATTAATA
210079 ATAATA
1 ATAATA
210085 AATTTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
9 1 0.02
10 8 0.18
11 2 0.04
12 33 0.73
13 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:210172 original size:2 final size:2
Alignment explanation
Indices: 210165--210216 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
210155 AGTTTAGTCT
210165 TA TA TA TA TA TA 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 TA TA TA TA TA TA
210207 TA TA TA TA TA
1 TA TA TA TA TA
210217 GTTGTACTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:218447 original size:2 final size:2
Alignment explanation
Indices: 218440--218498 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
218430 TCTTTTTAAA
218440 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
218482 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
218499 TATATATATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:218503 original size:2 final size:2
Alignment explanation
Indices: 218498--218526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
218488 ACACACACAC
218498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218527 CTCCCATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218795 original size:24 final size:24
Alignment explanation
Indices: 218700--218786 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
218690 ATCAAAACAT
*
218700 AATCCATGTCAAGTA-TC-ATCAG
1 AATCCAGGTCAAGTATTCGATCAG
218722 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
218746 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
218770 AATCCAGGTCATGTATT
1 AATCCAGGTCAAGTATT
218787 TTAATAGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 14 0.24
23 2 0.03
24 43 0.73
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCGATCAG
Found at i:227272 original size:42 final size:41
Alignment explanation
Indices: 227196--227274 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
227186 CAGATTTTAA
* * *
227196 TAGGGGTATCGATACCCTTGGCAGGGTACCGATACCTCAGT
1 TAGGGGTACCGATACCCTTAGCAGGATACCGATACCTCAGT
*
227237 TAGGGTGTACCGATACCCTTTAG-AGGATACTGATACCT
1 TAGGG-GTACCGATACCC-TTAGCAGGATACCGATACCT
227275 ACTTTAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.16
42 24 0.75
43 3 0.09
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (41 bp):
TAGGGGTACCGATACCCTTAGCAGGATACCGATACCTCAGT
Found at i:227985 original size:22 final size:22
Alignment explanation
Indices: 227949--228005 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
227939 CTACGCGGTT
*
227949 CTTCGGGACATATACAGAGGTC
1 CTTCGGGACAAATACAGAGGTC
* *
227971 CTTGGGGACAAATACATAGGTC
1 CTTCGGGACAAATACAGAGGTC
227993 CTTCGGGACAAAT
1 CTTCGGGACAAAT
228006 TTCACATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (22 bp):
CTTCGGGACAAATACAGAGGTC
Found at i:228962 original size:12 final size:11
Alignment explanation
Indices: 228945--228988 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
228935 TTAGCATTTG
228945 GTATTGTTCAAA
1 GTATTGTTC-AA
228957 GTATTGTTC-A
1 GTATTGTTCAA
*
228967 TTATTGTTCACA
1 GTATTGTTCA-A
228979 GTATTGTTCA
1 GTATTGTTCA
228989 TACCGTATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (11 bp):
GTATTGTTCAA
Found at i:228974 original size:22 final size:22
Alignment explanation
Indices: 228946--228989 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
228936 TAGCATTTGG
228946 TATTGTTCAAAGTATTGTTCAT
1 TATTGTTCAAAGTATTGTTCAT
*
228968 TATTGTTCACAGTATTGTTCAT
1 TATTGTTCAAAGTATTGTTCAT
228990 ACCGTATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (22 bp):
TATTGTTCAAAGTATTGTTCAT
Found at i:230121 original size:3 final size:3
Alignment explanation
Indices: 230106--230217 Score: 86
Period size: 3 Copynumber: 36.3 Consensus size: 3
230096 GTTTAGTAAG
* * *
230106 TAT TAT TAG TAT TAT TAT TAGT TAT AATT TAC TAT GGT-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT --TAT TAT TAT TAT
* * * *
230154 TAT TAT TAT TAT TAT TGT TAT TAC TAC TAT TA- TAT CAT TAT TAT GGTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT
230203 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
230218 GTTACTATGC
Statistics
Matches: 88, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
2 5 0.06
3 73 0.83
4 6 0.07
5 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:230297 original size:16 final size:16
Alignment explanation
Indices: 230276--230317 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
230266 TTTTATTATT
*
230276 ATATATTACACATTAA
1 ATATATTAAACATTAA
230292 ATATATTAAACATTAA
1 ATATATTAAACATTAA
230308 ATATATTAAA
1 ATATATTAAA
230318 TACATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATTAAACATTAA
Found at i:232793 original size:2 final size:2
Alignment explanation
Indices: 232786--232815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
232776 TACCAAATGA
232786 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
232816 GTAAATCACA
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):
AT
Found at i:235902 original size:20 final size:20
Alignment explanation
Indices: 235877--235969 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
235867 TTTTCCCAAT
235877 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
235897 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
235917 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
235938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
235959 TCGCAATGCGA
1 TCGCAATGCGA
235970 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:235919 original size:41 final size:41
Alignment explanation
Indices: 235874--235969 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
235864 CGATTTTCCC
235874 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
235915 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
235956 AAATCGCAATGCGA
1 AATTCGCAATGCGA
235970 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:235923 original size:21 final size:20
Alignment explanation
Indices: 235877--235969 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
235867 TTTTCCCAAT
*
235877 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
235897 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
235917 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
235938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
235959 TCGCAATGCGA
1 TCGCAATGCGA
235970 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:236025 original size:20 final size:21
Alignment explanation
Indices: 236000--236051 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
235990 TAATAAAAAA
*
236000 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTGACTT
236020 TCGCAAC-ACGATACTGACTT
1 TCGCAACGACGATACTGACTT
236040 TCGCAACG-CGAT
1 TCGCAACGACGAT
236052 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTGACTT
Found at i:236032 original size:41 final size:41
Alignment explanation
Indices: 235955--236032 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
235945 GCGAATTGGG
* * **
235955 AAAATCGCAATGCGATACTGACTATTGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATTGCAACACGATAATAA
*
235996 AAAATCGCAACGAGATACTTACT-TTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATT-GCAACACGATA
236033 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.06
41 29 0.94
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATTGCAACACGATAATAA
Found at i:236628 original size:19 final size:19
Alignment explanation
Indices: 236604--236648 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
236594 GCAACGAGAT
*
236604 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
236623 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
236642 AATCGCA
1 AATCGCA
236649 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:236666 original size:19 final size:19
Alignment explanation
Indices: 236644--236808 Score: 161
Period size: 19 Copynumber: 9.1 Consensus size: 19
236634 GAAACCAAAA
*
236644 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
236663 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
236682 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
236701 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
236721 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
236737 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
236754 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
236768 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
236787 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
236807 TC
1 TC
236809 AACCAAAAGA
Statistics
Matches: 121, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.49
20 34 0.28
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.