Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 15 of 206
Found at i:4534694 original size:40 final size:40
Alignment explanation
Indices: 4534650--4534759 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
4534640 AGCTTTTGTG
* * *
4534650 GCATTAACGGCACTTTTTGAAAAACGCCGCTACATATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTACAGATCGA
* * *
4534690 GCATTAGTGGCGTTTTTTGAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTACAGATCGA
4534730 GCATTAGCGGCGCTTTTTGAAAAACGCCGC
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGC
4534760 AAAAAAATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTACAGATCGA
Found at i:4534835 original size:115 final size:115
Alignment explanation
Indices: 4534690--4534989 Score: 384
Period size: 115 Copynumber: 2.6 Consensus size: 115
4534680 TACATATCGA
*
4534690 GCATTAGTGGCGTTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
1 GCATTAGAGGCGTTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
* * *
4534755 GCCGCAAAAAAATTAAACACAACGCCGTCGTTTTGTGTTAACCTTTAGTG
66 GCCGCAAAAAAATTAAACACAACACCATCGTTTTATGTTAACCTTTAGTG
* ** * * * *
4534805 GCATTAGAGGCGTTTTTTGGAAAATACCGCTATATATCGAGCATTAGCGGTGCTTTTAGAAAAAT
1 GCATTAGAGGCGTTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
* * * **
4534870 GCCGCAAAAAATTTAAGCACAACACCATCGTTTTATGTTGAGTTTTAGTG
66 GCCGCAAAAAAATTAAACACAACACCATCGTTTTATGTTAACCTTTAGTG
* * * * * * * *
4534920 GCATTAGCGGCGCTTTTAGTAAAACGTCGCTAGAGATGGAGCATTAGCGGCGCGTTTTGAAAAAC
1 GCATTAGAGGCGTTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
4534985 GCCGC
66 GCCGC
4534990 TATAGATCGA
Statistics
Matches: 155, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 155 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (115 bp):
GCATTAGAGGCGTTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
GCCGCAAAAAAATTAAACACAACACCATCGTTTTATGTTAACCTTTAGTG
Found at i:4534842 original size:155 final size:153
Alignment explanation
Indices: 4534499--4534874 Score: 466
Period size: 155 Copynumber: 2.4 Consensus size: 153
4534489 TAGATCGATT
* * * * * * * * *
4534499 ATTAGCGGCGCTTTCTGAAAAACGCTGCTATAGATCGAGCATTAGCGGCACATTTTGAAAAACGA
1 ATTAACGGCACTTTTTGAAAAACACCGCTATATATCGAGCATTAGCGGCGCTTTTTGAAAAACGC
* *
4534564 CGCTATAGGTCAAACATTAGCGGCGCTTTTTGATAACACCGCAAAAAATTAAACACAACGCAGTC
66 CGCTATAGATCAAACATTAGCGGCGCTTTTTGAAAACACCGCAAAAAATTAAACACAACGCAGTC
* *
4534629 GTTTTGTGTTAAGCTTTTGTGGC
131 GTTTTGTGTTAACCTTTAGTGGC
* * * *
4534652 ATTAACGGCACTTTTTGAAAAACGCCGCTACATATCGAGCATTAGTGGCGTTTTTTGAAAAACGC
1 ATTAACGGCACTTTTTGAAAAACACCGCTATATATCGAGCATTAGCGGCGCTTTTTGAAAAACGC
* * * *
4534717 CGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAACACAACGCCG
66 CGCTATAGATCAAACATTAGCGGCGCTTTTTG-AAAACACCGC-AAAAAATTAAACACAACGCAG
4534782 TCGTTTTGTGTTAACCTTTAGTGGC
129 TCGTTTTGTGTTAACCTTTAGTGGC
** * * * * *
4534807 ATTAGA-GGCGTTTTTTGGAAAATACCGCTATATATCGAGCATTAGCGGTGCTTTTAGAAAAATG
1 ATTA-ACGGCACTTTTTGAAAAACACCGCTATATATCGAGCATTAGCGGCGCTTTTTGAAAAACG
4534871 CCGC
65 CCGC
4534875 AAAAAATTTA
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
153 83 0.44
154 8 0.04
155 98 0.52
156 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (153 bp):
ATTAACGGCACTTTTTGAAAAACACCGCTATATATCGAGCATTAGCGGCGCTTTTTGAAAAACGC
CGCTATAGATCAAACATTAGCGGCGCTTTTTGAAAACACCGCAAAAAATTAAACACAACGCAGTC
GTTTTGTGTTAACCTTTAGTGGC
Found at i:4534984 original size:40 final size:40
Alignment explanation
Indices: 4534920--4535015 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
4534910 AGTTTTAGTG
* * *
4534920 GCATTAGCGGCGCTTTTAGTAAAACGTCGCTAGAGATGGA
1 GCATTAGCGGCGCTTTTAGAAAAACGCCGCTAGAGATCGA
*
4534960 GCATTAGCGGCGCGTTTT-GAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGC-TTTTAGAAAAACGCCGCTAGAGATCGA
* *
4535000 GCTTTAGCGTCGCTTT
1 GCATTAGCGGCGCTTT
4535016 ATCGAAAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 3 0.06
40 42 0.86
41 4 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTAGAAAAACGCCGCTAGAGATCGA
Found at i:4535354 original size:21 final size:21
Alignment explanation
Indices: 4535330--4535371 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4535320 TAGTTTAGAG
*
4535330 TTTAGGGTATAAGGCTTAGGA
1 TTTAAGGTATAAGGCTTAGGA
* *
4535351 TTTAAGGTTTAAGGTTTAGGA
1 TTTAAGGTATAAGGCTTAGGA
4535372 GTTATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.31, T:0.38
Consensus pattern (21 bp):
TTTAAGGTATAAGGCTTAGGA
Found at i:4535428 original size:21 final size:21
Alignment explanation
Indices: 4535404--4535450 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4535394 ATTATGGGTG
4535404 TAGGGATT-ATAGTTTAAGGTT
1 TAGGGATTGA-AGTTTAAGGTT
* *
4535425 TAGGGGTTGAGGTTTAAGGTT
1 TAGGGATTGAAGTTTAAGGTT
4535446 TAGGG
1 TAGGG
4535451 GTTAAGGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (21 bp):
TAGGGATTGAAGTTTAAGGTT
Found at i:4535451 original size:21 final size:21
Alignment explanation
Indices: 4535415--4535469 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
4535405 AGGGATTATA
*
4535415 GTTTAAGGTTTAGGGGTTGAG
1 GTTTAAGGTTTAGGGGTTAAG
4535436 GTTTAAGGTTTAGGGGTTAAG
1 GTTTAAGGTTTAGGGGTTAAG
*
4535457 GGTTAAGGGTTTA
1 GTTTAA-GGTTTA
4535470 TGTTTTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (21 bp):
GTTTAAGGTTTAGGGGTTAAG
Found at i:4536038 original size:3 final size:3
Alignment explanation
Indices: 4536030--4536060 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4536020 ACATGTAACT
4536030 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4536061 CACTTCAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4538557 original size:20 final size:19
Alignment explanation
Indices: 4538528--4538568 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4538518 ATTTAAAAAG
4538528 TAAAAATTATTAAATTATTT
1 TAAAAATTATTAAATT-TTT
*
4538548 TAAAATTTATTAAATTTTT
1 TAAAAATTATTAAATTTTT
4538567 TA
1 TA
4538569 GAATATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAAATTATTAAATTTTT
Found at i:4541363 original size:3 final size:3
Alignment explanation
Indices: 4541355--4541395 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
4541345 AAAATTTAAG
* * *
4541355 AAT AAT AAT ATT AAT AAT AAT GAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4541396 AATTTAAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4541886 original size:21 final size:20
Alignment explanation
Indices: 4541860--4541916 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
4541850 AATAGCTTCG
*
4541860 AAAAAAAAGGAAGAAAATAA
1 AAAAAAAAGGAAGAAAAAAA
* *
4541880 AATAAAAA-TAATGAAAAAAA
1 AAAAAAAAGGAA-GAAAAAAA
4541900 AAACAAAAAGGAAGAAA
1 AAA-AAAAAGGAAGAAA
4541917 CACCTTAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.07
20 16 0.55
21 9 0.31
22 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGGAAGAAAAAAA
Found at i:4542234 original size:16 final size:18
Alignment explanation
Indices: 4542213--4542256 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
4542203 TGGGCCATTA
4542213 GGGCTT-TT-TGTAATTT
1 GGGCTTGTTGTGTAATTT
4542229 GGGCTTGTTGGATGTAATTT
1 GGGCTTGTT-G-TGTAATTT
4542249 GGGCTTGT
1 GGGCTTGT
4542257 AGGGCTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
20 16 0.67
ACGTcount: A:0.11, C:0.07, G:0.34, T:0.48
Consensus pattern (18 bp):
GGGCTTGTTGTGTAATTT
Found at i:4553159 original size:9 final size:9
Alignment explanation
Indices: 4553142--4553176 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4553132 AATAAATATT
4553142 AATTAATTA
1 AATTAATTA
*
4553151 AATTCATTA
1 AATTAATTA
*
4553160 AATTAAATA
1 AATTAATTA
4553169 AATTAATT
1 AATTAATT
4553177 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:4554473 original size:23 final size:24
Alignment explanation
Indices: 4554460--4554509 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
4554450 TAATTTTTAA
4554460 ATTTTGAATTATTT-AGTGATAAT
1 ATTTTGAATTATTTAAGTGATAAT
4554483 ATTTTGAATTATTT-AGTGATAAT
1 ATTTTGAATTATTTAAGTGATAAT
4554506 ATTT
1 ATTT
4554510 AGGAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (24 bp):
ATTTTGAATTATTTAAGTGATAAT
Found at i:4554510 original size:13 final size:13
Alignment explanation
Indices: 4554469--4554511 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
4554459 AATTTTGAAT
4554469 TATTTAGTGATAA
1 TATTTAGTGATAA
*
4554482 TATTT--TGA-AT
1 TATTTAGTGATAA
4554492 TATTTAGTGATAA
1 TATTTAGTGATAA
4554505 TATTTAG
1 TATTTAG
4554512 GAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:4562982 original size:20 final size:20
Alignment explanation
Indices: 4562944--4562983 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4562934 AGGCAACCGA
*
4562944 CATTTATTTTTATTTATTTT
1 CATTTATTTTAATTTATTTT
4562964 CATTTA-TTTAATTTAATTTT
1 CATTTATTTTAATTT-ATTTT
4562984 GAATTCTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTATTTTAATTTATTTT
Found at i:4564457 original size:23 final size:23
Alignment explanation
Indices: 4564409--4564458 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
4564399 ATTTTTGAAT
*
4564409 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTAATAATA
4564431 TTTAGAATTATTTAGTAATAATA
1 TTTAGAATTATTTAGTAATAATA
4564454 TTTAG
1 TTTAG
4564459 GAAAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTAGAATTATTTAGTAATAATA
Found at i:4565890 original size:17 final size:17
Alignment explanation
Indices: 4565868--4565925 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
4565858 GAGGTTTTTT
4565868 TAAAAATATTTTATTTA
1 TAAAAATATTTTATTTA
*
4565885 TAAAAATATTGTT-TTAA
1 TAAAAATATT-TTATTTA
4565902 TAAATAA-ATTTTATGTTA
1 TAAA-AATATTTTAT-TTA
*
4565920 GAAAAA
1 TAAAAA
4565926 AGAGAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 2 0.06
17 23 0.68
18 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TAAAAATATTTTATTTA
Found at i:4573215 original size:46 final size:46
Alignment explanation
Indices: 4573162--4573301 Score: 262
Period size: 46 Copynumber: 3.0 Consensus size: 46
4573152 CCATGGCAAA
4573162 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
4573208 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
4573254 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
4573300 TT
1 TT
4573302 ATAGCATTGT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:4580584 original size:88 final size:89
Alignment explanation
Indices: 4580478--4580654 Score: 266
Period size: 89 Copynumber: 2.0 Consensus size: 89
4580468 GCATATGTCT
*
4580478 GGTTACATGTAAAATATTACAGTTAATTATTATCGGATG-TAACCTTATTAGCAGATTGAATATA
1 GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATGTTAACCTTATTAGCAGATTGAATATA
4580542 CTATGACATAGTATTTCATTTCTC
66 CTATGACATAGTATTTCATTTCTC
* * * * *
4580566 GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATATA
1 GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATGTTAACCTTATTAGCAGATTGAATATA
* * *
4580631 GTATGACATTGTATTTCCTTTCTC
66 CTATGACATAGTATTTCATTTCTC
4580655 AAGGAAAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 35 0.44
89 44 0.56
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (89 bp):
GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATGTTAACCTTATTAGCAGATTGAATATA
CTATGACATAGTATTTCATTTCTC
Found at i:4581092 original size:79 final size:79
Alignment explanation
Indices: 4580993--4581150 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
4580983 ATTTAGACGG
4580993 AACTTCCTGTCACAATTATGGTTGGGTTATTGATGTCTGGGAATAATATAGTTTAAGACTTTGAA
1 AACTTCCTGTCACAATTATGGTTGGGTTATTGATGTCTGGGAATAATATAGTTTAAGACTTTGAA
4581058 ATTTGTTCATATGT
66 ATTTGTTCATATGT
4581072 AACTTCCTGTCACAATTATGGTTGGGTTATTGATGTCTGGGAATAATATAGTTTAAGACTTTGAA
1 AACTTCCTGTCACAATTATGGTTGGGTTATTGATGTCTGGGAATAATATAGTTTAAGACTTTGAA
4581137 ATTTGTTCATATGT
66 ATTTGTTCATATGT
4581151 TGTACTCGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (79 bp):
AACTTCCTGTCACAATTATGGTTGGGTTATTGATGTCTGGGAATAATATAGTTTAAGACTTTGAA
ATTTGTTCATATGT
Found at i:4591308 original size:30 final size:30
Alignment explanation
Indices: 4591274--4591333 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
4591264 ATTTTTATTA
4591274 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
4591304 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
4591334 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:4596007 original size:18 final size:18
Alignment explanation
Indices: 4595979--4596028 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
4595969 AAAAACATTA
4595979 AAAAAATTTTAAAATTTAC
1 AAAAAA-TTTAAAATTTAC
* *
4595998 AAAAAATTTAGAATTTTC
1 AAAAAATTTAAAATTTAC
*
4596016 AAAAAAGTTAAAA
1 AAAAAATTTAAAA
4596029 AAGAATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAAATTTAAAATTTAC
Found at i:4596020 original size:19 final size:20
Alignment explanation
Indices: 4595978--4596021 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4595968 TAAAAACATT
4595978 AAAAAAATTTTAAAATTTAC
1 AAAAAAATTTTAAAATTTAC
* *
4595998 -AAAAAA-TTTAGAATTTTC
1 AAAAAAATTTTAAAATTTAC
4596016 AAAAAA
1 AAAAAA
4596022 GTTAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAAAATTTTAAAATTTAC
Found at i:4596044 original size:21 final size:23
Alignment explanation
Indices: 4596007--4596052 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
4595997 CAAAAAATTT
4596007 AGAATTTTCAAAAAAGTTA-AAAA
1 AGAATTTTC-AAAAAGTTATAAAA
4596030 AGAATTTTC-AAAAGTTATAAAA
1 AGAATTTTCAAAAAGTTATAAAA
4596052 A
1 A
4596053 AAACTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 9 0.41
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (23 bp):
AGAATTTTCAAAAAGTTATAAAA
Found at i:4596155 original size:9 final size:9
Alignment explanation
Indices: 4596143--4596219 Score: 52
Period size: 9 Copynumber: 8.1 Consensus size: 9
4596133 GAAAAAAGCA
4596143 AAAAATTAT
1 AAAAATTAT
4596152 -AAAA-TACT
1 AAAAATTA-T
*
4596160 AAAAATAAT
1 AAAAATTAT
4596169 ACAAAATTATT
1 A-AAAATTA-T
4596180 AAAAATTTGTAT
1 AAAAA--T-TAT
*
4596192 AACAATTAT
1 AAAAATTAT
4596201 AAAAA-TAT
1 AAAAATTAT
4596209 AACAAATTAT
1 AA-AAATTAT
4596219 A
1 A
4596220 GGAGACATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
7 2 0.04
8 10 0.19
9 16 0.30
10 16 0.30
11 2 0.04
12 6 0.11
13 2 0.04
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4596506 original size:20 final size:22
Alignment explanation
Indices: 4596481--4596520 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4596471 GGAAATTCTA
4596481 ATTTTT-AAT-AATTTTATATT
1 ATTTTTAAATAAATTTTATATT
4596501 ATTTTTAAATAAATTTTATA
1 ATTTTTAAATAAATTTTATA
4596521 AGTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTAAATAAATTTTATATT
Found at i:4596590 original size:18 final size:18
Alignment explanation
Indices: 4596555--4596589 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4596545 TTTTTTTAAA
4596555 AAAAATTCCTATTATTTT
1 AAAAATTCCTATTATTTT
*
4596573 AAAAATT-CTTTTATTTT
1 AAAAATTCCTATTATTTT
4596590 TTTGCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAAATTCCTATTATTTT
Found at i:4603353 original size:38 final size:38
Alignment explanation
Indices: 4603297--4603411 Score: 221
Period size: 38 Copynumber: 3.0 Consensus size: 38
4603287 GTATTTACAA
4603297 ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
1 ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
*
4603335 ATTACCACACCTTTTGGCCAATTTATTACCCCATTTTT
1 ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
4603373 ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
1 ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
4603411 A
1 A
4603412 CTTGTTTTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.43
Consensus pattern (38 bp):
ATTATCACACCTTTTGGCCAATTTATTACCCCATTTTT
Found at i:4607616 original size:2 final size:2
Alignment explanation
Indices: 4607611--4607642 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4607601 TTTCCGAATA
4607611 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
4607643 GAATGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4607983 original size:12 final size:12
Alignment explanation
Indices: 4607968--4608008 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
4607958 GAACATAGAG
*
4607968 ATAATGATAGTA
1 ATAATGATAATA
4607980 ATAATGATAATA
1 ATAATGATAATA
4607992 TATAAT-ATAATA
1 -ATAATGATAATA
4608004 ATAAT
1 ATAAT
4608009 AATGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
ATAATGATAATA
Found at i:4608236 original size:27 final size:26
Alignment explanation
Indices: 4608196--4608255 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
4608186 AGATGGGCCA
4608196 AATTGAAACAAAAACGAAATATGAGGCTT
1 AATTGAAACAAAAAC-AAA-ATG-GGCTT
4608225 AATT-AAA-AAAAACAAAATGGGCTT
1 AATTGAAACAAAAACAAAATGGGCTT
*
4608249 GATTGAA
1 AATTGAA
4608256 GCGCGTCGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 8 0.28
25 5 0.17
26 3 0.10
27 6 0.21
28 3 0.10
29 4 0.14
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (26 bp):
AATTGAAACAAAAACAAAATGGGCTT
Found at i:4609619 original size:44 final size:44
Alignment explanation
Indices: 4609566--4610490 Score: 797
Period size: 44 Copynumber: 20.9 Consensus size: 44
4609556 AAGACTTGTA
* * * * *
4609566 TCTTCGATCTACTTCACGCTAATACATGAAGACAAGACCTGCTA
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
*
4609610 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* *
4609654 TCTTTGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
*
4609698 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC-GACTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-CTT
* * *** *
4609742 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* *
4609786 GTATTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTG-TA
1 -TCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTT
* * * * * * * * *
4609830 TCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTA
1 TCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGCTT
* * * **
4609875 TCTTCGATCTACTTCACGCCAGTACATGAAGATAATATCTATTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *** *
4609919 TCTTCGATCTA-TTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTT-CA-CGCCAGTACATGAAGACAAGATCTGCTT
* *
4609963 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * * * *** *
4610007 TCTTCGATCTGCTTCGTCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
* *
4610052 TATTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
** * *** * *
4610096 TCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGATCTGGTA
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* *
4610141 TCTTTGATCTATTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * * *** * *
4610185 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
**
4610230 TCTTTGATCTACTTCACGCCAGTACATGAAGACACTATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *** * * * *
4610274 T-TTCCGATCTACTTCACCACCAGTATGGGAAGATAAAATTTG-TA
1 TCTT-TGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* * * * * * * * * *
4610318 TATTCGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTGCTA
1 TCTTTGATCTACTTCAC-GCCAG-TACATGAAGACAAGATCTGCTT
* * **
4610363 TCTTTGATCTACTTCACGCCAGTACATGAAGATAATATCTATTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
*
4610407 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *
4610451 TCCTTGATCTACTTTACGCCAATACATGAAGACAAGATCT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
4610491 ATTATCTTTC
Statistics
Matches: 710, Mismatches: 149, Indels: 44
0.79 0.17 0.05
Matches are distributed among these distances:
43 42 0.06
44 459 0.65
45 208 0.29
46 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
Found at i:4609824 original size:89 final size:89
Alignment explanation
Indices: 4609593--4610499 Score: 949
Period size: 89 Copynumber: 10.2 Consensus size: 89
4609583 GCTAATACAT
* * *
4609593 GAAGACAAGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * ***
4609658 TGATCTACTTCA-CGCCAATACAT
66 CGATCTACTTCACCACCAGTATGG
* *
4609681 AAAGACAAGATCTGCTT-TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC-GACTTTC
1 GAAGACAAGATCTG-TTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-CTTTC
* *
4609744 TTTGATCTACTCCACCACCAGTATGG
64 TTCGATCTACTTCACCACCAGTATGG
* * * *
4609770 GGAGACAAGATCTGTTGTATTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTG-TATCT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCT
* * * * *
4609833 TCGATCCACTTCGCTACCAATATAG
65 TCGATCTACTTCACCACCAGTATGG
* * * * * **
4609858 GAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAGTACATGAAGATAATATCTATTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
4609923 CGATCTA-TTCCACCACCAGTATGG
66 CGATCTACTT-CACCACCAGTATGG
* * *
4609947 GGAGACAAGATCTGTT-TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* **
4610011 CGATCTGCTTCGTCACCAGTATGG
66 CGATCTACTTCACCACCAGTATGG
* * *
4610035 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
4610100 CAATCTACTTCACCACCAGTATGG
66 CGATCTACTTCACCACCAGTATGG
* * *
4610124 GAAGACAAGATCTGGTATCTTTGATCTATTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * *
4610189 TGATCTGCTTCGCCACCAGTATGG
66 CGATCTACTTCACCACCAGTATGG
* **
4610213 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACACTATCTGCTTT-TT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
4610277 CCGATCTACTTCACCACCAGTATGG
66 -CGATCTACTTCACCACCAGTATGG
* * * * * * * * * * * * *
4610302 GAAGATAAAATTTG-TATATTCGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTGCTATC
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCAC-GCCAG-TACATGAAGACAAGATCTGCTTTC
* * ***
4610365 TTTGATCTACTTCA-CGCCAGTACAT
64 TTCGATCTACTTCACCACCAGTATGG
* * * * *
4610390 GAAGATAATATCTATTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCCT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-CT
* * * ***
4610455 T-GATCTACTTTA-CGCCAATACAT
65 TCGATCTACTTCACCACCAGTATGG
*
4610478 GAAGACAAGATCTATTATCTTT
1 GAAGACAAGATCTGTTATCTTT
4610500 CAACCTGCTC
Statistics
Matches: 693, Mismatches: 108, Indels: 36
0.83 0.13 0.04
Matches are distributed among these distances:
87 1 0.00
88 312 0.45
89 377 0.54
90 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (89 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCACCACCAGTATGG
Found at i:4609891 original size:177 final size:176
Alignment explanation
Indices: 4609593--4610463 Score: 980
Period size: 177 Copynumber: 4.9 Consensus size: 176
4609583 GCTAATACAT
* * *
4609593 GAAGACAAGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATATTTGATCTACTTCACGCC-ATACATGAAGACAAGATCTGCTTTCTT
* * * * ** * *
4609658 TGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATAC
65 TGATCTACTTCGCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTAC
*
4609723 ATGAAGACAAGATC-GACTTTCTTTGATCTACTCCACCACCAGTATGG
130 ATGAAGACAAGATCTG-CTTTCTTCGATCTACTCCACCACCAGTATGG
* * *
4609770 GGAGACAAGATCTGTTGTATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTG-TATCTT
1 GAAGACAAGATCTGTTATATTTGATCTACTTCACGCC-ATACATGAAGACAAGATCTGCTTTCTT
* * * * *
4609834 CGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAGTA
65 TGATCTACTTCGC-ACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTA
* * ** *
4609899 CATGAAGATAATATCTATTTTCTTCGATCTATTCCACCACCAGTATGG
129 CATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * * *
4609947 GGAGACAAGATCTGTT-TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATATTTGATCTACTTCACGCCA-TACATGAAGACAAGATCTGCTTTCTT
* * * *
4610011 CGATCTGCTTCGTCACCAGTATGGGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAGTA
65 TGATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTA
* * *
4610076 CATGAAGACAAGATCTGTTTTCTTCAATCTACTTCACCACCAGTATGG
129 CATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
* * * *
4610124 GAAGACAAGATCTGGTATCTTTGATCTATTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATATTTGATCTACTTCACGCCA-TACATGAAGACAAGATCTGCTTTCTT
* * *
4610189 TGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTA
65 TGATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTA
** *
4610254 CATGAAGACACTATCTGCTTT-TTCCGATCTACTTCACCACCAGTATGG
129 CATGAAGACAAGATCTGCTTTCTT-CGATCTACTCCACCACCAGTATGG
* * * * * * * * * * * *
4610302 GAAGATAAAATTTG-TATATTCGATCCACTTCGCTACCGATATAGGAAGACAGGACCTGCTATCT
1 GAAGACAAGATCTGTTATATTTGATCTACTTCAC-GCC-ATACATGAAGACAAGATCTGCTTTCT
* * * * * * ** * *
4610366 TTGATCTACTTCACGCCAGTACATGAAGATAATATCTATTTTCTTTGATCTACTTCACGCCAATA
64 TTGATCTACTTCGCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTA
4610431 CATGAAGACAAGATCTGCTTTCCTT-GATCTACT
129 CATGAAGACAAGATCTGCTTT-CTTCGATCTACT
4610464 TTACGCCAAT
Statistics
Matches: 602, Mismatches: 81, Indels: 22
0.85 0.11 0.03
Matches are distributed among these distances:
175 1 0.00
176 52 0.09
177 354 0.59
178 192 0.32
179 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (176 bp):
GAAGACAAGATCTGTTATATTTGATCTACTTCACGCCATACATGAAGACAAGATCTGCTTTCTTT
GATCTACTTCGCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACA
TGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGG
Found at i:4612057 original size:13 final size:13
Alignment explanation
Indices: 4612039--4612064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4612029 AAAGAGATTT
4612039 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
4612052 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
4612065 AAATTGAACA
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:4612134 original size:19 final size:20
Alignment explanation
Indices: 4612097--4612136 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4612087 TCTCTTCGCA
* *
4612097 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
4612117 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
4612136 T
1 T
4612137 AAGCACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:4616262 original size:44 final size:44
Alignment explanation
Indices: 4616196--4616609 Score: 382
Period size: 44 Copynumber: 9.3 Consensus size: 44
4616186 TACTGGTGGC
* * *
4616196 GAAGCAGATCAAAGAAAGCAGATCTTATCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
4616240 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* *
4616285 GAAGCAGATCAAAGAAAACAGATCTTGTCTTTATGTACTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
4616329 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
** * *
4616374 GAAGTAGATTGAAGAAAGCAGATCTTGTCTTCATGTACTAGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* * * *** * *
4616418 GAAGTAGATCAAATATAGCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * * *
4616463 GAAATAGATCGAAGAAAACAAATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
* *** *
4616507 GAAGTAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGT
* * *
4616551 GGAA-TAGATCGAAGAAAATAGATCTTATCTTCATGTACTGGCGT
1 -GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
4616595 GAAGTAGATCAAAGA
1 GAAGTAGATCAAAGA
4616610 TAGTAGGTCC
Statistics
Matches: 286, Mismatches: 77, Indels: 14
0.76 0.20 0.04
Matches are distributed among these distances:
43 23 0.08
44 139 0.49
45 124 0.43
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGT
Found at i:4616323 original size:89 final size:89
Alignment explanation
Indices: 4616163--4616701 Score: 674
Period size: 89 Copynumber: 6.1 Consensus size: 89
4616153 GAGCAGGTTG
* * * * * *
4616163 AAGATA-CAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTATCTT
1 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTT
4616227 CATGTACTGGCGTGAAGTAGATCA
66 CATGTACTGGCGTGAAGTAGATCA
* *
4616251 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTT
1 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTT
*
4616316 TATGTACTGGCGTGAAGTAGATCA
66 CATGTACTGGCGTGAAGTAGATCA
* *
4616340 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTGAAGAAAGCAGATCTTGTCTT
1 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTT
*
4616405 CATGTACTAGCGTGAAGTAGATCA
66 CATGTACTGGCGTGAAGTAGATCA
* * * *
4616429 AATATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCGAAGAAAACAAATCTTGTCTT
1 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTT
*
4616494 CATGTATTGGCGTGAAGTAGATCA
66 CATGTACTGGCGTGAAGTAGATCA
* * * * *
4616518 AAGA-AACAGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCGAAGAAAATAGATCTTATCT
1 AAGATACCAGATCTTGTCTTCCCATACTGGTGG-CGAAGTAGATCGAAGAAAACAGATCTTGTCT
4616581 TCATGTACTGGCGTGAAGTAGATCA
65 TCATGTACTGGCGTGAAGTAGATCA
** * * * * * * * * *
4616606 AAGATAGTAGGTCCTGTCTTCCTATA-TCGGTAGCGAAGTGGATCGAA-TATACAGATTTTATCT
1 AAGATACCAGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCT
*** * *
4616669 TCCCATACTGGTGGTGAAGTAGATCG
65 TCATGTACTGG-CGTGAAGTAGATCA
4616695 AAGATAC
1 AAGATAC
4616702 AAGTCTTATC
Statistics
Matches: 399, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
88 107 0.27
89 292 0.73
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (89 bp):
AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTT
CATGTACTGGCGTGAAGTAGATCA
Found at i:4616712 original size:44 final size:45
Alignment explanation
Indices: 4616163--4616708 Score: 361
Period size: 44 Copynumber: 12.3 Consensus size: 45
4616153 GAGCAGGTTG
* * *
4616163 AAGATACAA-ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCA
1 AAGATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* * *** *
4616207 AAGAAAGC-AGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCA
1 AAGATA-CAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* * *
4616251 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCA
1 AAGATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* **** *
4616296 AAGA-AAACAGATCTTGTCTTTATGTACTGG-CGTGAAGTAGATCA
1 AAGATACA-AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* * **
4616340 AAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTG
1 AAGATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* *** * *
4616385 AAGAAAGC-AGATCTTGTCTTCATGTACTAG-CGTGAAGTAGATCA
1 AAGATA-CAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* * * *
4616429 AATATAGC-AGATCTTGTCTTCCCATACTGGTGGCGAAATAGATCG
1 AAGATA-CAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* *** * *
4616474 AAGAAAACAA-ATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCA
1 AAG-ATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
* * *
4616518 AAGAAAC-AGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCG
1 AAGATACAAGATCTTGTCTTCCCATACTGGTGGT-GAAGTAGATCA
* * *** *
4616562 AAGA-AAATAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCA
1 AAGATACA-AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
** * * * * * * *
4616606 AAGATAGTAGGTCCTGTCTTCCTATA-TCGGTAGCGAAGTGGATCG
1 AAGATACAAGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCA
* * * *
4616651 AATATAC-AGATTTTATCTTCCCATACTGGTGGTGAAGTAGATCG
1 AAGATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
4616695 AAGATACAAG-TCTT
1 AAGATACAAGATCTT
4616709 ATCTCCCTGA
Statistics
Matches: 377, Mismatches: 103, Indels: 44
0.72 0.20 0.08
Matches are distributed among these distances:
42 1 0.00
43 25 0.07
44 196 0.52
45 151 0.40
46 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
AAGATACAAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA
Found at i:4618150 original size:3 final size:3
Alignment explanation
Indices: 4618123--4618174 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
4618113 TTTAAACATA
* *
4618123 ATT ATC ATT ATT A-T ATT ATGCT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT--T ATT ATT ATT ATT ATT ATT ATT ATT
*
4618169 TTT ATT
1 ATT ATT
4618175 TTTTTACAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
5 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:4618267 original size:11 final size:11
Alignment explanation
Indices: 4618253--4618294 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
4618243 CGTATATTGG
4618253 TACATATTTTA
1 TACATATTTTA
4618264 TACATATTTTA
1 TACATATTTTA
4618275 T---TATTTTA
1 TACATATTTTA
*
4618283 TACATAGTTTA
1 TACATATTTTA
4618294 T
1 T
4618295 TATTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 8 0.30
11 19 0.70
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (11 bp):
TACATATTTTA
Found at i:4618316 original size:22 final size:19
Alignment explanation
Indices: 4618257--4618302 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
4618247 TATTGGTACA
4618257 TATTTTATACATATTTTAT
1 TATTTTATACATATTTTAT
*
4618276 TATTTTATACATAGTTTAT
1 TATTTTATACATATTTTAT
4618295 TATTTTAT
1 TATTTTAT
4618303 TTCATCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTATACATATTTTAT
Found at i:4619612 original size:167 final size:167
Alignment explanation
Indices: 4619336--4619669 Score: 641
Period size: 167 Copynumber: 2.0 Consensus size: 167
4619326 AATTTTGAGA
4619336 AATTGTACCCTAACGTATTGGGACTCGATTTCTTTACATGTCTTGAACAATTGATTATCCTTTTC
1 AATTGTACCCTAACGTATTGGGACTCGATTTCTTTACATGTCTTGAACAATTGATTATCCTTTTC
4619401 TGATTTCATCATTTGTTTTTTTAAAACTGCTTTTTAACCCACGACACTAAGACATTAAATAATCG
66 TGATTTCATCATTTGTTTTTTTAAAACTGCTTTTTAACCCACGACACTAAGACATTAAATAATCG
4619466 ATTTGGTACCAATTTTGGGCGTTACGAGGGTGCTAAC
131 ATTTGGTACCAATTTTGGGCGTTACGAGGGTGCTAAC
*
4619503 AATTGTACCCTAACGTATTGGGACTCGATTTCTTTACATGTCTTGAACAATTGATTATCTTTTTC
1 AATTGTACCCTAACGTATTGGGACTCGATTTCTTTACATGTCTTGAACAATTGATTATCCTTTTC
* *
4619568 TGATTTCATCATTTGTTTTTTTAAAACTGCTTTTTAGCCCACGACACTAAGACATTAAATAATTG
66 TGATTTCATCATTTGTTTTTTTAAAACTGCTTTTTAACCCACGACACTAAGACATTAAATAATCG
4619633 ATTTGGTACCAATTTTGGGCGTTACGAGGGTGCTAAC
131 ATTTGGTACCAATTTTGGGCGTTACGAGGGTGCTAAC
4619670 CCTTCCTCGT
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 164 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (167 bp):
AATTGTACCCTAACGTATTGGGACTCGATTTCTTTACATGTCTTGAACAATTGATTATCCTTTTC
TGATTTCATCATTTGTTTTTTTAAAACTGCTTTTTAACCCACGACACTAAGACATTAAATAATCG
ATTTGGTACCAATTTTGGGCGTTACGAGGGTGCTAAC
Found at i:4625857 original size:2 final size:2
Alignment explanation
Indices: 4625852--4625977 Score: 84
Period size: 2 Copynumber: 64.5 Consensus size: 2
4625842 AGGAAGAATA
*
4625852 AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
* * * * * * * *
4625894 AT AT GA- AT GT AT AT -T TT AG A- AT AT GT AT GT AT AA AA AA AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
4625934 CAGG A- AG A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4625975 AT A
1 AT A
4625978 AAATACGTAT
Statistics
Matches: 102, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
1 6 0.06
2 93 0.91
3 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (2 bp):
AT
Found at i:4625900 original size:93 final size:93
Alignment explanation
Indices: 4625803--4625977 Score: 341
Period size: 93 Copynumber: 1.9 Consensus size: 93
4625793 GCTATAGGGA
4625803 ATGAATGTATATTTTAGAATATGTATGTATAAAAAAATCAGGAAGAATAATATATATATATATAT
1 ATGAATGTATATTTTAGAATATGTATGTATAAAAAAATCAGGAAGAATAATATATATATATATAT
4625868 ATATATATATAGATATATATATATATAT
66 ATATATATATAGATATATATATATATAT
4625896 ATGAATGTATATTTTAGAATATGTATGTATAAAAAAATCAGGAAGAATAATATATATATATATAT
1 ATGAATGTATATTTTAGAATATGTATGTATAAAAAAATCAGGAAGAATAATATATATATATATAT
*
4625961 ATATATATATATATATA
66 ATATATATATAGATATA
4625978 AAATACGTAT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (93 bp):
ATGAATGTATATTTTAGAATATGTATGTATAAAAAAATCAGGAAGAATAATATATATATATATAT
ATATATATATAGATATATATATATATAT
Found at i:4626252 original size:12 final size:12
Alignment explanation
Indices: 4626237--4626277 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
4626227 GAACATAGAG
*
4626237 ATAATGATAGTA
1 ATAATGATAATA
4626249 ATAATGATAATA
1 ATAATGATAATA
4626261 TATAAT-ATAATA
1 -ATAATGATAATA
4626273 ATAAT
1 ATAAT
4626278 AATGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
ATAATGATAATA
Found at i:4630836 original size:11 final size:11
Alignment explanation
Indices: 4630820--4630844 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4630810 TCTAGACCCC
4630820 AAAAAAGAAAA
1 AAAAAAGAAAA
4630831 AAAAAAGAAAA
1 AAAAAAGAAAA
4630842 AAA
1 AAA
4630845 GAATCATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:4632533 original size:23 final size:23
Alignment explanation
Indices: 4632486--4632533 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
4632476 GTGGGTGGCT
* *
4632486 TGCTTATGTCACAAGCTTAAGCA
1 TGCTTATGTCACAACCTAAAGCA
*
4632509 TGCTTATGTCACAACCTAAATCA
1 TGCTTATGTCACAACCTAAAGCA
4632532 TG
1 TG
4632534 ATTTTAAATA
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (23 bp):
TGCTTATGTCACAACCTAAAGCA
Found at i:4633389 original size:46 final size:46
Alignment explanation
Indices: 4633285--4633445 Score: 251
Period size: 46 Copynumber: 3.6 Consensus size: 46
4633275 TACTTATGAT
*
4633285 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-A-GACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATG-CTAC
4633328 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
4633374 CACTTATCACTTTGTCACTTGATCAGGTAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
4633420 CACTTATCACTTTATCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4633446 AGTACTCAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
43 10 0.09
44 5 0.05
45 27 0.25
46 67 0.61
47 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:4642912 original size:20 final size:20
Alignment explanation
Indices: 4642887--4642931 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4642877 TAATTATTAT
4642887 ATTTTAAAAAATTTAAATAA
1 ATTTTAAAAAATTTAAATAA
* **
4642907 ATTTTAAAAATTTTACCTAA
1 ATTTTAAAAAATTTAAATAA
4642927 ATTTT
1 ATTTT
4642932 TTATGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTAAAAAATTTAAATAA
Found at i:4642961 original size:15 final size:16
Alignment explanation
Indices: 4642941--4642974 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4642931 TTTATGTAAG
4642941 AAAATTAAAAT-ATAT
1 AAAATTAAAATAATAT
*
4642956 AAAATTATAATAATAT
1 AAAATTAAAATAATAT
4642972 AAA
1 AAA
4642975 TACTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATTAAAATAATAT
Found at i:4643932 original size:2 final size:2
Alignment explanation
Indices: 4643925--4643963 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4643915 TAACATAATG
* *
4643925 AT AT AT AT GT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4643964 AATTAATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4649805 original size:23 final size:21
Alignment explanation
Indices: 4649767--4649811 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
4649757 ACAATAATTA
*
4649767 TTATATATTTTTTAAAAATAAT
1 TTATATAGTTTTT-AAAATAAT
4649789 TTATGATAGTTTTTAAAATAAT
1 TTAT-ATAGTTTTTAAAATAAT
4649811 T
1 T
4649812 ATCTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATATAGTTTTTAAAATAAT
Found at i:4649848 original size:21 final size:21
Alignment explanation
Indices: 4649801--4649848 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
4649791 ATGATAGTTT
*
4649801 TTAAAATAATTATCTTTTAAA
1 TTAAAATAATTATCTTATAAA
*
4649822 TT-AAATAATTTATC-TATGAA
1 TTAAAATAA-TTATCTTATAAA
4649842 TTAAAAT
1 TTAAAAT
4649849 TTAATATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TTAAAATAATTATCTTATAAA
Found at i:4656190 original size:2 final size:2
Alignment explanation
Indices: 4656183--4656211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4656173 CATATTCTAT
4656183 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 T
4656212 GGGCAAATCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4657995 original size:2 final size:2
Alignment explanation
Indices: 4657988--4658017 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4657978 CAGCATTTGC
4657988 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
4658018 AAAACAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4666767 original size:27 final size:27
Alignment explanation
Indices: 4666737--4666790 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4666727 TAACCGTTAT
* *
4666737 TTGGTGGATTCAGCACTTAGCAACCCC
1 TTGGGGGAATCAGCACTTAGCAACCCC
*
4666764 TTGGGGGAATCAGTACTTAGCAACCCC
1 TTGGGGGAATCAGCACTTAGCAACCCC
4666791 CCTTTTACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (27 bp):
TTGGGGGAATCAGCACTTAGCAACCCC
Found at i:4666858 original size:33 final size:33
Alignment explanation
Indices: 4666816--4666942 Score: 130
Period size: 33 Copynumber: 3.6 Consensus size: 33
4666806 AAAATATGGT
4666816 GGAATCAGCACTTAGCAACCACCAATGATTCGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
* *
4666849 GGAATCAGCACTTAGCAACGCCTTATACAATCCG-TTACAGT
1 GGAATCAGCACTTAGCAA--CC--A-CCAAT--GATT-C-GG
* *
4666890 GGAATCAGCACTTAGCAACCACCGATGATTTGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
4666923 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
4666943 CCCCTTTTGC
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
33 39 0.50
34 1 0.01
35 4 0.05
36 3 0.04
37 2 0.03
38 4 0.05
39 4 0.05
40 2 0.03
41 19 0.24
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGATTCGG
Found at i:4666993 original size:80 final size:79
Alignment explanation
Indices: 4666767--4667024 Score: 346
Period size: 80 Copynumber: 3.3 Consensus size: 79
4666757 CAACCCCTTG
* *
4666767 GGGGAATCAGTACTTAGCAACCCCCCTTTTACACATTAAAAAATATGGTGGAATCAGCACTTAGC
1 GGGGAATCAGCACTTAGCAACCCCCCTTTT-CACATTCAAAAATATGGTGGAATCAGCACTTAGC
* *
4666832 AACCACCAATGATTC
65 AACCACCGATGATTT
* * * *** **
4666847 GGGGAATCAGCACTTAGCAA--CGCCTTAT-ACAATC--CGTTACAGTGGAATCAGCACTTAGCA
1 GGGGAATCAGCACTTAGCAACCCCCCTTTTCACATTCAAAAATATGGTGGAATCAGCACTTAGCA
4666907 ACCACCGATGATTT
66 ACCACCGATGATTT
4666921 GGGGAATCAGCACTTAGCAACCCCCCTTTTGCACATTCAAAAATATGGTGGAATCAGCACTTAGC
1 GGGGAATCAGCACTTAGCAACCCCCCTTTT-CACATTCAAAAATATGGTGGAATCAGCACTTAGC
*
4666986 AACCACCGATAATTT
65 AACCACCGATGATTT
4667001 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
4667025 TTGGGGGAAT
Statistics
Matches: 151, Mismatches: 21, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
74 53 0.35
76 10 0.07
78 11 0.07
80 77 0.51
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (79 bp):
GGGGAATCAGCACTTAGCAACCCCCCTTTTCACATTCAAAAATATGGTGGAATCAGCACTTAGCA
ACCACCGATGATTT
Found at i:4672735 original size:13 final size:13
Alignment explanation
Indices: 4672705--4672763 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
4672695 AAATAATACG
*
4672705 AAAAATCTTAA-T
1 AAAAATATTAATT
4672717 -AAAATATTAATT
1 AAAAATATTAATT
*
4672729 AAAAATATTTATCT
1 AAAAATATTAAT-T
*
4672743 -AAATTAATTAATT
1 AAAAAT-ATTAATT
4672756 AAAAATAT
1 AAAAATAT
4672764 CACCAACAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
11 9 0.24
12 1 0.03
13 17 0.46
14 10 0.27
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAATATTAATT
Found at i:4676092 original size:21 final size:21
Alignment explanation
Indices: 4676068--4676114 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4676058 CAAAATAATT
4676068 AAAATAATTT-TCAAAAATTCA
1 AAAATAATTTAT-AAAAATTCA
*
4676089 AAAAT-ATTTATAAAAATTCC
1 AAAATAATTTATAAAAATTCA
4676109 AAAATA
1 AAAATA
4676115 TAAAGAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATAATTTATAAAAATTCA
Found at i:4676465 original size:24 final size:24
Alignment explanation
Indices: 4676432--4676480 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4676422 AGGACTCGTC
4676432 AACTCAATTAACTTAAAATCTTTT
1 AACTCAATTAACTTAAAATCTTTT
* * * *
4676456 AACTCGATTAATTTGAAATTTTTT
1 AACTCAATTAACTTAAAATCTTTT
4676480 A
1 A
4676481 CTTAATTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (24 bp):
AACTCAATTAACTTAAAATCTTTT
Found at i:4676612 original size:30 final size:30
Alignment explanation
Indices: 4676576--4676638 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
4676566 ACTGATAGCC
4676576 AAATACAGTAGTACTAATATTCACTTAAGT
1 AAATACAGTAGTACTAATATTCACTTAAGT
4676606 AAATACAGTAGTACTAATATTCACTTAAGT
1 AAATACAGTAGTACTAATATTCACTTAAGT
4676636 AAA
1 AAA
4676639 CATATCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATACAGTAGTACTAATATTCACTTAAGT
Found at i:4679757 original size:96 final size:96
Alignment explanation
Indices: 4679593--4679788 Score: 374
Period size: 96 Copynumber: 2.0 Consensus size: 96
4679583 TATATCTCTC
*
4679593 AAAACACCTAGACAACTTGCACTATCCTCATTTGCTATCCCACATACATTGAACTTTAATCCTGT
1 AAAACACCTAGACAACTTGCACAATCCTCATTTGCTATCCCACATACATTGAACTTTAATCCTGT
*
4679658 TTTGATGAGTTTGAGGATAATACTCGTCCTT
66 TTTGATAAGTTTGAGGATAATACTCGTCCTT
4679689 AAAACACCTAGACAACTTGCACAATCCTCATTTGCTATCCCACATACATTGAACTTTAATCCTGT
1 AAAACACCTAGACAACTTGCACAATCCTCATTTGCTATCCCACATACATTGAACTTTAATCCTGT
4679754 TTTGATAAGTTTGAGGATAATACTCGTCCTT
66 TTTGATAAGTTTGAGGATAATACTCGTCCTT
4679785 AAAA
1 AAAA
4679789 TTTTTGGGAT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (96 bp):
AAAACACCTAGACAACTTGCACAATCCTCATTTGCTATCCCACATACATTGAACTTTAATCCTGT
TTTGATAAGTTTGAGGATAATACTCGTCCTT
Found at i:4680914 original size:50 final size:50
Alignment explanation
Indices: 4680839--4680939 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
4680829 CCGCAGGTAA
4680839 ACGCACCGCCCATCCAAACTCACCCTAAGTCAACATTTACAGATATTGAG
1 ACGCACCGCCCATCCAAACTCACCCTAAGTCAACATTTACAGATATTGAG
4680889 ACGCACCGCCCATCCAAACTCACCCTAAGTCAACATTTACAGATATTGAG
1 ACGCACCGCCCATCCAAACTCACCCTAAGTCAACATTTACAGATATTGAG
4680939 A
1 A
4680940 GGAAAATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.35, C:0.34, G:0.12, T:0.20
Consensus pattern (50 bp):
ACGCACCGCCCATCCAAACTCACCCTAAGTCAACATTTACAGATATTGAG
Found at i:4685931 original size:21 final size:24
Alignment explanation
Indices: 4685905--4685952 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
4685895 ATAAAAATTA
*
4685905 AATTGAATT-TTT-AGTTAA-TCG
1 AATTGAATTATTTGAGTCAATTCG
4685926 AATTGAATTATTTGAGTCAATTCG
1 AATTGAATTATTTGAGTCAATTCG
4685950 AAT
1 AAT
4685953 AAGTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 5 0.22
24 6 0.26
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (24 bp):
AATTGAATTATTTGAGTCAATTCG
Found at i:4689533 original size:29 final size:30
Alignment explanation
Indices: 4689474--4689531 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4689464 TCCGAGCCTT
**
4689474 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATAAAAAAGTTTA
* *
4689504 GGGGCAAAATTGTAATTTTAAAAAAGTT
1 GGGGCAAAAATGTAATTATAAAAAAGTT
4689532 AGAGTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATAAAAAAGTTTA
Found at i:4689762 original size:13 final size:13
Alignment explanation
Indices: 4689744--4689774 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4689734 TTCCAGCAAC
4689744 TATGAATTTATTT
1 TATGAATTTATTT
4689757 TATGAATTTATTT
1 TATGAATTTATTT
*
4689770 GATGA
1 TATGA
4689775 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:4689983 original size:50 final size:50
Alignment explanation
Indices: 4689869--4690110 Score: 295
Period size: 50 Copynumber: 4.7 Consensus size: 50
4689859 ATTTGGGTAA
* * *
4689869 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
4689925 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * *
4689975 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
4690025 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
4690075 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
4690111 TTTGGCATGT
Statistics
Matches: 168, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 94 0.56
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:4690056 original size:100 final size:103
Alignment explanation
Indices: 4689869--4690118 Score: 362
Period size: 100 Copynumber: 2.4 Consensus size: 103
4689859 ATTTGGGTAA
4689869 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
4689934 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
4689975 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
4690037 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
4690075 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4690119 GTTATTATCA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 41 0.31
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:4690680 original size:78 final size:79
Alignment explanation
Indices: 4690584--4690758 Score: 284
Period size: 79 Copynumber: 2.2 Consensus size: 79
4690574 TTTTGCAGCG
4690584 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAAT-G-GCTATTTTTTTTAAAGTAAAAT
1 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTA-TTTTTTTAAAGTAAAAT
4690647 TATTTTTTGTGGCGT
65 TATTTTTTGTGGCGT
* *
4690662 TTTTTATAAAAACGCCGCTAAATTTTTTGCTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
1 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
4690727 ATTTTTTGTGGCGT
66 ATTTTTTGTGGCGT
*
4690741 TTTTCT-TTAAAACGCCGC
1 TTTT-TATAAAAACGCCGC
4690759 AAAAAATTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
78 38 0.42
79 48 0.53
80 5 0.05
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.45
Consensus pattern (79 bp):
TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
ATTTTTTGTGGCGT
Found at i:4691771 original size:96 final size:93
Alignment explanation
Indices: 4691653--4691838 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 93
4691643 CTAACTCTTA
*
4691653 ACCCCAAACCCTAAACCACTAA-CCTCTAAACCTTATTTAATATAGAAATTAAAAAAACACTAAT
1 ACCCCAAACCCTAAACCACTAACCCT-TAAACATTATTTAATATAGAAATT-AAAAAACACTAAT
*
4691717 TAATCTAAATCATAAACCCTAACCCTAACCCG
64 TAATCTAAACCATAAACCC-AA-CCTAACCCG
* * *
4691749 ACCCCAAATCCCTAATCC-CTAACCCTTAAACATTATTTAATATATAAATTAAAATACACTAATT
1 ACCCCAAA-CCCTAAACCACTAACCCTTAAACATTATTTAATATAGAAATTAAAAAACACTAATT
*
4691813 AATCTAAACCCTAAACCCAACCTAAC
65 AATCTAAACCATAAACCCAACCTAAC
4691839 TTATTTAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
93 6 0.07
94 2 0.02
95 29 0.35
96 34 0.41
97 11 0.13
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (93 bp):
ACCCCAAACCCTAAACCACTAACCCTTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
ATCTAAACCATAAACCCAACCTAACCCG
Found at i:4692043 original size:89 final size:89
Alignment explanation
Indices: 4691931--4692106 Score: 244
Period size: 89 Copynumber: 2.0 Consensus size: 89
4691921 CTAACTCTTA
* * * *
4691931 ACCCCAAACCCCAAACTACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACATTAATCA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
*
4691996 ATCTAAATCATAAACCCTAACTCG
66 ATCTAAACCATAAACCCTAACTCG
* * * * * *
4692020 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
*
4692085 ATCTAAACCCTAAACCCTAACT
66 ATCTAAACCATAAACCCTAACT
4692107 TGACACTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (89 bp):
ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
ATCTAAACCATAAACCCTAACTCG
Found at i:4692104 original size:278 final size:275
Alignment explanation
Indices: 4691556--4692101 Score: 893
Period size: 278 Copynumber: 2.0 Consensus size: 275
4691546 ATTATATAAG
* *
4691556 AACTTATTTAATATATAAATTAAAAAAATACTAATTAATCTAAACCTTAAACCCTAACTCGACCC
1 AACTTATTTAAGATATAAATT-AAAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCC
* * * *
4691621 TGAATCTTTAAACCCTAGATAACTAACTCTTAACCCCAAACCCTAAACCACTAACCTCTAAACCT
65 CGAATCTCTAAACCCTAAATAACTAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCT
*
4691686 TATTTAATATAGAAATTAAAAAAACACTAATTAATCTAAATCATAAACCCTAACCCTAACCCGAC
130 TATTTAATATAGAAATTAAAAAAACACTAATCAATCTAAATCATAAACCCTAA-CCT-A--CGAC
* * *
4691751 CCCAAATCCCTAATCCCTAACCCTTAAACATTATTTAATATATAAATTAAAATACACTAATTAAT
191 CCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAAT
4691816 CTAAACCCTAAACCCAACCT
256 CTAAACCCTAAACCCAACCT
*
4691836 AACTTATTTAAGATATAAATT-AAAAATACTAATTAATCTAAACCTTAAAACTTAACTCGACCCC
1 AACTTATTTAAGATATAAATTAAAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCCC
* *
4691900 GAATCTCTAAACCCTAAATCACTAACTCTTAACCCCAAACCCCAAACTACTAACCTCTAAACCTT
66 GAATCTCTAAACCCTAAATAACTAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCTT
*
4691965 ATTTAATATAGAAATT-AAAAAACATTAATCAATCTAAATCATAAACCCTAA-CT-CGACCCCAA
131 ATTTAATATAGAAATTAAAAAAACACTAATCAATCTAAATCATAAACCCTAACCTACGACCCCAA
4692027 ATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAA
196 ATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAA
4692092 CCCTAAACCC
261 CCCTAAACCC
4692102 TAACTTGACA
Statistics
Matches: 252, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
271 81 0.32
275 2 0.01
277 33 0.13
278 116 0.46
280 20 0.08
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (275 bp):
AACTTATTTAAGATATAAATTAAAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCCC
GAATCTCTAAACCCTAAATAACTAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCTT
ATTTAATATAGAAATTAAAAAAACACTAATCAATCTAAATCATAAACCCTAACCTACGACCCCAA
ATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAA
CCCTAAACCCAACCT
Found at i:4692129 original size:89 final size:89
Alignment explanation
Indices: 4691949--4692130 Score: 238
Period size: 89 Copynumber: 2.0 Consensus size: 89
4691939 CCCCAAACTA
* * * *
4691949 CTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACATTAATCAATCTAAATCATAAACCCT
1 CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
* * *
4692014 AACTCGACCCCAAATCCCTAACCC
66 AACTCGACACCAAATCCATAAACC
* * * *
4692038 CTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCT
1 CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
* * *
4692103 AACTTGACACTAAATCTATAAACC
66 AACTCGACACCAAATCCATAAACC
4692127 CTAA
1 CTAA
4692131 ATCCCTAACT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (89 bp):
CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
AACTCGACACCAAATCCATAAACC
Found at i:4692158 original size:14 final size:14
Alignment explanation
Indices: 4692123--4692187 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
4692113 TAAATCTATA
* *
4692123 AACCCTAAATCCCT
1 AACCCTTAACCCCT
* *
4692137 AACTCTTAACCTCT
1 AACCCTTAACCCCT
4692151 AACCCTTAACCCCT
1 AACCCTTAACCCCT
* *
4692165 AACCCCTAACCCAT
1 AACCCTTAACCCCT
*
4692179 AAACCTTAA
1 AACCCTTAA
4692188 ATCACAACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTTAACCCCT
Found at i:4692226 original size:14 final size:15
Alignment explanation
Indices: 4692207--4692239 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
4692197 CTTAAATTAG
4692207 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
4692221 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
4692236 AATC
1 AATC
4692240 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:4692596 original size:42 final size:42
Alignment explanation
Indices: 4692444--4692625 Score: 262
Period size: 41 Copynumber: 4.4 Consensus size: 42
4692434 CCTTGTGGGT
* * ***
4692444 CTTTAGCGGCG-TTTTTCAAGAAGCGTCTCTAATGCGTGGAC
1 CTTTAGCGGCGTTTTTTCAAGAAGCGCCGCTAATGCACAGAC
*
4692485 CTTTAGCGGCGTTTTTT-AAGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTTCAAGAAGCGCCGCTAATGCACAGAC
* *
4692526 CTTTAGCGGCG-TTTTTCAGGAAGCGCCGCTAATGCACTGAC
1 CTTTAGCGGCGTTTTTTCAAGAAGCGCCGCTAATGCACAGAC
*
4692567 CTTTAGCGGCGTTTTTTCATGAAGCGCCGCTAATGCACAGAC
1 CTTTAGCGGCGTTTTTTCAAGAAGCGCCGCTAATGCACAGAC
4692609 CTTTAGCGGCGTTTTTT
1 CTTTAGCGGCGTTTTTT
4692626 GTAAAGCGCC
Statistics
Matches: 129, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
40 5 0.04
41 74 0.57
42 50 0.39
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTTCAAGAAGCGCCGCTAATGCACAGAC
Found at i:4693471 original size:22 final size:22
Alignment explanation
Indices: 4693443--4693595 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
4693433 TGTTGATAGT
*
4693443 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
4693465 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
4693487 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
4693509 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
4693531 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
4693553 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
4693575 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
4693596 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:4695043 original size:14 final size:14
Alignment explanation
Indices: 4695024--4695052 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4695014 TTTTTGTAAG
4695024 TCTTATACATAATT
1 TCTTATACATAATT
4695038 TCTTATACATAATT
1 TCTTATACATAATT
4695052 T
1 T
4695053 TTTTCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
TCTTATACATAATT
Found at i:4696234 original size:43 final size:43
Alignment explanation
Indices: 4696173--4696308 Score: 236
Period size: 43 Copynumber: 3.2 Consensus size: 43
4696163 GACCTATAGT
*
4696173 GGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
1 GGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
4696216 GGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
1 GGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
* * *
4696259 GGCGTTTGTCGTAAAAGCGCCGCTAAATGTCATGGTCTTTAGC
1 GGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
4696302 GGCGTTT
1 GGCGTTT
4696309 ATTTTTGAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (43 bp):
GGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGC
Found at i:4696397 original size:22 final size:22
Alignment explanation
Indices: 4696369--4696411 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4696359 TTGCGGCGCT
*
4696369 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
4696391 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
4696412 GTTTTGGTGT
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:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:4701060 original size:72 final size:72
Alignment explanation
Indices: 4700975--4701118 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
4700965 TATAAAAATA
*
4700975 ACCTAAGTTTAAAAATAATCACCAAAATAACCTAAAATAAACAGTACTCACTCTTTTTTTGCACC
1 ACCTAAGTTTAAAAATAATCACCAAAATAACCTAAAATAAACAGTACCCACTCTTTTTTTGCACC
4701040 AATGATT
66 AATGATT
4701047 ACCTAAGTTTAAAAATAATCACCAAAATAACCTAAAATAAACAGTACCCACTCTTTTTTTGCACC
1 ACCTAAGTTTAAAAATAATCACCAAAATAACCTAAAATAAACAGTACCCACTCTTTTTTTGCACC
4701112 AATGATT
66 AATGATT
4701119 GGCTAATCAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (72 bp):
ACCTAAGTTTAAAAATAATCACCAAAATAACCTAAAATAAACAGTACCCACTCTTTTTTTGCACC
AATGATT
Found at i:4716635 original size:17 final size:16
Alignment explanation
Indices: 4716609--4716640 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4716599 TTAGTATTAA
4716609 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
4716625 AAAAATATATAAAAAA
1 AAAAAT-TATAAAAAA
4716641 ATTGATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:4718187 original size:29 final size:29
Alignment explanation
Indices: 4718147--4718221 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
4718137 TCTAAGAATT
*
4718147 AAAATTACATTTTTAAATA-AAAAAGTAAA
1 AAAATTAAATTTTTAAATATAAAAA-TAAA
* *
4718176 TAGATTAAATTTCTTAAA-ATAAAAATAAA
1 AAAATTAAATTT-TTAAATATAAAAATAAA
4718205 AAAATTAAA-TTTTAAAT
1 AAAATTAAATTTTTAAAT
4718222 GCACAAATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.13
28 2 0.05
29 21 0.55
30 10 0.26
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTAAATTTTTAAATATAAAAATAAA
Found at i:4724338 original size:80 final size:80
Alignment explanation
Indices: 4724205--4724367 Score: 326
Period size: 80 Copynumber: 2.0 Consensus size: 80
4724195 AGTCTGCTGG
4724205 ATTGCTTGGGAGACCTCAGGTAAACAAACAAATAAAATGAGAATCTTTGACGATAGTTAGGAGCT
1 ATTGCTTGGGAGACCTCAGGTAAACAAACAAATAAAATGAGAATCTTTGACGATAGTTAGGAGCT
4724270 TGAATTATGAATTTA
66 TGAATTATGAATTTA
4724285 ATTGCTTGGGAGACCTCAGGTAAACAAACAAATAAAATGAGAATCTTTGACGATAGTTAGGAGCT
1 ATTGCTTGGGAGACCTCAGGTAAACAAACAAATAAAATGAGAATCTTTGACGATAGTTAGGAGCT
4724350 TGAATTATGAATTTA
66 TGAATTATGAATTTA
4724365 ATT
1 ATT
4724368 TTTGTTAAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (80 bp):
ATTGCTTGGGAGACCTCAGGTAAACAAACAAATAAAATGAGAATCTTTGACGATAGTTAGGAGCT
TGAATTATGAATTTA
Found at i:4738094 original size:38 final size:38
Alignment explanation
Indices: 4738034--4738118 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
4738024 TATTTTGAAA
* *
4738034 ATATTTTTAATTAATATATTTAA-A-ATTTTAAAAAAT
1 ATATTTTTAATTAAAATATTTAACAGAATTTAAAAAAT
*
4738070 ATATTTTGTACATTAAAATTTTTAACAGAATTTAAAAAAT
1 ATATTTT-TA-ATTAAAATATTTAACAGAATTTAAAAAAT
4738110 AT-TTTTTAA
1 ATATTTTTAA
4738119 CAGACGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 7 0.17
37 3 0.07
38 14 0.33
39 5 0.12
40 13 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (38 bp):
ATATTTTTAATTAAAATATTTAACAGAATTTAAAAAAT
Found at i:4741076 original size:2 final size:2
Alignment explanation
Indices: 4741036--4741066 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4741026 AACTTTTTTA
4741036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4741067 AGTCATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4741788 original size:15 final size:16
Alignment explanation
Indices: 4741768--4741798 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4741758 GTAAGGACAG
4741768 CATACATT-ACATATA
1 CATACATTCACATATA
4741783 CATACATTCACATATA
1 CATACATTCACATATA
4741799 TGTTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (16 bp):
CATACATTCACATATA
Found at i:4757074 original size:19 final size:19
Alignment explanation
Indices: 4757050--4757087 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4757040 AAAAGAAGAA
4757050 AAAAAAATCTTATAGCTAC
1 AAAAAAATCTTATAGCTAC
4757069 AAAAAAATCTTATAGCTAC
1 AAAAAAATCTTATAGCTAC
4757088 TCTCTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAAAATCTTATAGCTAC
Found at i:4771608 original size:131 final size:131
Alignment explanation
Indices: 4771373--4771635 Score: 438
Period size: 131 Copynumber: 2.0 Consensus size: 131
4771363 TTGTCAGTAC
*
4771373 TTCAAATATACATTTGAAAATTGGTTTGGTTACCAAAGACATCAAAAATTTTCGTATAAAACAAG
1 TTCAAATATACATTTGAAAATTGGTTTGGTTACCAAAGA-ATCAAAAATTTTCATATAAAACAAG
*
4771438 AAGCTGTCTTAAAGACAGACAGTGAGGTAAAACCGGTGGTGTTGATGTAATAATTGGAACTGTGT
65 AAGCTGTCTTAAAGACAGACAGTGAGGTAAAACCGGTGGTGTTGAAGTAATAATTGGAACTGTGT
4771503 TG
130 TG
* *
4771505 TTCAAATATACATTTGAAAATTGGTTTGGTTACTAAAG-ATTAAAAGATTTTCATATAAAACAAG
1 TTCAAATATACATTTGAAAATTGGTTTGGTTACCAAAGAATCAAAA-ATTTTCATATAAAACAAG
* * *
4771569 AAGCTGTCTTATAGACAGACAGTGAGGTAAAGCTGGTGGTGTTGAAGTAATAATTGGAACTGTGT
65 AAGCTGTCTTAAAGACAGACAGTGAGGTAAAACCGGTGGTGTTGAAGTAATAATTGGAACTGTGT
4771634 TG
130 TG
4771636 GTTTGTTTTA
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
130 6 0.05
131 80 0.65
132 37 0.30
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (131 bp):
TTCAAATATACATTTGAAAATTGGTTTGGTTACCAAAGAATCAAAAATTTTCATATAAAACAAGA
AGCTGTCTTAAAGACAGACAGTGAGGTAAAACCGGTGGTGTTGAAGTAATAATTGGAACTGTGTT
G
Found at i:4777451 original size:29 final size:30
Alignment explanation
Indices: 4777393--4777452 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
4777383 TAGATCTGAT
* * *
4777393 TTTTGAAAATTGAAAAGTAAATGGATTAAA
1 TTTTGAAAAATGAAAAATAAATGGACTAAA
*
4777423 TTTTGAAAAAT-AAAAATATATGGACTAAA
1 TTTTGAAAAATGAAAAATAAATGGACTAAA
4777452 T
1 T
4777453 ACTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTGAAAAATGAAAAATAAATGGACTAAA
Found at i:4778783 original size:24 final size:23
Alignment explanation
Indices: 4778751--4778799 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
4778741 CATAACGAGC
*
4778751 ATCTTAAGTGTGTCTGTATATAGT
1 ATCTTAAGTGTGTCTGCATA-AGT
4778775 ATCTTAAGTGTGTCTGCATAAGT
1 ATCTTAAGTGTGTCTGCATAAGT
4778798 AT
1 AT
4778800 GCTGCAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (23 bp):
ATCTTAAGTGTGTCTGCATAAGT
Found at i:4786576 original size:31 final size:31
Alignment explanation
Indices: 4786538--4786607 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
4786528 TTTGATCTGG
4786538 ATACCAAATTAAACATT-AAAATCAAACTCAA
1 ATACCAAATTAAACATTGAAAAT-AAACTCAA
* *
4786569 ATACCAAATTGAACTTTGAAAATAAACTCAA
1 ATACCAAATTAAACATTGAAAATAAACTCAA
*
4786600 TTACCAAA
1 ATACCAAA
4786608 CATTGCATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (31 bp):
ATACCAAATTAAACATTGAAAATAAACTCAA
Found at i:4786837 original size:2 final size:2
Alignment explanation
Indices: 4786830--4786865 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4786820 TAATTCATCA
4786830 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
4786866 TCATCTTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4788097 original size:14 final size:14
Alignment explanation
Indices: 4788080--4788109 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4788070 TATTTTTATA
4788080 TATATGTATGCATG
1 TATATGTATGCATG
*
4788094 TATATGTATGTATG
1 TATATGTATGCATG
4788108 TA
1 TA
4788110 GGGATTCCAT
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:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (14 bp):
TATATGTATGCATG
Found at i:4791858 original size:18 final size:18
Alignment explanation
Indices: 4791827--4791871 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
4791817 AATAATAAAG
*
4791827 TAAATAAACATAAAAGAAA
1 TAAAGAAACATAAAAG-AA
4791846 TAAAGAAAC-TAAAAGAA
1 TAAAGAAACATAAAAGAA
4791863 TAAAAGAAA
1 T-AAAGAAA
4791872 GAAATGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (18 bp):
TAAAGAAACATAAAAGAA
Found at i:4792302 original size:17 final size:18
Alignment explanation
Indices: 4792280--4792313 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4792270 TAAATGAGTT
4792280 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
4792297 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
4792314 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:4797448 original size:17 final size:17
Alignment explanation
Indices: 4797426--4797468 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
4797416 ATCTTCCTTT
4797426 AAACCATTTTTTAGTGA
1 AAACCATTTTTTAGTGA
4797443 AAACCATTTTTTAGTGA
1 AAACCATTTTTTAGTGA
4797460 AAACCATTT
1 AAACCATTT
4797469 CTTTCAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (17 bp):
AAACCATTTTTTAGTGA
Found at i:4797932 original size:29 final size:30
Alignment explanation
Indices: 4797900--4797958 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
4797890 TTTGAAATAA
* *
4797900 TAATTGACTCATTAAAAATGATAAA-ATTT
1 TAATTAACCCATTAAAAATGATAAATATTT
* *
4797929 TAATTAACCCTTTAAAAATTATAAATATTT
1 TAATTAACCCATTAAAAATGATAAATATTT
4797959 AAGTTAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATTAACCCATTAAAAATGATAAATATTT
Found at i:4803011 original size:3 final size:3
Alignment explanation
Indices: 4803003--4803032 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4802993 TTGTAGTTTC
4803003 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
4803033 GGAAAAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4813303 original size:15 final size:15
Alignment explanation
Indices: 4813283--4813312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4813273 TTGCTTTCAA
4813283 TTAAAATTATAAATT
1 TTAAAATTATAAATT
*
4813298 TTAAAATTATTAATT
1 TTAAAATTATAAATT
4813313 AAATTTTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAATTATAAATT
Found at i:4813367 original size:26 final size:25
Alignment explanation
Indices: 4813298--4813367 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 25
4813288 ATTATAAATT
**
4813298 TTAAAA-TTATTAATTAAATTTTATTA
1 TTAAAATTTATT-A-TAAATTTTAAAA
* *
4813324 TTAAATATTTAATCTAAATATTTAAAA
1 TTAAA-ATTTATTATAAAT-TTTAAAA
4813351 TTAAAATTTATTATAAA
1 TTAAAATTTATTATAAA
4813368 ATTAAATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 20 0.57
27 11 0.31
28 4 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAAATTTATTATAAATTTTAAAA
Found at i:4815100 original size:119 final size:121
Alignment explanation
Indices: 4814945--4815165 Score: 286
Period size: 119 Copynumber: 1.8 Consensus size: 121
4814935 CTTCCAAAGC
* * * **
4814945 AATCGAAACATCTTAACAATGCATACATAGATGCATTAAAAACTTGCATCAGTTCCTAAAC-T-C
1 AATCGAAACACCTTAACAAAGCACACATAGATGCATTAAAAACTCACATCAGTTCCTAAACTTAC
* *
4815008 GAAAGAAAGA-GGAAACCAAATGATACACAAGTATACTCACAAGACAAAGAAAGGCT
66 GAAAGAAA-ACGGAAACCAAAAGACACACAAGTATACTCACAAGACAAAGAAAGGCT
* * * * *
4815064 AATCGAGACACCTTAACAAAGTACACATAGATGCATTAGAAACTCATATCTGTTCCTAAACTTAC
1 AATCGAAACACCTTAACAAAGCACACATAGATGCATTAAAAACTCACATCAGTTCCTAAACTTAC
* *
4815129 GAAAGAAAACGGATATCAAAAGACACACAAGTATACT
66 GAAAGAAAACGGAAACCAAAAGACACACAAGTATACT
4815166 TATTAGTAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
119 51 0.60
120 2 0.02
121 32 0.38
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (121 bp):
AATCGAAACACCTTAACAAAGCACACATAGATGCATTAAAAACTCACATCAGTTCCTAAACTTAC
GAAAGAAAACGGAAACCAAAAGACACACAAGTATACTCACAAGACAAAGAAAGGCT
Found at i:4816409 original size:22 final size:23
Alignment explanation
Indices: 4816367--4816411 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4816357 AGGTAAGATT
4816367 TTTTTTTAAAAATTATTAAATCAA
1 TTTTTTTAAAAATTA-TAAATCAA
*
4816391 TTTTTTTAATAATTA-AAATCA
1 TTTTTTTAAAAATTATAAATCA
4816412 TACTGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
24 14 0.70
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTTTAAAAATTATAAATCAA
Found at i:4818505 original size:17 final size:17
Alignment explanation
Indices: 4818483--4818546 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
4818473 TATGAATGGC
*
4818483 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
4818500 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
4818519 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
4818536 TACAATTAGAA
1 TACAATTAGAA
4818547 CTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:4818525 original size:19 final size:19
Alignment explanation
Indices: 4818501--4818554 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
4818491 AAAGCTGTAT
4818501 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
4818520 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
4818537 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
4818555 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:4818532 original size:36 final size:36
Alignment explanation
Indices: 4818484--4818554 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
4818474 ATGAATGGCT
4818484 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
4818520 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
4818555 TTACATAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:4819246 original size:22 final size:22
Alignment explanation
Indices: 4819218--4819260 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4819208 ATAATTTATA
4819218 TTTTAATTATTAAAA-TAATAAT
1 TTTTAA-TATTAAAACTAATAAT
4819240 TTTTAATATTAAAACTAATAA
1 TTTTAATATTAAAACTAATAA
4819261 AATTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAATATTAAAACTAATAAT
Found at i:4819266 original size:21 final size:21
Alignment explanation
Indices: 4819220--4819272 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
4819210 AATTTATATT
**
4819220 TTAATTATTAAAATAATAATTT
1 TTAA-TATTAAAATAATAATAA
4819242 TTAATATTAAAACTAATAA-AA
1 TTAATATTAAAA-TAATAATAA
*
4819263 TTAAAATTAA
1 TTAATATTAA
4819273 TGTTTTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATATTAAAATAATAATAA
Found at i:4837724 original size:16 final size:15
Alignment explanation
Indices: 4837705--4837734 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4837695 TTCAACCGTT
4837705 AAAAAAAAGAAAAAAG
1 AAAAAAAA-AAAAAAG
4837721 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
4837735 CAAGGTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:4838395 original size:14 final size:15
Alignment explanation
Indices: 4838376--4838405 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4838366 TTAAAATAAT
4838376 ATAAAATTAT-ATTA
1 ATAAAATTATAATTA
4838390 ATAAAATTATAATTA
1 ATAAAATTATAATTA
4838405 A
1 A
4838406 AAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTATAATTA
Found at i:4838403 original size:20 final size:20
Alignment explanation
Indices: 4838358--4838404 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4838348 ATTGTGGAGA
4838358 ATAATTATTTAAAATAATAT
1 ATAATTATTTAAAATAATAT
*
4838378 AAAATTATATTAATAA-AAT-T
1 ATAATTAT-TTAA-AATAATAT
4838398 ATAATTA
1 ATAATTA
4838405 AAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 7 0.30
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTATTTAAAATAATAT
Found at i:4845148 original size:96 final size:95
Alignment explanation
Indices: 4844975--4845163 Score: 306
Period size: 96 Copynumber: 2.0 Consensus size: 95
4844965 AACTGGCCTA
* *
4844975 ATTCCAAGAAATGTTTGAAAAGCCTGTAAGATTGAAGCTTGGTGGCCCAATGATGAAAATATGAC
1 ATTCCAAGAAATGTTGGAAAAGCCTGTAAGATTGAAGCTGGGTGGCCCAATGATGAAAATATGAC
*
4845040 AACACAGGCTATCTTGGTAAATATGGGATG
66 AACACAGACTATCTTGGTAAATATGGGATG
* * *
4845070 ATTCCAAGAAATGTTGGAGAAGCCTGTCAGATTGAAGCCTGGGTGGCCCAATGATGAAAATATGG
1 ATTCCAAGAAATGTTGGAAAAGCCTGTAAGATTGAAG-CTGGGTGGCCCAATGATGAAAATATGA
*
4845135 CAACATAGACTATCTTGGTAAATATGGGA
65 CAACACAGACTATCTTGGTAAATATGGGA
4845164 ACTAATCTTA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
95 34 0.40
96 52 0.60
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (95 bp):
ATTCCAAGAAATGTTGGAAAAGCCTGTAAGATTGAAGCTGGGTGGCCCAATGATGAAAATATGAC
AACACAGACTATCTTGGTAAATATGGGATG
Found at i:4848097 original size:15 final size:14
Alignment explanation
Indices: 4848064--4848114 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 14
4848054 ATTATGTTGC
*
4848064 ATTTTAAAAATT--
1 ATTTTAAAATTTCA
4848076 ATTTTAAAATTTCA
1 ATTTTAAAATTTCA
*
4848090 AGTTTTAAAATTTTA
1 A-TTTTAAAATTTCA
4848105 A-TTTAAAATT
1 ATTTTAAAATT
4848115 ATTTCTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 11 0.32
13 9 0.26
14 1 0.03
15 13 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTTTAAAATTTCA
Found at i:4864076 original size:34 final size:35
Alignment explanation
Indices: 4864016--4864082 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
4864006 CAAACACCAG
*
4864016 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
4864051 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
4864083 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4866060 original size:4 final size:4
Alignment explanation
Indices: 4866051--4866085 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
4866041 AATATCTATT
4866051 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
4866086 TACTTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:4867090 original size:54 final size:54
Alignment explanation
Indices: 4867024--4867127 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
4867014 ATTCCAGACA
* *
4867024 CAACCAATTTTTCATTCCCCAAATTTCAAAT-CTCTGATCTCTCTCATAATTACT
1 CAACCAAATTTTCATTCCCCAAATTGCAAATGCT-TGATCTCTCTCATAATTACT
* * * *
4867078 CAACCAAATTTTCCTTCTCCAACTTGCAAATGGTTGATCTCTCTCATAAT
1 CAACCAAATTTTCATTCCCCAAATTGCAAATGCTTGATCTCTCTCATAAT
4867128 GACTTCACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.38
Consensus pattern (54 bp):
CAACCAAATTTTCATTCCCCAAATTGCAAATGCTTGATCTCTCTCATAATTACT
Found at i:4870830 original size:12 final size:12
Alignment explanation
Indices: 4870813--4870841 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4870803 GCACATAGTG
4870813 TGTATCACCTGA
1 TGTATCACCTGA
4870825 TGTATCACCTGA
1 TGTATCACCTGA
4870837 -GTATC
1 TGTATC
4870842 CTGCGATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (12 bp):
TGTATCACCTGA
Done.