Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 73
Found at i:4442790 original size:12 final size:13
Alignment explanation
Indices: 4442747--4442793 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
4442737 ATTATATCCC
4442747 TTTCATTTATTATAA
1 TTTCATTTATT-T-A
* *
4442762 TTTTATTTATTTC
1 TTTCATTTATTTA
4442775 TTTCATTT-TTTA
1 TTTCATTTATTTA
4442787 TTTCATT
1 TTTCATT
4442794 AAACCAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 1 0.04
15 10 0.36
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCATTTATTTA
Found at i:4448174 original size:27 final size:27
Alignment explanation
Indices: 4448144--4448209 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
4448134 ACATGCATGG
* *
4448144 CACATGCGTGGCTGGTCATGAGGATCT
1 CACATGGGTGGCTGGTCATGAGGAACT
*
4448171 CACATGGGTGGATGGTCATGAGGAACT
1 CACATGGGTGGCTGGTCATGAGGAACT
*
4448198 CATATGGGTGGC
1 CACATGGGTGGC
4448210 ATAGGATGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (27 bp):
CACATGGGTGGCTGGTCATGAGGAACT
Found at i:4477049 original size:22 final size:21
Alignment explanation
Indices: 4477023--4477064 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4477013 TGGCTTCGAA
4477023 TTGATGGCATTGATGGATGAAG
1 TTGATGGCATTGAT-GATGAAG
**
4477045 TTGATGGTGTTGATGATGAA
1 TTGATGGCATTGATGATGAA
4477065 ATAGAGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (21 bp):
TTGATGGCATTGATGATGAAG
Found at i:4481492 original size:90 final size:89
Alignment explanation
Indices: 4481332--4481496 Score: 276
Period size: 90 Copynumber: 1.8 Consensus size: 89
4481322 CTAACACACA
* *
4481332 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTGTATTATTTCAAATGAATTAAATCTATAT
1 CTTTTATAGCCAAGATACCCTAATCATATTAGGGTTGTATTATTTCAAATGAATTAAATCTACAT
4481397 TTAATTAATTTGAATTTAATAATC
66 TTAATTAATTTGAATTTAATAATC
* * *
4481421 CTTTTATATCCAAGATACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTACA
1 CTTTTATAGCCAAGATACCCTAATCATATTAGGG-TTGTATTATTTCAAATGAATTAAATCTACA
4481486 TTTAATTAATT
65 TTTAATTAATT
4481497 AAAATTAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.46
90 38 0.54
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (89 bp):
CTTTTATAGCCAAGATACCCTAATCATATTAGGGTTGTATTATTTCAAATGAATTAAATCTACAT
TTAATTAATTTGAATTTAATAATC
Found at i:4484188 original size:15 final size:13
Alignment explanation
Indices: 4484176--4484205 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
4484166 TCATAATAAC
4484176 TATATATATAATA
1 TATATATATAATA
4484189 TATATATATACATA
1 TATATATATA-ATA
4484203 TAT
1 TAT
4484206 GAAAATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATATATAATA
Found at i:4486880 original size:19 final size:20
Alignment explanation
Indices: 4486830--4486872 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4486820 GAAGCCCCTT
4486830 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
4486850 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
4486869 TGAA
1 TGAA
4486873 TGTACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4488206 original size:14 final size:12
Alignment explanation
Indices: 4488180--4488232 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 12
4488170 GGTCTAGAAG
*
4488180 TGTGTCATTCTT
1 TGTGTCGTTCTT
4488192 TGTTGATCGTTCTT
1 TG-TG-TCGTTCTT
*
4488206 TGTGTCATTCTT
1 TGTGTCGTTCTT
4488218 TGCTGGTCGTTCTT
1 TG-T-GTCGTTCTT
4488232 T
1 T
4488233 ATCCTTGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.32
13 5 0.15
14 18 0.53
ACGTcount: A:0.06, C:0.17, G:0.21, T:0.57
Consensus pattern (12 bp):
TGTGTCGTTCTT
Found at i:4488210 original size:26 final size:26
Alignment explanation
Indices: 4488180--4488232 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4488170 GGTCTAGAAG
*
4488180 TGTGTCATTCTTTGTTGATCGTTCTT
1 TGTGTCATTCTTTGCTGATCGTTCTT
*
4488206 TGTGTCATTCTTTGCTGGTCGTTCTT
1 TGTGTCATTCTTTGCTGATCGTTCTT
4488232 T
1 T
4488233 ATCCTTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.06, C:0.17, G:0.21, T:0.57
Consensus pattern (26 bp):
TGTGTCATTCTTTGCTGATCGTTCTT
Found at i:4488218 original size:12 final size:12
Alignment explanation
Indices: 4488180--4488219 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4488170 GGTCTAGAAG
4488180 TGTGTCATTCTT
1 TGTGTCATTCTT
*
4488192 TGTTGATCGTTCTT
1 TG-TG-TCATTCTT
4488206 TGTGTCATTCTT
1 TGTGTCATTCTT
4488218 TG
1 TG
4488220 CTGGTCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.46
13 4 0.17
14 9 0.38
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.57
Consensus pattern (12 bp):
TGTGTCATTCTT
Found at i:4493104 original size:6 final size:6
Alignment explanation
Indices: 4493093--4493128 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
4493083 AGACCCATAT
* *
4493093 GTCATG GTCATG GTCATG GTAATG GTCACG GTCATG
1 GTCATG GTCATG GTCATG GTCATG GTCATG GTCATG
4493129 ACACAAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (6 bp):
GTCATG
Found at i:4498663 original size:48 final size:45
Alignment explanation
Indices: 4498567--4498700 Score: 135
Period size: 48 Copynumber: 2.9 Consensus size: 45
4498557 GTAACCATGC
* * * * * * *
4498567 AAATAAGCTTATGAGCTTACGAAAT-AATGGCAAGTATATAGGAA
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
* *
4498611 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTA
1 AAATAAACTTACGAGCTTATGGAA---TAAATGGTAAGTATTTTGGAA
*
4498659 AAATAAACTTACGAGCTTATGGGATAAATGGTAAGATATTTT
1 AAATAAACTTACGAGCTTATGGAATAAATGGTAAG-TATTTT
4498701 ATATTATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
44 21 0.28
45 11 0.14
46 6 0.08
47 1 0.01
48 37 0.49
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
Found at i:4499566 original size:15 final size:15
Alignment explanation
Indices: 4499532--4499577 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
4499522 TATGAAATAA
*
4499532 GAAATGGAATAAGAACG
1 GAAAT-GAA-AAGAAAG
4499549 GAAATGAAAAGAAAG
1 GAAATGAAAAGAAAG
*
4499564 GAAATGGAAAGAAA
1 GAAATGAAAAGAAA
4499578 TGATATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 19 0.70
16 3 0.11
17 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.28, T:0.09
Consensus pattern (15 bp):
GAAATGAAAAGAAAG
Found at i:4500151 original size:19 final size:19
Alignment explanation
Indices: 4500107--4500154 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4500097 AACCCCTTGT
**
4500107 AAAATACATGATTTTTATA
1 AAAATACATGATTTAAATA
*
4500126 AAAATACATGATTTAAATG
1 AAAATACATGATTTAAATA
*
4500145 AAGATACATG
1 AAAATACATG
4500155 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAATACATGATTTAAATA
Found at i:4504314 original size:19 final size:20
Alignment explanation
Indices: 4504267--4504317 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4504257 AAACCCCTTT
**
4504267 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
4504287 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4504306 TGAAGATACATG
1 TGAAAATACATG
4504318 CACTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4518222 original size:78 final size:78
Alignment explanation
Indices: 4518093--4518248 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
4518083 AAAGGTGCGA
4518093 TTTCACAAAATTTGACTTAGGACAAATTTGAAGTGTCCTCAGTGGTGATGATGATGGTACAGATC
1 TTTCACAAAATTTGACTTAGGACAAATTTGAAGTGTCCTCAGTGGTGATGATGATGGTACAGATC
4518158 CCCAGCTGAATTC
66 CCCAGCTGAATTC
4518171 TTTCACAAAATTTGACTTAGGACAAATTTGAAGTGTCCTCAGTGGTGATGATGATGGTACAGATC
1 TTTCACAAAATTTGACTTAGGACAAATTTGAAGTGTCCTCAGTGGTGATGATGATGGTACAGATC
4518236 CCCAGCTGAATTC
66 CCCAGCTGAATTC
4518249 AAGTCATCTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (78 bp):
TTTCACAAAATTTGACTTAGGACAAATTTGAAGTGTCCTCAGTGGTGATGATGATGGTACAGATC
CCCAGCTGAATTC
Found at i:4545189 original size:20 final size:20
Alignment explanation
Indices: 4545153--4545191 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4545143 AAATGTGATG
*
4545153 ATGAATCATGCTTAGCTAAA
1 ATGAATCATGCTGAGCTAAA
4545173 ATGAATGCATG-TGAGCTAA
1 ATGAAT-CATGCTGAGCTAA
4545192 TGAATGATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (20 bp):
ATGAATCATGCTGAGCTAAA
Found at i:4547542 original size:13 final size:13
Alignment explanation
Indices: 4547526--4547550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4547516 ATCACCAACT
4547526 TATATATATATTA
1 TATATATATATTA
4547539 TATATATATATT
1 TATATATATATT
4547551 TCGCTGCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATATTA
Found at i:4549250 original size:229 final size:229
Alignment explanation
Indices: 4548849--4549310 Score: 924
Period size: 229 Copynumber: 2.0 Consensus size: 229
4548839 GTTGGTGAAT
4548849 AGTTTTTAGTTAAATGAGGCATAATTCAATAAGTGACAATAAGAACACCAAGGTGACTATTGGGC
1 AGTTTTTAGTTAAATGAGGCATAATTCAATAAGTGACAATAAGAACACCAAGGTGACTATTGGGC
4548914 CACAAACACATACATTGCACATGGAGAGTTTGGAACCAAAATGAACAAGTAGAAGACTATTTTGC
66 CACAAACACATACATTGCACATGGAGAGTTTGGAACCAAAATGAACAAGTAGAAGACTATTTTGC
4548979 CTAAAGGGAGGTTCATTCATCTTAGCTTAATCATCATACCCTTTTTAAAGAGTTAGCCAAACCAA
131 CTAAAGGGAGGTTCATTCATCTTAGCTTAATCATCATACCCTTTTTAAAGAGTTAGCCAAACCAA
4549044 CACAAGGCCTAAATACATATGCATTCATTTAATA
196 CACAAGGCCTAAATACATATGCATTCATTTAATA
4549078 AGTTTTTAGTTAAATGAGGCATAATTCAATAAGTGACAATAAGAACACCAAGGTGACTATTGGGC
1 AGTTTTTAGTTAAATGAGGCATAATTCAATAAGTGACAATAAGAACACCAAGGTGACTATTGGGC
4549143 CACAAACACATACATTGCACATGGAGAGTTTGGAACCAAAATGAACAAGTAGAAGACTATTTTGC
66 CACAAACACATACATTGCACATGGAGAGTTTGGAACCAAAATGAACAAGTAGAAGACTATTTTGC
4549208 CTAAAGGGAGGTTCATTCATCTTAGCTTAATCATCATACCCTTTTTAAAGAGTTAGCCAAACCAA
131 CTAAAGGGAGGTTCATTCATCTTAGCTTAATCATCATACCCTTTTTAAAGAGTTAGCCAAACCAA
4549273 CACAAGGCCTAAATACATATGCATTCATTTAATA
196 CACAAGGCCTAAATACATATGCATTCATTTAATA
4549307 AGTT
1 AGTT
4549311 ATGTACCTTA
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 233 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (229 bp):
AGTTTTTAGTTAAATGAGGCATAATTCAATAAGTGACAATAAGAACACCAAGGTGACTATTGGGC
CACAAACACATACATTGCACATGGAGAGTTTGGAACCAAAATGAACAAGTAGAAGACTATTTTGC
CTAAAGGGAGGTTCATTCATCTTAGCTTAATCATCATACCCTTTTTAAAGAGTTAGCCAAACCAA
CACAAGGCCTAAATACATATGCATTCATTTAATA
Found at i:4549425 original size:12 final size:12
Alignment explanation
Indices: 4549408--4549453 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
4549398 AGAGTCTTAC
4549408 CTTATTTTATTA
1 CTTATTTTATTA
*
4549420 CTTATTTAGTCTTA
1 CTTATTT--TATTA
4549434 CCTTATTTTATTA
1 -CTTATTTTATTA
4549447 CTTATTT
1 CTTATTT
4549454 ATGCATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (12 bp):
CTTATTTTATTA
Found at i:4549438 original size:27 final size:27
Alignment explanation
Indices: 4549400--4549454 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4549390 ATTCTAAGAG
4549400 AGTCTTACCTTATTTTATTACTTATTT
1 AGTCTTACCTTATTTTATTACTTATTT
4549427 AGTCTTACCTTATTTTATTACTTATTT
1 AGTCTTACCTTATTTTATTACTTATTT
4549454 A
1 A
4549455 TGCATTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (27 bp):
AGTCTTACCTTATTTTATTACTTATTT
Found at i:4550726 original size:2 final size:2
Alignment explanation
Indices: 4550719--4550770 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
4550709 ATCACCAACT
* *
4550719 TA TA TA TA TA TA TA CA CA TA TA T- 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
4550760 TA TA TA TA TA T
1 TA TA TA TA TA T
4550771 CCCGCTGTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4550731 original size:21 final size:23
Alignment explanation
Indices: 4550718--4550770 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
4550708 TATCACCAAC
4550718 TTATATATATATATACACATATA
1 TTATATATATATATACACATATA
* *
4550741 TTATATATATATATATATATATA
1 TTATATATATATATACACATATA
4550764 -TATATAT
1 TTATATAT
4550771 CCCGCTGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATATATATATATACACATATA
Found at i:4558372 original size:2 final size:2
Alignment explanation
Indices: 4558365--4558393 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4558355 TATAGATGTA
4558365 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4558394 GAATATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4558375 original size:17 final size:17
Alignment explanation
Indices: 4558355--4558400 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
4558345 TCATTATAAC
*
4558355 TATAGATGTAATATATA
1 TATATATGTAATATATA
*
4558372 TATATATAT-ATA-ATA
1 TATATATGTAATATATA
4558387 TATATATG-AATATA
1 TATATATGTAATATA
4558401 ACTATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 13 0.54
16 4 0.17
17 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (17 bp):
TATATATGTAATATATA
Found at i:4558377 original size:19 final size:19
Alignment explanation
Indices: 4558355--4558393 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4558345 TCATTATAAC
*
4558355 TATAGATGTAATATATATA
1 TATAGATATAATATATATA
*
4558374 TATATATATAATATATATA
1 TATAGATATAATATATATA
4558393 T
1 T
4558394 GAATATAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TATAGATATAATATATATA
Found at i:4558399 original size:19 final size:19
Alignment explanation
Indices: 4558363--4558417 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
4558353 ACTATAGATG
4558363 TAATATATATAT-ATATATA
1 TAATATATATATGA-ATATA
4558382 TAATATATATATGAATATA
1 TAATATATATATGAATATA
*
4558401 -ACTATAT-TATAGAATAT
1 TAATATATATAT-GAATAT
4558418 GAAATTAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 17 0.52
20 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
TAATATATATATGAATATA
Found at i:4558415 original size:18 final size:17
Alignment explanation
Indices: 4558364--4558417 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
4558354 CTATAGATGT
4558364 AATAT-ATATATATAT-
1 AATATAATATATATATG
4558379 -ATATAATATATATATG
1 AATATAATATATATATG
4558395 AATATAACTATAT-TATAG
1 AATATAA-TATATATAT-G
4558413 AATAT
1 AATAT
4558418 GAAATTAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.12
15 10 0.29
17 9 0.26
18 11 0.32
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
AATATAATATATATATG
Found at i:4560351 original size:108 final size:108
Alignment explanation
Indices: 4560162--4560374 Score: 426
Period size: 108 Copynumber: 2.0 Consensus size: 108
4560152 TAGATCAACT
4560162 TGAGCAACATTTTTGAGGGGGTTACCGGTGTCCAAAACTTTTGGAAAATTTCTTGAATGTCTTTT
1 TGAGCAACATTTTTGAGGGGGTTACCGGTGTCCAAAACTTTTGGAAAATTTCTTGAATGTCTTTT
4560227 GATGAGTCAATAAACCGTCTGTAAAATTTCAGAACCAAATGAG
66 GATGAGTCAATAAACCGTCTGTAAAATTTCAGAACCAAATGAG
4560270 TGAGCAACATTTTTGAGGGGGTTACCGGTGTCCAAAACTTTTGGAAAATTTCTTGAATGTCTTTT
1 TGAGCAACATTTTTGAGGGGGTTACCGGTGTCCAAAACTTTTGGAAAATTTCTTGAATGTCTTTT
4560335 GATGAGTCAATAAACCGTCTGTAAAATTTCAGAACCAAAT
66 GATGAGTCAATAAACCGTCTGTAAAATTTCAGAACCAAAT
4560375 ACCATGAGTA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (108 bp):
TGAGCAACATTTTTGAGGGGGTTACCGGTGTCCAAAACTTTTGGAAAATTTCTTGAATGTCTTTT
GATGAGTCAATAAACCGTCTGTAAAATTTCAGAACCAAATGAG
Found at i:4571376 original size:42 final size:41
Alignment explanation
Indices: 4571329--4571412 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
4571319 AGTTCTAAAG
4571329 GTCTTAA-ATAACTAATGAATAAAATAATAATAAACTAAAAAT
1 GTCTTAACATAACTAAT-AATAAAATAATAAT-AACTAAAAAT
* **
4571371 GTCTTAACTCTAACTCCTAATAAAATAATAATAACTAAAAAT
1 GTCTTAAC-ATAACTAATAATAAAATAATAATAACTAAAAAT
4571413 AATGTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 17 0.46
43 14 0.38
44 6 0.16
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.30
Consensus pattern (41 bp):
GTCTTAACATAACTAATAATAAAATAATAATAACTAAAAAT
Found at i:4575252 original size:20 final size:20
Alignment explanation
Indices: 4575229--4575272 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4575219 TTTTTAAAAA
4575229 TTTTGGCTTTGTTTTTATTT
1 TTTTGGCTTTGTTTTTATTT
*
4575249 TTTTGGCTTTTTTTTTATTT
1 TTTTGGCTTTGTTTTTATTT
4575269 TTTT
1 TTTT
4575273 AAACAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTTGGCTTTGTTTTTATTT
Found at i:4581584 original size:19 final size:20
Alignment explanation
Indices: 4581537--4581576 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
4581527 ACCATTTTGC
4581537 AAATACATGATTTTTAATGA
1 AAATACATGATTTTTAATGA
4581557 AAATACATGA-TTTTAATGA
1 AAATACATGATTTTTAATGA
4581576 A
1 A
4581577 GGTACATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATACATGATTTTTAATGA
Found at i:4582601 original size:20 final size:20
Alignment explanation
Indices: 4582578--4582615 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4582568 TATGTTATGC
4582578 ATGAAAATCATATAGTATAT
1 ATGAAAATCATATAGTATAT
4582598 ATGAAAATCATATAGTAT
1 ATGAAAATCATATAGTAT
4582616 GCAAGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGAAAATCATATAGTATAT
Found at i:4584601 original size:32 final size:34
Alignment explanation
Indices: 4584539--4584603 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 34
4584529 CAACTCTATT
* *
4584539 CATTTCTTGTATTTCATTACTTATCTTATTTATC
1 CATTTCTTGTATTCCATTACTTATCCTATTTATC
4584573 CATTTC-T-TATTCCATTA-TTAATCCTATTTAT
1 CATTTCTTGTATTCCATTACTT-ATCCTATTTAT
4584604 TTTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.07
32 19 0.68
33 1 0.04
34 6 0.21
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.57
Consensus pattern (34 bp):
CATTTCTTGTATTCCATTACTTATCCTATTTATC
Found at i:4585542 original size:43 final size:45
Alignment explanation
Indices: 4585440--4585545 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 45
4585430 AGGATTAGAT
*
4585440 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATT-A--ATGAGTTAAAAC--TATGTTTAGTTA
4585490 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACTATGTTTAG-TTA
4585533 TTATTATTTTATT
1 TTATTATTTTATT
4585546 CATTAGTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 7 0.13
43 16 0.30
45 10 0.19
46 1 0.02
50 20 0.37
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACTATGTTTAGTTA
Found at i:4589891 original size:16 final size:18
Alignment explanation
Indices: 4589862--4589899 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4589852 TGTAGGAGTC
4589862 TTTTCTTTTATCTT-TTT
1 TTTTCTTTTATCTTCTTT
4589879 TTTTCTTTT-TCTTCTTT
1 TTTTCTTTTATCTTCTTT
4589896 TTTT
1 TTTT
4589900 TCATTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTCTTTTATCTTCTTT
Found at i:4597820 original size:13 final size:13
Alignment explanation
Indices: 4597802--4597840 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
4597792 ATAGGCGTGA
4597802 ATGGTGATGGAAG
1 ATGGTGATGGAAG
4597815 ATGGTGATGGAAAG
1 ATGGTGATGG-AAG
*
4597829 ATGGTAATGGAA
1 ATGGTGATGGAA
4597841 AGATAGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:4597831 original size:14 final size:14
Alignment explanation
Indices: 4597802--4597844 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
4597792 ATAGGCGTGA
4597802 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
4597815 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
*
4597829 ATGGTAATGGAAAG
1 ATGGTGATGGAAAG
4597843 AT
1 AT
4597845 AGTATCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:4598217 original size:19 final size:19
Alignment explanation
Indices: 4598179--4598234 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
4598169 GAAACCTTTT
*
4598179 TGAAAATACATCATTTTTAA
1 TGAAAATACATGA-TTTTAA
4598199 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
* *
4598218 TGAAGATACATGCTTTT
1 TGAAAATACATGATTTT
4598235 GGTCGAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:4599160 original size:20 final size:20
Alignment explanation
Indices: 4599135--4599173 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4599125 CCATGATATG
4599135 TAAATG-ATATCAAAACATAA
1 TAAATGAATAT-AAAACATAA
4599155 TAAATGAATATAAAACATA
1 TAAATGAATATAAAACATA
4599174 TGTAGACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:4619053 original size:15 final size:15
Alignment explanation
Indices: 4619042--4619070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4619032 ACTCAAAAAG
4619042 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
4619057 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
4619071 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:4625191 original size:24 final size:24
Alignment explanation
Indices: 4625149--4625207 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
4625139 AAAATCAGCA
* *
4625149 AAGAAATTG-AAGCACTCAAAA-G
1 AAGAAATAGAAAGCAATCAAAAGG
4625171 AAGAAAATAGAAAGCAATCAAAAGG
1 AAG-AAATAGAAAGCAATCAAAAGG
4625196 AAGAAATAGAAA
1 AAGAAATAGAAA
4625208 AGAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.09
23 5 0.16
24 20 0.62
25 4 0.12
ACGTcount: A:0.63, C:0.08, G:0.19, T:0.10
Consensus pattern (24 bp):
AAGAAATAGAAAGCAATCAAAAGG
Found at i:4630343 original size:19 final size:19
Alignment explanation
Indices: 4630319--4630360 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
4630309 GCTAGCTTCA
4630319 AGCTTGCAAGTGTATAGCT
1 AGCTTGCAAGTGTATAGCT
4630338 AGCTTGCAAGTGTATAGCT
1 AGCTTGCAAGTGTATAGCT
4630357 AGCT
1 AGCT
4630361 AGGAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (19 bp):
AGCTTGCAAGTGTATAGCT
Found at i:4641107 original size:18 final size:18
Alignment explanation
Indices: 4641086--4641127 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4641076 CTGGAACTGG
*
4641086 TGCTGGACTATGAACTAC
1 TGCTGGACTAGGAACTAC
*
4641104 TGCTGGACTAGGAACTGC
1 TGCTGGACTAGGAACTAC
4641122 TGCTGG
1 TGCTGG
4641128 GACTGGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (18 bp):
TGCTGGACTAGGAACTAC
Found at i:4651540 original size:15 final size:14
Alignment explanation
Indices: 4651517--4651554 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4651507 ATCATTGCAC
4651517 TTTTC-TTTTCTTT
1 TTTTCATTTTCTTT
4651530 TCTTTCATTTTCTTT
1 T-TTTCATTTTCTTT
*
4651545 TTTTTATTTT
1 TTTTCATTTT
4651555 GGGAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 9 0.41
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCATTTTCTTT
Found at i:4651574 original size:20 final size:19
Alignment explanation
Indices: 4651542--4651586 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
4651532 TTTCATTTTC
4651542 TTTTTTTTATTTTGGGAATT
1 TTTTTTTTATTTT-GGAATT
4651562 TTGTTTTTT-TTTTGGAATT
1 TT-TTTTTTATTTTGGAATT
4651581 TTTTTT
1 TTTTTT
4651587 ACTTTCAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 8 0.33
20 6 0.25
21 6 0.25
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (19 bp):
TTTTTTTTATTTTGGAATT
Found at i:4654651 original size:9 final size:9
Alignment explanation
Indices: 4654639--4654679 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
4654629 TAACTGAAAT
4654639 AAGAAATGA
1 AAGAAATGA
4654648 AAG-AATGA
1 AAGAAATGA
4654656 AATGAAATGA
1 AA-GAAATGA
4654666 TAAGAAATGA
1 -AAGAAATGA
4654676 AAGA
1 AAGA
4654680 GATAGAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.24
9 8 0.28
10 12 0.41
11 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (9 bp):
AAGAAATGA
Found at i:4654656 original size:20 final size:20
Alignment explanation
Indices: 4654641--4654677 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
4654631 ACTGAAATAA
4654641 GAAATGA-AAG-AATGAAAT
1 GAAATGATAAGAAATGAAAT
4654659 GAAATGATAAGAAATGAAA
1 GAAATGATAAGAAATGAAA
4654678 GAGATAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (20 bp):
GAAATGATAAGAAATGAAAT
Found at i:4660078 original size:19 final size:17
Alignment explanation
Indices: 4660045--4660087 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
4660035 GATGTATGAG
4660045 TCTTTTTTTTTTCTTTT
1 TCTTTTTTTTTTCTTTT
4660062 TCTTTTTCTTCTTTCTTTT
1 TCTTTTT-TT-TTTCTTTT
*
4660081 TGTTTTT
1 TCTTTTT
4660088 GTTGCATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
19 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (17 bp):
TCTTTTTTTTTTCTTTT
Found at i:4660090 original size:6 final size:6
Alignment explanation
Indices: 4660045--4660087 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
4660035 GATGTATGAG
*
4660045 TCTTTT T-TTTT TCTTTT TCTTTT TCTTCTT TCTTTT TGTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
4660088 GTTGCATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
7 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:4662787 original size:16 final size:16
Alignment explanation
Indices: 4662761--4662793 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4662751 AGTATGAACA
4662761 GGAAAATAAAA-AAAT
1 GGAAAATAAAAGAAAT
4662776 GGAAACATAAAAGAAAT
1 GGAAA-ATAAAAGAAAT
4662793 G
1 G
4662794 ATTTAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.12
Consensus pattern (16 bp):
GGAAAATAAAAGAAAT
Found at i:4675967 original size:20 final size:20
Alignment explanation
Indices: 4675942--4675986 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
4675932 TTGTTTGGCC
4675942 TCTTAGAGCTTTT-AGATTTT
1 TCTTAGAGCTTTTAAG-TTTT
4675962 TCTTAGAGCTTTTAAGTTTT
1 TCTTAGAGCTTTTAAGTTTT
4675982 TCTTA
1 TCTTA
4675987 TTGCCTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.56
Consensus pattern (20 bp):
TCTTAGAGCTTTTAAGTTTT
Found at i:4681999 original size:2 final size:2
Alignment explanation
Indices: 4681992--4682039 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
4681982 AGTTATTTTC
*
4681992 AT AT AT AT AT AT AT AT AT A- AT A- ACT AT AG AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
4682032 AT AT AT AT
1 AT AT AT AT
4682040 TATCTATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 36 0.90
3 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4689232 original size:23 final size:24
Alignment explanation
Indices: 4689183--4689232 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
4689173 TCTTTCTTCT
* *
4689183 TTTTCTTGTTTTTGAATGTTTTCA
1 TTTTCTTGCTTTTGAATGCTTTCA
* *
4689207 TTTTCTT-CTTTTGAGTGCTTTGA
1 TTTTCTTGCTTTTGAATGCTTTCA
4689230 TTT
1 TTT
4689233 CTTTGTTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.10, C:0.10, G:0.14, T:0.66
Consensus pattern (24 bp):
TTTTCTTGCTTTTGAATGCTTTCA
Found at i:4691460 original size:17 final size:17
Alignment explanation
Indices: 4691438--4691477 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4691428 TTCTTTAATT
*
4691438 AAACTATTTCATTCATC
1 AAACTAGTTCATTCATC
* *
4691455 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
4691472 AAACTA
1 AAACTA
4691478 ACTCTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:4700075 original size:11 final size:11
Alignment explanation
Indices: 4700053--4700089 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4700043 GCAACCTAAC
4700053 TCATCATTTCT
1 TCATCATTTCT
* *
4700064 TTATCCTTTCT
1 TCATCATTTCT
4700075 TCATCATTTCT
1 TCATCATTTCT
4700086 TCAT
1 TCAT
4700090 TCTTTATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (11 bp):
TCATCATTTCT
Found at i:4700078 original size:22 final size:22
Alignment explanation
Indices: 4700053--4700100 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
4700043 GCAACCTAAC
* *
4700053 TCATCATTTCTTTATCCTTTCT
1 TCATCATTTCTTCATCCTTTAT
*
4700075 TCATCATTTCTTCATTCTTTAT
1 TCATCATTTCTTCATCCTTTAT
4700097 TCAT
1 TCAT
4700101 AATTGCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (22 bp):
TCATCATTTCTTCATCCTTTAT
Found at i:4706507 original size:24 final size:25
Alignment explanation
Indices: 4706480--4706528 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
4706470 ATGATGCTAA
4706480 TTTCATATAT-TATA-ATATAGTTAT
1 TTTCATATATATATATATATA-TTAT
4706504 TTTCATATATATATATATATATTAT
1 TTTCATATATATATATATATATTAT
4706529 CTATAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
25 8 0.35
26 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTCATATATATATATATATATTAT
Found at i:4709713 original size:27 final size:27
Alignment explanation
Indices: 4709674--4709734 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
4709664 TGACCATGAA
4709674 GAAGAAGTAGCACCAAATGAAGTCGAG
1 GAAGAAGTAGCACCAAATGAAGTCGAG
*
4709701 TAAGAAGTAGCACCAAATGAAGTCGAG
1 GAAGAAGTAGCACCAAATGAAGTCGAG
4709728 GAAGAAG
1 GAAGAAG
4709735 CAGAAATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.30, T:0.11
Consensus pattern (27 bp):
GAAGAAGTAGCACCAAATGAAGTCGAG
Found at i:4712243 original size:15 final size:16
Alignment explanation
Indices: 4712223--4712260 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4712213 ATGGGTTAGT
*
4712223 GAAAAAAATAAAA-AA
1 GAAAAAAAGAAAACAA
4712238 GAAAAAAAGAAAACAA
1 GAAAAAAAGAAAACAA
4712254 -AAAAAAA
1 GAAAAAAA
4712261 ACAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.03
Consensus pattern (16 bp):
GAAAAAAAGAAAACAA
Found at i:4713114 original size:19 final size:19
Alignment explanation
Indices: 4713092--4713142 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
4713082 AAAAACAAAC
4713092 GAGAGTTGAAAA-AGACATT
1 GAGAGTTGAAAAGAGA-ATT
*
4713111 GAGAGCATTGAAAAGAGATTT
1 GAGAG--TTGAAAAGAGAATT
4713132 GAGAG-TGAAAA
1 GAGAGTTGAAAA
4713143 TGAACACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
21 14 0.50
22 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.20
Consensus pattern (19 bp):
GAGAGTTGAAAAGAGAATT
Found at i:4718285 original size:27 final size:27
Alignment explanation
Indices: 4718247--4718310 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
4718237 CCTTTAAGAA
* *
4718247 GAAGAAGTAGCACCAAATGAAGTTGAG
1 GAAGAAGTAGCACCAAATAAAGTCGAG
4718274 GAAGAAGTAGCACCAAATAAAGTCGAG
1 GAAGAAGTAGCACCAAATAAAGTCGAG
4718301 GAAGAAGTAG
1 GAAGAAGTAG
4718311 AAATTGGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.47, C:0.11, G:0.30, T:0.12
Consensus pattern (27 bp):
GAAGAAGTAGCACCAAATAAAGTCGAG
Found at i:4720807 original size:13 final size:13
Alignment explanation
Indices: 4720783--4720820 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
4720773 GGTTAGTGAA
4720783 AAAAATAAAAAATC
1 AAAAA-AAAAAATC
*
4720797 AAAAAAGAAAA-C
1 AAAAAAAAAAATC
4720809 AAAAAAAAAAAT
1 AAAAAAAAAAAT
4720821 TAAAGAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 5 0.24
14 5 0.24
ACGTcount: A:0.84, C:0.05, G:0.03, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAATC
Found at i:4726978 original size:22 final size:23
Alignment explanation
Indices: 4726921--4726975 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
4726911 TTTATTTTTT
* *
4726921 TCTTCTTTTTCTTCTTTTTAGTG
1 TCTTCATTTTCTTCTTTTGAGTG
*
4726944 TTTTCATTTTCTTCTTTTGAGTG
1 TCTTCATTTTCTTCTTTTGAGTG
4726967 -CTTCGATTT
1 TCTTC-ATTT
4726976 CTTTTTGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.07, C:0.16, G:0.11, T:0.65
Consensus pattern (23 bp):
TCTTCATTTTCTTCTTTTGAGTG
Found at i:4728437 original size:9 final size:9
Alignment explanation
Indices: 4728423--4728454 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
4728413 TTTCTTTATT
4728423 TTTTTCTTC
1 TTTTTCTTC
4728432 TTTTTCTTC
1 TTTTTCTTC
4728441 TTTTTCTTC
1 TTTTTCTTC
4728450 TTTTT
1 TTTTT
4728455 AGTGTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:4728462 original size:18 final size:18
Alignment explanation
Indices: 4728423--4728462 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4728413 TTTCTTTATT
**
4728423 TTTTTCTTCTTTTTCTTC
1 TTTTTCTTCTTTTTAGTC
*
4728441 TTTTTCTTCTTTTTAGTG
1 TTTTTCTTCTTTTTAGTC
4728459 TTTT
1 TTTT
4728463 CATTTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTCTTCTTTTTAGTC
Found at i:4728493 original size:22 final size:23
Alignment explanation
Indices: 4728436--4728490 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
4728426 TTCTTCTTTT
* *
4728436 TCTTCTTTTTCTTCTTTTTAGTG
1 TCTTCATTTTCTTCTTTTGAGTG
*
4728459 TTTTCATTTTCTTCTTTTGAGTG
1 TCTTCATTTTCTTCTTTTGAGTG
4728482 -CTTCGATTT
1 TCTTC-ATTT
4728491 CTTTTTGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.07, C:0.16, G:0.11, T:0.65
Consensus pattern (23 bp):
TCTTCATTTTCTTCTTTTGAGTG
Found at i:4730713 original size:17 final size:17
Alignment explanation
Indices: 4730693--4730732 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4730683 TTCTTTAACT
4730693 AAACTAGTTCATTCATC
1 AAACTAGTTCATTCATC
* *
4730710 AAACTAGTTCATTGATT
1 AAACTAGTTCATTCATC
4730727 AAACTA
1 AAACTA
4730733 ACACTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:4736858 original size:17 final size:17
Alignment explanation
Indices: 4736836--4736868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4736826 GTTGGCTAAA
*
4736836 AGAAATGGTTATGGTAT
1 AGAAATGGGTATGGTAT
4736853 AGAAATGGGTATGGTA
1 AGAAATGGGTATGGTA
4736869 AATGTAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (17 bp):
AGAAATGGGTATGGTAT
Found at i:4739225 original size:11 final size:11
Alignment explanation
Indices: 4739203--4739251 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
4739193 GCAACCTAAC
*
4739203 TCATCATTTCT
1 TCATCCTTTCT
*
4739214 TTATCCTTTCT
1 TCATCCTTTCT
*
4739225 TCATCATTTCT
1 TCATCCTTTCT
*
4739236 TCATCCTTTAT
1 TCATCCTTTCT
4739247 TCATC
1 TCATC
4739252 ATTGCTTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (11 bp):
TCATCCTTTCT
Found at i:4739228 original size:22 final size:22
Alignment explanation
Indices: 4739203--4739262 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
4739193 GCAACCTAAC
*
4739203 TCATCATTTCTTTATCCTTTCT
1 TCATCATTTCTTTATCCTTTAT
*
4739225 TCATCATTTCTTCATCCTTTAT
1 TCATCATTTCTTTATCCTTTAT
*
4739247 TCATCATTGC-TTATCC
1 TCATCATTTCTTTATCC
4739263 ATTTTTGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.17, C:0.28, G:0.02, T:0.53
Consensus pattern (22 bp):
TCATCATTTCTTTATCCTTTAT
Found at i:4739478 original size:16 final size:16
Alignment explanation
Indices: 4739459--4739489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4739449 TTGAAAATAC
4739459 AAAAAATCAAAAATTA
1 AAAAAATCAAAAATTA
*
4739475 AAAAAATTAAAAATT
1 AAAAAATCAAAAATT
4739490 TTCGAAAATT
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:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATCAAAAATTA
Found at i:4746586 original size:17 final size:17
Alignment explanation
Indices: 4746557--4746622 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
4746547 TAAGATCTAG
*
4746557 TTTAATAAATGAACTAA
1 TTTAATGAATGAACTAA
* *
4746574 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAA
*
4746591 TTTAATTAATGAACTAA
1 TTTAATGAATGAACTAA
* *
4746608 CTTTATTCAATGAAC
1 -TTTAATGAATGAAC
4746623 AAGAACTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 28 0.70
18 12 0.30
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAA
Found at i:4750666 original size:17 final size:17
Alignment explanation
Indices: 4750638--4750688 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
4750628 TTAAGATTTG
*
4750638 GTTTAATAAATGAACTA
1 GTTTAATGAATGAACTA
*
4750655 GTTTGATGAATGAACTA
1 GTTTAATGAATGAACTA
*
4750672 GTTTAATTAATGAACTA
1 GTTTAATGAATGAACTA
4750689 ACTTTATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (17 bp):
GTTTAATGAATGAACTA
Found at i:4750809 original size:18 final size:17
Alignment explanation
Indices: 4750764--4750829 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
4750754 TTATATAAAT
*
4750764 ATGCATAAATGAACTAC
1 ATGCATAAATGAACTGC
* * *
4750781 TTCCCTAAATGAACTAG-
1 ATGCATAAATGAACT-GC
4750798 ATGCATTAAATGCAA-TGC
1 ATGCA-TAAATG-AACTGC
4750816 ATGCATAAATGAAC
1 ATGCATAAATGAAC
4750830 AACACACTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
18 12 0.32
19 2 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (17 bp):
ATGCATAAATGAACTGC
Found at i:4754860 original size:22 final size:22
Alignment explanation
Indices: 4754835--4754879 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4754825 CTATCAGTCA
4754835 AGCATTCAGATGACTCCTTATG
1 AGCATTCAGATGACTCCTTATG
4754857 AGCATTCAGATGACTCCTTATG
1 AGCATTCAGATGACTCCTTATG
4754879 A
1 A
4754880 ATCCTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
AGCATTCAGATGACTCCTTATG
Found at i:4762087 original size:43 final size:43
Alignment explanation
Indices: 4762033--4762115 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
4762023 ATTATGTTGT
*
4762033 GTTAATCACTATTGCTAGTCATTACAAATATCATGATTGTGAA
1 GTTAATCACTATTACTAGTCATTACAAATATCATGATTGTGAA
* * *
4762076 GTTAATCACTATTATTAGTCATTACATATATCGTGATTGT
1 GTTAATCACTATTACTAGTCATTACAAATATCATGATTGT
4762116 CGTGATTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (43 bp):
GTTAATCACTATTACTAGTCATTACAAATATCATGATTGTGAA
Found at i:4762726 original size:2 final size:2
Alignment explanation
Indices: 4762719--4762747 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4762709 TTAAAATCAT
4762719 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
4762748 TAATTTAAAT
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:4771412 original size:38 final size:38
Alignment explanation
Indices: 4771370--4771499 Score: 179
Period size: 38 Copynumber: 3.4 Consensus size: 38
4771360 AAGAAAAAAA
* * *
4771370 ATCTCAAGTGAGATAAATCTTATGTTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAATCTTCTATTTTGAGTGAAACT
* *
4771408 ATCTCAAGCGAGATTAAAATCATCTATTTCGAGTGAAACT
1 ATCTCAAGCGAGA-T-AAATCTTCTATTTTGAGTGAAACT
*
4771448 ATCTCAAGCGAGATAAATATTCTATTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAATCTTCTATTTTGAGTGAAACT
*
4771486 ATCTCAAGTGAGAT
1 ATCTCAAGCGAGAT
4771500 GTAGATCCCT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 46 0.57
39 2 0.02
40 33 0.41
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (38 bp):
ATCTCAAGCGAGATAAATCTTCTATTTTGAGTGAAACT
Found at i:4771459 original size:19 final size:19
Alignment explanation
Indices: 4771398--4771459 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
4771388 CTTATGTTTT
4771398 GAGTGAAACTATCTCAAGC
1 GAGTGAAACTATCTCAAGC
* * **
4771417 GAGATTAAAATCATCT-ATTTC
1 GAG-TGAAACT-ATCTCA-AGC
4771438 GAGTGAAACTATCTCAAGC
1 GAGTGAAACTATCTCAAGC
4771457 GAG
1 GAG
4771460 ATAAATATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
19 11 0.35
20 12 0.39
21 8 0.26
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (19 bp):
GAGTGAAACTATCTCAAGC
Found at i:4771575 original size:59 final size:60
Alignment explanation
Indices: 4771506--4771630 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 60
4771496 AGATGTAGAT
* *
4771506 CCCTCAAGTGATG-CGTCCCTAATTCAAAATATCGTGAATCGAGCAA-AGGAAATGTTATC
1 CCCTCTAGTGA-GACGTCCCTAATTCAAAATATCGTGAATCGAGCAATAGGAAATGTTAAC
** * * * * * *
4771565 CCCTCTAGTGAGACGTTGCTGATTCGAAGTGTTGTGAATTGAGCAATAGGAAATGTTAAC
1 CCCTCTAGTGAGACGTCCCTAATTCAAAATATCGTGAATCGAGCAATAGGAAATGTTAAC
4771625 CCCTCT
1 CCCTCT
4771631 GGTGGGGCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 35 0.65
60 18 0.33
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (60 bp):
CCCTCTAGTGAGACGTCCCTAATTCAAAATATCGTGAATCGAGCAATAGGAAATGTTAAC
Found at i:4771815 original size:58 final size:59
Alignment explanation
Indices: 4771725--4771838 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
4771715 GATCCCTCAA
* *
4771725 GTGAGGCGTCACTGATTCAAAATGTCATGAATCGAGCAA-AGGAAATGTTAGCCCCCTG
1 GTGAGGCGTCACTGATTCAAAATGTCATGAATCGAGCAATAGGAAATATTAACCCCCTG
** * * **
4771783 GTGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATATTAACCCC
1 GTGAGGCGTCACTGATTCAAAATGTCATGAATCGAGCAATAGGAAATATTAACCCC
4771839 TTTGGTGGGG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
58 33 0.70
59 14 0.30
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (59 bp):
GTGAGGCGTCACTGATTCAAAATGTCATGAATCGAGCAATAGGAAATATTAACCCCCTG
Found at i:4771871 original size:212 final size:212
Alignment explanation
Indices: 4771443--4771923 Score: 739
Period size: 212 Copynumber: 2.3 Consensus size: 212
4771433 ATTTCGAGTG
* * * *
4771443 AAACTATCTCAAGCGAGATAAATATTCTATTTTGAGTGAAACTATCTCAAGTGAGATGTAGATCC
1 AAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGATGTAGATCC
* * * *
4771508 CTCAAGTGATGCGTCCCTAATTCAAAATATCGTGAATCGAGCAAAGGAAATGTTATCCCCTCTAG
66 CTCAAGTGAGGCGTCACTAATTCAAAATATCATGAATCGAGCAAAGGAAATGTTAGCCCCTCTAG
* *
4771573 TGAGACGTTGCTGATTCGAAGTGTTGTGAATTGAGCAATAGGAAATGTTAACCCCTCTGGTGGGG
131 TGAGACGTTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATATTAACCCCTCTGGTGGGG
*
4771638 CATTGTTTCTTTAAGAA
196 CATAGTTTCTTTAAGAA
* * *
4771655 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGTTGATCC
1 AAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGATGTAGATCC
* * *
4771720 CTCAAGTGAGGCGTCACTGATTCAAAATGTCATGAATCGAGCAAAGGAAATGTTAGCCCC-CTGG
66 CTCAAGTGAGGCGTCACTAATTCAAAATATCATGAATCGAGCAAAGGAAATGTTAGCCCCTCTAG
* *
4771784 TGAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATATTAACCCCTTTGGTGGGG
131 TGAGACGTTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATATTAACCCCTCTGGTGGGG
* * *
4771849 CGTAGTTTGTTTTAATAA
196 CATAGTTT-CTTTAAGAA
*
4771867 AAACAATCTCAAGTGACATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGAT
1 AAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGAT
4771924 AAAATCACCT
Statistics
Matches: 243, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
211 70 0.29
212 173 0.71
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (212 bp):
AAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGATGTAGATCC
CTCAAGTGAGGCGTCACTAATTCAAAATATCATGAATCGAGCAAAGGAAATGTTAGCCCCTCTAG
TGAGACGTTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATATTAACCCCTCTGGTGGGG
CATAGTTTCTTTAAGAA
Found at i:4771926 original size:38 final size:39
Alignment explanation
Indices: 4771867--4771962 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 39
4771857 GTTTTAATAA
* * ** *
4771867 AAACAATCTCAAGTGACAT-AAATCTTCTATTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCACCTATTTCAAGTG
*
4771905 AAACTATCTCAAGTGAGATAAAATCACCTGTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCACCTATTTCAAGTG
* *
4771944 AAACTATCTCGAGCGAGAT
1 AAACTATCTCAAGTGAGAT
4771963 GTTGATCCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 17 0.35
39 32 0.65
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (39 bp):
AAACTATCTCAAGTGAGATAAAATCACCTATTTCAAGTG
Found at i:4772287 original size:54 final size:55
Alignment explanation
Indices: 4772155--4772434 Score: 252
Period size: 58 Copynumber: 5.1 Consensus size: 55
4772145 AGGACTTACT
* * ** *
4772155 CATCAAGAAACCCTTGAAAATCAAGCTTAGTTTC-TTAAAATCATTCGTTTTCAGTTAT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTAAAA-CATTC-TTTT--GAAAA
*
4772213 CATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAACA-TCTTTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTAAAACATTCTTTTGAAAA
* * * * *
4772267 AATCAAGAAACCCTTGAAAATCAGGCATAGTTTC--TAAAA-ACTCATTTG-AAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTAAAACATTCTTTTGAAAA
* * * * *
4772318 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTCTTAAAA-ATTCATTGGAAATGA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT-TTAAAACATTCTTTTGAAA--A
* * *
4772375 TTTATCAAGAAACCCCTGAAAATCATGCTTAGTTTCTTTAAAA-ATTCTTTTGAAAG
1 --CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTAAAACATTCTTTTGAAAA
4772431 CATC
1 CATC
4772435 TCGTTGTTTG
Statistics
Matches: 184, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
51 32 0.17
52 11 0.06
54 47 0.26
55 2 0.01
56 4 0.02
57 3 0.02
58 49 0.27
59 36 0.20
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (55 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTAAAACATTCTTTTGAAAA
Found at i:4774844 original size:13 final size:13
Alignment explanation
Indices: 4774826--4774861 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4774816 GCACATGCAA
4774826 ATGCAAAATGGGC
1 ATGCAAAATGGGC
4774839 ATGCAAAATGGGC
1 ATGCAAAATGGGC
* *
4774852 GTGTAAAATG
1 ATGCAAAATG
4774862 CGAGATGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.31, T:0.19
Consensus pattern (13 bp):
ATGCAAAATGGGC
Found at i:4775389 original size:29 final size:31
Alignment explanation
Indices: 4775332--4775392 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
4775322 CAATAAGACT
* *
4775332 AGACAAAAGGAAATTAATGTTAGTAGAAATA
1 AGACAAAAAGAAATCAATGTTAGTAGAAATA
*
4775363 AGACAAAAAG-AATCAA-GTTAGTTGAAATA
1 AGACAAAAAGAAATCAATGTTAGTAGAAATA
4775392 A
1 A
4775393 TTAGTCCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
30 5 0.19
31 9 0.33
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (31 bp):
AGACAAAAAGAAATCAATGTTAGTAGAAATA
Found at i:4777518 original size:2 final size:2
Alignment explanation
Indices: 4777511--4777543 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4777501 AGACACTTGC
4777511 TA TA TA TA TA TA -A 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
4777544 ATTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4777553 original size:21 final size:21
Alignment explanation
Indices: 4777511--4777557 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4777501 AGACACTTGC
*
4777511 TATATATATATAATATATATA
1 TATATATATATAATATAAATA
*
4777532 TATATATATATAATTTAAATA
1 TATATATATATAATATAAATA
4777553 T-TATA
1 TATATA
4777558 GCATACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATATATATAATATAAATA
Found at i:4781842 original size:158 final size:158
Alignment explanation
Indices: 4781554--4781871 Score: 627
Period size: 158 Copynumber: 2.0 Consensus size: 158
4781544 TTGTAAAGTG
4781554 AATTGTGTAAGTAACCCTTTTTGTTCTTTTCTTTCTATTTCTAAGCCACCCTTTCAATTATATTT
1 AATTGTGTAAGTAACCCTTTTTGTTCTTTTCTTTCTATTTCTAAGCCACCCTTTCAATTATATTT
4781619 TGCTTTCCTTCCTACTAACCCTTTTGCAGCCGACGCCAAACAAGTAAAATTTACTTGATATAGTC
66 TGCTTTCCTTCCTACTAACCCTTTTGCAGCCGACGCCAAACAAGTAAAATTTACTTGATATAGTC
*
4781684 TTGAGTAAAGTTCTCTATAACTTAAGAC
131 TTGAGTAAAGTTCTCTAGAACTTAAGAC
4781712 AATTGTGTAAGTAACCCTTTTTGTTCTTTTCTTTCTATTTCTAAGCCACCCTTTCAATTATATTT
1 AATTGTGTAAGTAACCCTTTTTGTTCTTTTCTTTCTATTTCTAAGCCACCCTTTCAATTATATTT
4781777 TGCTTTCCTTCCTACTAACCCTTTTGCAGCCGACGCCAAACAAGTAAAATTTACTTGATATAGTC
66 TGCTTTCCTTCCTACTAACCCTTTTGCAGCCGACGCCAAACAAGTAAAATTTACTTGATATAGTC
4781842 TTGAGTAAAGTTCTCTAGAACTTAAGAC
131 TTGAGTAAAGTTCTCTAGAACTTAAGAC
4781870 AA
1 AA
4781872 GAGAATCGAT
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (158 bp):
AATTGTGTAAGTAACCCTTTTTGTTCTTTTCTTTCTATTTCTAAGCCACCCTTTCAATTATATTT
TGCTTTCCTTCCTACTAACCCTTTTGCAGCCGACGCCAAACAAGTAAAATTTACTTGATATAGTC
TTGAGTAAAGTTCTCTAGAACTTAAGAC
Found at i:4789612 original size:32 final size:33
Alignment explanation
Indices: 4789576--4789660 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 33
4789566 ATATATATAT
4789576 ATATATATAATATAGTTTTT-CATTTTGAAAAC
1 ATATATATAATATAGTTTTTACATTTTGAAAAC
*
4789608 ATATATATAATATATAGTTTTTGGAAATATTTTGAAAAC
1 ATATATAT-A-ATATAGTTTTT----ACATTTTGAAAAC
4789647 ATATATATAATATA
1 ATATATATAATATA
4789661 TAGTTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
32 8 0.18
33 1 0.02
34 11 0.24
37 5 0.11
38 1 0.02
39 19 0.42
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (33 bp):
ATATATATAATATAGTTTTTACATTTTGAAAAC
Found at i:4789684 original size:26 final size:27
Alignment explanation
Indices: 4789637--4789688 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
4789627 TTTGGAAATA
* *
4789637 TTTTGAAAACATATATATAATATATAG
1 TTTTAAAAAAATATATATAATATATAG
*
4789664 TTTTAAAAAAATATTTA-AATATATA
1 TTTTAAAAAAATATATATAATATATA
4789689 TTATATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (27 bp):
TTTTAAAAAAATATATATAATATATAG
Found at i:4789689 original size:37 final size:38
Alignment explanation
Indices: 4789597--4789679 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 38
4789587 ATAGTTTTTC
***
4789597 ATTTTGAAAACATATATATAATATATAGTTTTTGGAAAT
1 ATTTT-AAAACATATATATAATATATAGTTTTAAAAAAT
4789636 ATTTTGAAAACATATATATAATATATAGTTTTAAAAAAAT
1 ATTTT-AAAACATATATATAATATATAGTTTT-AAAAAAT
4789676 ATTT
1 ATTT
4789680 AAATATATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 32 0.80
40 8 0.20
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (38 bp):
ATTTTAAAACATATATATAATATATAGTTTTAAAAAAT
Found at i:4789695 original size:7 final size:7
Alignment explanation
Indices: 4789683--4789734 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
4789673 AATATTTAAA
4789683 TATATAT
1 TATATAT
4789690 TATATAT
1 TATATAT
4789697 TATA-A-
1 TATATAT
4789702 TACTATAT
1 TA-TATAT
*
4789710 TATTTAT
1 TATATAT
4789717 TATATATT
1 TATATA-T
4789725 TATATAT
1 TATATAT
4789732 TAT
1 TAT
4789735 TTTCAATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 25 0.64
8 9 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:4789722 original size:22 final size:19
Alignment explanation
Indices: 4789681--4789736 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 19
4789671 AAAATATTTA
*
4789681 AATATATATTATATATTAT
1 AATATATATTATTTATTAT
4789700 AATACTATATTATTTATTAT
1 AATA-TATATTATTTATTAT
4789720 ATATTTATATATTATTT
1 A-A--TATATATTATTT
4789737 TCAATTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 15 0.47
21 1 0.03
22 10 0.31
23 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATATATTATTTATTAT
Found at i:4792998 original size:3 final size:3
Alignment explanation
Indices: 4792990--4793025 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4792980 AATACATTGA
4792990 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4793026 TTAGAACTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4794092 original size:37 final size:36
Alignment explanation
Indices: 4794037--4794122 Score: 127
Period size: 37 Copynumber: 2.4 Consensus size: 36
4794027 AAAGGTTTAT
** *
4794037 TTTCAAGAGAAATTGTCTCAAGCGAGAAAAAAATTTG
1 TTTCAAGAGAAACCGTCTCAAGCGAG-AAAAAATTCG
*
4794074 TTTCAAGAGAAACCGTCTCAAGCGAGACAAAATTCG
1 TTTCAAGAGAAACCGTCTCAAGCGAGAAAAAATTCG
4794110 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
4794123 AATCTTAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 21 0.47
37 24 0.53
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (36 bp):
TTTCAAGAGAAACCGTCTCAAGCGAGAAAAAATTCG
Found at i:4794094 original size:66 final size:66
Alignment explanation
Indices: 4793572--4794086 Score: 771
Period size: 66 Copynumber: 7.8 Consensus size: 66
4793562 GATTAATTTT
* * ** *
4793572 TGTTTTAAGAGAAACTGTCTCAAACGAGACAAAATTTTGTTTGGAGACAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTT
4793637 TA
65 TA
* * * * * * *
4793639 TATTTCAAGAGAAATTATCTCAAGCAAGAAAAAAATTTGTTTCAAGAGAAACAATCTCAAAAGAT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAG-ACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
4793704 TA
65 TA
* * *
4793706 TGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAATTTATTTCATGAGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
4793771 A
66 A
* * *
4793772 TGTTGCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAATAGAAACAATTTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
4793837 A
66 A
* *
4793838 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTGTTTCAATAGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
4793903 A
66 A
* * *
4793904 TGTTTCAAGAGAAACTATCTTAAGCGAGACAAAATTTGTTTCAAGAGAAACAATTTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
4793969 A
66 A
4793970 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
4794035 A
66 A
* *
4794036 T-TTTCAAGAGAAATTGTCTCAAGCGAGAAAAAAATTTGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGCGAG-ACAAAATTTGTTTCAAGAGAAAC
4794087 CGTCTCAAGC
Statistics
Matches: 409, Mismatches: 37, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
65 25 0.06
66 305 0.75
67 74 0.18
68 5 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
A
Found at i:4794140 original size:66 final size:66
Alignment explanation
Indices: 4794070--4794235 Score: 224
Period size: 66 Copynumber: 2.5 Consensus size: 66
4794060 GAGAAAAAAA
* * * *
4794070 TTTGTTTCAAGAGAAACCGTCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAATCTTAAAGGT
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTCATTCCAAGAGAAACAATCTCAAAGGT
4794135 T
66 T
* * *
4794136 TTTGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGGGAAACAATCTCAAAGGT
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTCATTCCAAGAGAAACAATCTCAAAGGT
4794201 T
66 T
* * * * *
4794202 TATATATCCAGAGAAACTGTCTCAATCGAGACAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAA
4794236 CACTCATTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (66 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTCATTCCAAGAGAAACAATCTCAAAGGT
T
Found at i:4794197 original size:168 final size:169
Alignment explanation
Indices: 4793904--4794232 Score: 518
Period size: 168 Copynumber: 2.0 Consensus size: 169
4793894 CAAAGGTTTA
* * *
4793904 TGTTTCAAGAGAAACTATCTTAAGCGAGACAAAATTTGTTTCAAGAGAAACAATTTCAAAGGTTT
1 TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAATTTCAAAGGTTT
* * *
4793969 ATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
66 ATGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGTT
* *
4794034 TAT-TTTCAAGAGAAATTGTCTCAAGCGAGAAAAAAATT
131 TATATATCAAGAGAAACTGTCTCAAGCGAGAAAAAAATT
*
4794072 TGTTTCAAGAGAAACCGTCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAATCTT-AAAGGTT
1 TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAAT-TTCAAAGGTT
* *
4794136 TTTGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGGGAAACAATCTCAAAGGT
65 TATGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGT
* *
4794201 TTATATATCCAGAGAAACTGTCTCAATCGAGA
130 TTATATATCAAGAGAAACTGTCTCAAGCGAGA
4794233 CAACACTCAT
Statistics
Matches: 146, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
168 121 0.83
169 25 0.17
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (169 bp):
TGTTTCAAGAGAAACCATCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAATTTCAAAGGTTT
ATGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGTT
TATATATCAAGAGAAACTGTCTCAAGCGAGAAAAAAATT
Found at i:4794263 original size:168 final size:165
Alignment explanation
Indices: 4793904--4794296 Score: 490
Period size: 168 Copynumber: 2.3 Consensus size: 165
4793894 CAAAGGTTTA
*
4793904 TGTTTCAAGAGAAACTATCTTAAGCGAGACAAAATTTGTTTCAAGAGAAACAATTTCAAAGGTTT
1 TGTTT-AAGAGAAACTATCTCAAGCGAGACAAAA-TTGTTTCAAGAGAAACAATTT-AAAGGTTT
* * *
4793969 ATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
63 ATGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGTT
* *
4794034 TATTTTCAAGAGAAATTGTCTCAAGCGAGAAAAAAATT
128 TATTATCAAGAGAAACTGTCTCAAGCGAGAAAAAAATT
**
4794072 TGTTTCAAGAGAAACCGTCTCAAGCGAGACAAAATTCGTTTCAAGAGAAACAATCTTAAAGGTTT
1 TGTTT-AAGAGAAACTATCTCAAGCGAGACAAAATT-GTTTCAAGAGAAACAAT-TTAAAGGTTT
* *
4794137 TTGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGGGAAACAATCTCAAAGGTT
63 ATGTTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGTT
* * * * *
4794202 TATATATCCAGAGAAACTGTCTCAATCGAGACAACACTCAT
128 TAT-TATCAAGAGAAACTGTCTCAAGCGAGAAAAAAAT--T
* * *
4794243 T-TTT-AG-GAAGACTATCTCAAGTGAGATCAATATT-TTT-AAGGGAAACAATTTAAA
1 TGTTTAAGAGAA-ACTATCTCAAGCGAGA-CAAAATTGTTTCAAGAGAAACAATTTAAA
4794297 AAATTGTATT
Statistics
Matches: 198, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
165 5 0.03
166 11 0.06
167 8 0.04
168 134 0.68
169 35 0.18
170 3 0.02
171 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (165 bp):
TGTTTAAGAGAAACTATCTCAAGCGAGACAAAATTGTTTCAAGAGAAACAATTTAAAGGTTTATG
TTTCAAGAGAAACTGTCTAAAGCGAGACAAAATTTATTCCAAGAGAAACAATCTCAAAGGTTTAT
TATCAAGAGAAACTGTCTCAAGCGAGAAAAAAATT
Found at i:4806170 original size:14 final size:14
Alignment explanation
Indices: 4806151--4806178 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4806141 GAATGAAGCC
4806151 TCCTTTATATAGGA
1 TCCTTTATATAGGA
4806165 TCCTTTATATAGGA
1 TCCTTTATATAGGA
4806179 GCTAAGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TCCTTTATATAGGA
Found at i:4816226 original size:21 final size:22
Alignment explanation
Indices: 4816182--4816226 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
4816172 CAAGTGTGGA
* *
4816182 AATTCAACAATGGGAACATTTG
1 AATTCAACAATAGGAACATATG
*
4816204 AATTCAACAA-AGGCACATATG
1 AATTCAACAATAGGAACATATG
4816225 AA
1 AA
4816227 ATTGTTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (22 bp):
AATTCAACAATAGGAACATATG
Found at i:4816229 original size:22 final size:23
Alignment explanation
Indices: 4816180--4816229 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
4816170 CACAAGTGTG
* *
4816180 GAAATTCAACAATGGGAACATTT
1 GAAATTCAACAATAGGAACATAT
*
4816203 G-AATTCAACAA-AGGCACATAT
1 GAAATTCAACAATAGGAACATAT
4816224 GAAATT
1 GAAATT
4816230 GTTTGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.35
22 14 0.61
23 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (23 bp):
GAAATTCAACAATAGGAACATAT
Found at i:4822685 original size:17 final size:17
Alignment explanation
Indices: 4822653--4822684 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4822643 AAATTGGAGT
4822653 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
4822670 ACAAAAAG-AAGAAAA
1 ACAAAAAGAAAGAAAA
4822685 AATTCCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:4845975 original size:24 final size:24
Alignment explanation
Indices: 4845947--4846027 Score: 153
Period size: 24 Copynumber: 3.3 Consensus size: 24
4845937 ATACATAATC
4845947 ATGCTATAATATAGTTATATTCAT
1 ATGCTATAATATAGTTATATTCAT
4845971 ATGCTATAATATAGTTATATTCAT
1 ATGCTATAATATAGTTATATTCAT
4845995 ATGCTATAATATAGTTATATTCAT
1 ATGCTATAATATAGTTATATTCAT
4846019 ATGCATATA
1 ATGC-TATA
4846028 TTACATCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 52 0.93
25 4 0.07
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (24 bp):
ATGCTATAATATAGTTATATTCAT
Found at i:4853829 original size:24 final size:24
Alignment explanation
Indices: 4853802--4853847 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4853792 GGTATGCTTG
* *
4853802 AAATGTTTATCTTTATGTTATTCC
1 AAATGCTTAGCTTTATGTTATTCC
*
4853826 AAATGCTTAGCTTTGTGTTATT
1 AAATGCTTAGCTTTATGTTATT
4853848 TTGGAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (24 bp):
AAATGCTTAGCTTTATGTTATTCC
Found at i:4858564 original size:90 final size:88
Alignment explanation
Indices: 4858448--4858623 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 88
4858438 TAATCCCGAA
* * *
4858448 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAGTATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAA-CCCTAATATGAT
4858513 TAGGATAACTTGGATATAAAAGGAT
64 TAGGATAACTTGGATATAAAAGGAT
4858538 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAACCCTAATATGATTA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAACCCTAATATGATTA
* *
4858603 GGGTAACTTGGCTATAAAAGG
66 GGATAACTTGGATATAAAAGG
4858624 GTGTGGTAGG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 32 0.40
89 3 0.04
90 46 0.57
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (88 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAACCCTAATATGATTA
GGATAACTTGGATATAAAAGGAT
Found at i:4869538 original size:22 final size:22
Alignment explanation
Indices: 4869513--4869554 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4869503 CCATTTCAAC
*
4869513 ATCAACACCATTAACATCTTCT
1 ATCAACACCATCAACATCTTCT
**
4869535 ATCAAGGCCATCAACATCTT
1 ATCAACACCATCAACATCTT
4869555 TATAATTCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.29
Consensus pattern (22 bp):
ATCAACACCATCAACATCTTCT
Found at i:4882530 original size:19 final size:18
Alignment explanation
Indices: 4882497--4882537 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4882487 TTTTAAATAC
*
4882497 TTATATATTGTATTTGTA
1 TTATATATTGTATTTATA
*
4882515 TTATATTTTGGTATTTATA
1 TTATATATT-GTATTTATA
4882534 TTAT
1 TTAT
4882538 GTCTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (18 bp):
TTATATATTGTATTTATA
Found at i:4888501 original size:17 final size:17
Alignment explanation
Indices: 4888479--4888529 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
4888469 AAGATAAGGT
4888479 AATGAAATAAGAAA-AAA
1 AATGAAATAA-AAAGAAA
* *
4888496 AATGAAAGAAAAAGGAA
1 AATGAAATAAAAAGAAA
*
4888513 AATGAAATAATAAGAAA
1 AATGAAATAAAAAGAAA
4888530 GTGAAGATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.12
Consensus pattern (17 bp):
AATGAAATAAAAAGAAA
Found at i:4888748 original size:18 final size:18
Alignment explanation
Indices: 4888721--4888759 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
4888711 GATGTAGGAG
4888721 TCTTTTC-T-TTTCTTTT
1 TCTTTTCTTCTTTCTTTT
4888737 T-TTTTCTTCTTTCTTTT
1 TCTTTTCTTCTTTCTTTT
4888754 TCTTTT
1 TCTTTT
4888760 TTGTTGCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.25
16 2 0.10
17 9 0.45
18 4 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TCTTTTCTTCTTTCTTTT
Found at i:4889130 original size:12 final size:14
Alignment explanation
Indices: 4889113--4889180 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 14
4889103 TGATGGTTCA
4889113 ATGGTGAT-GAA-G
1 ATGGTGATGGAATG
4889125 ATGGTGATGGAATG
1 ATGGTGATGGAATG
* *
4889139 ATGGTTAAGTTGGCATG
1 ATGG-T--GATGGAATG
* *
4889156 AAGGTGATGGACT-
1 ATGGTGATGGAATG
4889169 ATGGTGATGGAA
1 ATGGTGATGGAA
4889181 AGATAGTATC
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
12 8 0.19
13 13 0.30
14 10 0.23
15 1 0.02
16 1 0.02
17 10 0.23
ACGTcount: A:0.29, C:0.03, G:0.40, T:0.28
Consensus pattern (14 bp):
ATGGTGATGGAATG
Found at i:4889543 original size:19 final size:20
Alignment explanation
Indices: 4889505--4889547 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4889495 GAAACCCCTT
*
4889505 TGAAAACACATTATTTTTAA
1 TGAAAACACATTAATTTTAA
*
4889525 TGAAAATACA-TAATTTTAA
1 TGAAAACACATTAATTTTAA
4889544 TGAA
1 TGAA
4889548 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TGAAAACACATTAATTTTAA
Found at i:4892818 original size:17 final size:17
Alignment explanation
Indices: 4892798--4892850 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
4892788 TTTAGGGAAG
4892798 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
4892815 TAGTTCATTAATCAAAC
1 TAGTTCATTAATTAAAC
4892832 TAGTTCACTT-ATTAAAC
1 TAGTTCA-TTAATTAAAC
4892849 TA
1 TA
4892851 ACTCTTACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 31 0.94
18 2 0.06
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:4894059 original size:11 final size:11
Alignment explanation
Indices: 4894031--4894068 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4894021 TTAAAATTTT
4894031 GAAAAAAA-AA
1 GAAAAAAAGAA
4894041 -AAAAAAAGAA
1 GAAAAAAAGAA
4894051 GAAAAAAAGAA
1 GAAAAAAAGAA
4894062 GAGAAAA
1 GA-AAAA
4894069 GTGTAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 2 0.08
11 12 0.48
12 4 0.16
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAAAGAA
Found at i:4894227 original size:192 final size:194
Alignment explanation
Indices: 4893900--4894286 Score: 735
Period size: 192 Copynumber: 2.0 Consensus size: 194
4893890 TAACTTCCAT
4893900 TATCTTCCGTTCAAAGCAAGCAATTCAATCTCTTACTAGAATCATGATTGGGCAATCGTATCAAT
1 TATCTTCCGTTCAAAGCAAGCAATTCAATCTCTTACTAGAATCATGATTGGGCAATCGTATCAAT
*
4893965 TGGTATAAGAGCGATCTGATTCAATAAGCGTATCATTTTCTCGTACCTAGATTAGTTTAAAATTT
66 TGGTATAAGAGCGATCTGATTCAATAAGCGTATCATTTTCTCGTACCTAGATTAGTTAAAAATTT
4894030 TGAAAAAAAAAAAAAAAAGAAG-AAAAA-AAGAAGAGAAAAGTGTAAAG-AGGAGAAAGTAATTC
131 TGAAAAAAAAAAAAAAAAGAAGAAAAAAGAAGAAGA-AAAAGTGTAAAGAAGGAGAAAGTAATTC
4894092 TATCTTCCGTTCAAAGCAAGCAATTCAATCTCTTACTAGAATCATGATTGGGCAATCGTATCAAT
1 TATCTTCCGTTCAAAGCAAGCAATTCAATCTCTTACTAGAATCATGATTGGGCAATCGTATCAAT
4894157 TGGTATAAGAGCGATCTGATTCAATAAGCGTATCATTTTCTCGTACCTAGATTAGTTAAAAATTT
66 TGGTATAAGAGCGATCTGATTCAATAAGCGTATCATTTTCTCGTACCTAGATTAGTTAAAAATTT
4894222 TGAAAAAAAAAAAAAAAAGAAGAAAAAAGAAGAAGAAAAAGTGTAAAGAAGGAGAAAGTAATTC
131 TGAAAAAAAAAAAAAAAAGAAGAAAAAAGAAGAAGAAAAAGTGTAAAGAAGGAGAAAGTAATTC
4894286 T
1 T
4894287 TTTAATCTTT
Statistics
Matches: 191, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
192 151 0.79
193 17 0.09
194 23 0.12
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (194 bp):
TATCTTCCGTTCAAAGCAAGCAATTCAATCTCTTACTAGAATCATGATTGGGCAATCGTATCAAT
TGGTATAAGAGCGATCTGATTCAATAAGCGTATCATTTTCTCGTACCTAGATTAGTTAAAAATTT
TGAAAAAAAAAAAAAAAAGAAGAAAAAAGAAGAAGAAAAAGTGTAAAGAAGGAGAAAGTAATTC
Found at i:4894247 original size:13 final size:13
Alignment explanation
Indices: 4894231--4894261 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4894221 TTGAAAAAAA
4894231 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
*
4894244 AAAAAAGAAGAAG
1 AAAAAAAAAGAAG
4894257 AAAAA
1 AAAAA
4894262 GTGTAAAGAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:4899316 original size:17 final size:17
Alignment explanation
Indices: 4899296--4899344 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
4899286 GGGAAGTAGA
4899296 TCATTAATTAAACTAGT
1 TCATTAATTAAACTAGT
* *
4899313 TCATTCATCAAACTAGT
1 TCATTAATTAAACTAGT
*
4899330 TCATTTATTAAACTA
1 TCATTAATTAAACTA
4899345 ACTCTTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (17 bp):
TCATTAATTAAACTAGT
Found at i:4900211 original size:21 final size:21
Alignment explanation
Indices: 4900185--4900253 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
4900175 TTTTATTTTA
*
4900185 TCCATCTACTTCCTCTTCGAT
1 TCCATCTACTTCCACTTCGAT
4900206 TCCATCTACTTCCACTTCGAT
1 TCCATCTACTTCCACTTCGAT
*
4900227 TCCATTTACTTCCACTTCGA-
1 TCCATCTACTTCCACTTCGAT
4900247 TCCATCT
1 TCCATCT
4900254 CTTTATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 6 0.13
21 39 0.87
ACGTcount: A:0.17, C:0.38, G:0.04, T:0.41
Consensus pattern (21 bp):
TCCATCTACTTCCACTTCGAT
Found at i:4908562 original size:17 final size:17
Alignment explanation
Indices: 4908540--4908582 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4908530 TGAATAAATT
* *
4908540 TAGTTCATTAATTAAAG
1 TAGTTCATTAATCAAAC
*
4908557 TAGTTCATTCATCAAAC
1 TAGTTCATTAATCAAAC
4908574 TAGTTCATT
1 TAGTTCATT
4908583 TAATAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Done.