Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009589.1 Hibiscus syriacus cultivar Beakdansim tig00116968_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: 660543
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:568043 original size:14 final size:14
Alignment explanation
Indices: 567991--568047 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
567981 GCGAAATGAA
*
567991 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
568005 AATCACAATGCGAAATG
1 AATCGCAA--CGAAA-G
568022 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
568038 AATCGCAACG
1 AATCGCAACG
568048 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:568062 original size:19 final size:19
Alignment explanation
Indices: 567935--568069 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
567925 TAGTTTACTT
* *
567935 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
567955 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
567974 GCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
567993 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
568007 TCACAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
568026 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
568040 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
568059 TCGCAATGCGA
1 TCGCAACGCGA
568070 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:568087 original size:19 final size:19
Alignment explanation
Indices: 568065--568212 Score: 136
Period size: 19 Copynumber: 8.3 Consensus size: 19
568055 AAAATCGCAA
568065 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
568084 TGCGA--TT-CTTT--CGT
1 TGCGATTTTGGTTTCGCGT
** *
568098 TGCGATTTTCATTTCGCAT
1 TGCGATTTTGGTTTCGCGT
*
568117 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
568131 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
568150 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
568169 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
568188 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
568208 TGCGA
1 TGCGA
568213 AAGTAAACTA
Statistics
Matches: 106, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
14 18 0.17
16 6 0.06
17 6 0.06
19 63 0.59
20 13 0.12
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:568100 original size:14 final size:14
Alignment explanation
Indices: 568081--568137 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
568071 TTTGGTTTCG
568081 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
568095 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
568112 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
568128 CGTTGCGATT
1 CGTTGCGATT
568138 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:568113 original size:33 final size:33
Alignment explanation
Indices: 568065--568194 Score: 152
Period size: 33 Copynumber: 3.8 Consensus size: 33
568055 AAAATCGCAA
**
568065 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
* *
568098 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
*
568131 TGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGTTGCGA--TT-CTTT--CGT
**
568169 TGCGATTTTGGTTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
568195 TTAAGTTTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
33 52 0.63
35 2 0.02
36 4 0.05
38 25 0.30
ACGTcount: A:0.08, C:0.18, G:0.26, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
Found at i:568376 original size:93 final size:93
Alignment explanation
Indices: 568260--568728 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
568250 ATGGATTGCA
*
568260 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
568324 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
568352 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
568417 TAGCAGAATTGACAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
568445 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
568510 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
568538 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
568603 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
568631 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
568696 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
568724 TTACT
1 TTACT
568729 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 368 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:570473 original size:19 final size:20
Alignment explanation
Indices: 570429--570490 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
570419 TTTTGGTTGA
*
570429 AATGAAAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
** *
570449 AATGACTGTCGCAACGCGA-
1 AATGACAATCGCAACGAGAG
570468 AATGACAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
570488 AAT
1 AAT
570491 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAG
Found at i:570493 original size:14 final size:14
Alignment explanation
Indices: 570474--570530 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
570464 GCGAAATGAC
570474 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
570488 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
570507 AATCGCAACGAGAG
1 AATCGCAACGAGAG
570521 AATCGCAACG
1 AATCGCAACG
570531 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:570499 original size:33 final size:33
Alignment explanation
Indices: 570427--570547 Score: 170
Period size: 33 Copynumber: 3.5 Consensus size: 33
570417 TCTTTTGGTT
570427 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
*
570466 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
570499 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
570532 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
570548 TGACAGTCAT
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
33 56 0.71
36 1 0.01
38 1 0.01
39 21 0.27
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:570512 original size:19 final size:19
Alignment explanation
Indices: 570427--570547 Score: 91
Period size: 19 Copynumber: 6.8 Consensus size: 19
570417 TCTTTTGGTT
*
570427 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
***
570446 GAGAATGACTGTCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
570466 GAAATGACAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
570483 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
570499 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
570516 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
570532 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
570548 TGACAGTCAT
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 33 0.41
20 15 0.19
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:570709 original size:31 final size:32
Alignment explanation
Indices: 570671--570739 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
570661 AATACTAACT
570671 TGAAAATCGCAAC-GAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAGAGAATAGCAACGCGAAA
* *
570702 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAAC-AGAGAATAGCAACGCGAAA
570735 TGAAA
1 TGAAA
570740 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 13 0.38
33 21 0.62
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (32 bp):
TGAAAATCGCAACAGAGAATAGCAACGCGAAA
Found at i:570973 original size:22 final size:22
Alignment explanation
Indices: 570921--570975 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
570911 TGGTTGTGAG
**
570921 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
570943 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
570965 GGATTTCTTCG
1 GGATTTCTTCG
570976 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:571147 original size:20 final size:20
Alignment explanation
Indices: 571122--571315 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
571112 CTTTAAATAT
571122 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
571142 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
571164 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
571183 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
571203 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
571223 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
571243 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
571263 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
571283 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
571303 CGCGTTGCGATTT
1 CGCGTTGCGATTT
571316 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:571287 original size:60 final size:60
Alignment explanation
Indices: 571124--571295 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
571114 TTAAATATCG
* ** *
571124 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
571185 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
571245 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
571296 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:571309 original size:60 final size:60
Alignment explanation
Indices: 571121--571436 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
571111 GCTTTAAATA
* ** * *
571121 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
571182 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
571242 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
571302 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
571364 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
571423 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
571437 TGTTGGTCAT
Statistics
Matches: 208, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 78 0.38
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:571332 original size:21 final size:20
Alignment explanation
Indices: 571282--571379 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
571272 ATTTATGTGT
* * * *
571282 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
571302 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
571323 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
571343 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
571364 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
571380 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:571355 original size:61 final size:60
Alignment explanation
Indices: 571282--571438 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
571272 ATTTATGTGT
*
571282 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
571343 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
571404 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
571439 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:571374 original size:41 final size:41
Alignment explanation
Indices: 571282--571438 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
571272 ATTTATGTGT
* * *
571282 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
571323 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
571364 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
571404 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
571439 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:580250 original size:60 final size:60
Alignment explanation
Indices: 580123--580237 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
580113 ACAATCAAAT
* ** *
580123 GACCATTTTGTAACTTTTAATAATCAAAGAACTCAACGAAGTAATATCCTATAGTCGGAA
1 GACCATTTTGTAACTTTTAATAATCAAAGAACTCAACAAAACAACATCCTATAGTCGGAA
* *
580183 GACCATTTTGTAACTTTTAATAATCAAAGAACTTAATAAAACAACATCCTATAGT
1 GACCATTTTGTAACTTTTAATAATCAAAGAACTCAACAAAACAACATCCTATAGT
580238 TGAGGGACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATCAAAGAACTCAACAAAACAACATCCTATAGTCGGAA
Found at i:580608 original size:2 final size:2
Alignment explanation
Indices: 580601--580642 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
580591 GCAAAGAAAT
580601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
580643 ACCAGTGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:591663 original size:3 final size:3
Alignment explanation
Indices: 591649--591700 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
591639 ATGTAAAATG
* **
591649 TAA TAT TAA TAA TAA -AA TAA CGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
591696 -AA TAA
1 TAA TAA
591701 CGGGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:592080 original size:40 final size:40
Alignment explanation
Indices: 592026--592137 Score: 199
Period size: 40 Copynumber: 2.8 Consensus size: 40
592016 TTATCTAGGG
*
592026 TGACACGGCTCATACGTGATGAAGAGATCTGGT-CGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCCGGGG-A
592066 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCCGGGGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCCGGGGA
592106 TGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCATACGTGATGAAGAGTTCTGG
592138 CCATCTAAAG
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 65 0.93
41 5 0.07
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGTCCGGGGA
Found at i:592545 original size:66 final size:63
Alignment explanation
Indices: 592373--592551 Score: 171
Period size: 66 Copynumber: 2.8 Consensus size: 63
592363 CCAAAGCAAC
* * * * *
592373 TGTCTCGAAAGAGACAAGATTCGTTTCAAAGGAAAC-AACCCAAAGATGGCATTTAAAGGGAAT
1 TGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAAT
* * ** * * * * *
592436 TGTCTTAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGCGTTTCATGGGAA
1 TGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGCATTTAAAGGG-A
592501 AT
62 AT
592503 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
592552 TTTGTTTTGT
Statistics
Matches: 91, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
62 2 0.02
63 13 0.14
64 13 0.14
65 9 0.10
66 35 0.38
67 19 0.21
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (63 bp):
TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAAT
Found at i:592701 original size:1 final size:1
Alignment explanation
Indices: 592695--592721 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
592685 AAAGTTTCAA
592695 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
592722 GAAAAGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:593035 original size:39 final size:40
Alignment explanation
Indices: 592992--593070 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
592982 GTTTTAATAG
592992 AAACGATATCAAAGGT-GGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
*
593031 AAACGATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
593071 CGAGAGACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (40 bp):
AAACGATATCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
Found at i:593339 original size:27 final size:29
Alignment explanation
Indices: 593277--593340 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
593267 ATTTGTTTTT
* *
593277 AAAGAAATAAACTCAAAGATGATTTTGTTA
1 AAAGAAACAAACTCAAAGAT-ATTTTGTCA
* *
593307 AGAGAAACAGACTCAAAGAT-TTTT-TCA
1 AAAGAAACAAACTCAAAGATATTTTGTCA
593334 AAAGAAA
1 AAAGAAA
593341 TTGTCTCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 8 0.28
28 4 0.14
30 17 0.59
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (29 bp):
AAAGAAACAAACTCAAAGATATTTTGTCA
Found at i:593531 original size:36 final size:36
Alignment explanation
Indices: 593491--593563 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
593481 AAGAGACAAA
*
593491 ATTTTGTTATCAA-AGAAACATACTCAAAGATTTTTC
1 ATTTTGTT-TCAAGAGAAACAGACTCAAAGATTTTTC
* *
593527 ATTTTGTTTTAAGTGAAACAGACTCAAAGATTTTTC
1 ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTC
593563 A
1 A
593564 ATAAAATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (36 bp):
ATTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTC
Found at i:593600 original size:37 final size:36
Alignment explanation
Indices: 593574--593644 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
593564 ATAAAATATG
*
593574 TATC-AAGAGAGACAAAGTTTTGTTTCAAAAGAAAT
1 TATCTAAGAGAGACAAAATTTTGTTTCAAAAGAAAT
* *
593609 TATCTTAAGAGAGATAAAATTTTGTTTCCAAAGAAA
1 TATC-TAAGAGAGACAAAATTTTGTTTCAAAAGAAA
593645 CAGACTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 4 0.13
37 27 0.87
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (36 bp):
TATCTAAGAGAGACAAAATTTTGTTTCAAAAGAAAT
Found at i:593691 original size:30 final size:30
Alignment explanation
Indices: 593628--593690 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
593618 AGAGATAAAA
*
593628 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
593658 TTTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
593687 TTTT
1 TTTT
593691 TTACGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:593735 original size:53 final size:53
Alignment explanation
Indices: 593677--593781 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
593667 AAAAGAAACA
*
593677 ACTCAAAGATTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
1 ACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
593730 ACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
593782 AAATAAATAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:593902 original size:27 final size:27
Alignment explanation
Indices: 593792--594059 Score: 405
Period size: 27 Copynumber: 9.8 Consensus size: 27
593782 AAATAAATAG
*
593792 ACTCAAAGATTTTTTTTCAAAAGAAAC-A
1 ACTCAAAGA--TTTTTTCAAAAGGAACAA
593820 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
593849 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
**
593878 ACTCAAAGATTTTTTCAAGTGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
*
593905 ACTCAAAGATTTTTTCAAAAGAAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
* *
593932 ACTCAAAGA-TTTTTCAAAAGAAATAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
593958 ACTCAAAGATTTTTTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
593985 ACTCAAAGATTTTTTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
594012 ACTCAAAGATTTTTTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
594039 ACTCAAAGATTTTTTCAAAAG
1 ACTCAAAGATTTTTTCAAAAG
594060 AAATTGTCTT
Statistics
Matches: 226, Mismatches: 11, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
26 25 0.11
27 140 0.62
28 24 0.11
29 37 0.16
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:593993 original size:107 final size:110
Alignment explanation
Indices: 593792--594063 Score: 426
Period size: 107 Copynumber: 2.5 Consensus size: 110
593782 AAATAAATAG
* * *
593792 ACTCAAAGATTTTTTTTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAACAAACTCCAA
1 ACTCAAAGA--TTTTTTCAAAAGAAACAAACTCAAAGA-TTTT-TTCAAAAGAAATAAACTCAAA
**
593856 GATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGTGGAACAA
62 GATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
593905 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGA-TTTTTCAAAAGAAATAAACTCAAAGA-T
1 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAATAAACTCAAAGATT
593968 TTT-TTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
66 TTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
*
594012 ACTCAAAGATTTTTTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGAAAT
1 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAAT
594064 TGTCTTTAAA
Statistics
Matches: 151, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
107 74 0.49
108 19 0.13
109 20 0.13
110 3 0.02
111 16 0.11
112 10 0.07
113 9 0.06
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (110 bp):
ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAATAAACTCAAAGATT
TTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:594412 original size:36 final size:36
Alignment explanation
Indices: 594301--594419 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
594291 AGAAAATGAT
* * * * *
594301 GTCTCAAGCTAGACGAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
594335 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
594371 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
594406 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
594420 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 18 0.26
35 7 0.10
36 44 0.64
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:594566 original size:105 final size:105
Alignment explanation
Indices: 594414--594610 Score: 279
Period size: 105 Copynumber: 1.9 Consensus size: 105
594404 ACGATCTCAA
* * *
594414 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCA
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATCTGGATCTCAAAGGAAAAAGGTCTCA
594479 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
66 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
* * * * * *
594519 GTGAGATTAATTTTGTTTTAA-GTGAATCGAATTCAAAATCTGTATCTCAAAGGAAAAATGTCTC
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAAATCTGGATCTCAAAGGAAAAAGGTCTC
* *
594583 AAGCGAGACGAAGTTTGTTTTAAGAGAA
65 AAGCGAGACGAAATTTGTTTTAAAAGAA
594611 TTTGTCTCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 75 0.94
106 5 0.06
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATCTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
Found at i:594626 original size:36 final size:36
Alignment explanation
Indices: 594577--594713 Score: 152
Period size: 36 Copynumber: 3.8 Consensus size: 36
594567 AAAGGAAAAA
* * * *
594577 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAACGAGACAAAATTTGTTTTAAGAGAAAT
* **
594613 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAACGAGACAAAATTTGTTTTAAGAGAAAT
* * *
594648 TGTTTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAACGAGACAAAATTTG-TTTTAAGAGAAAT
594684 TGTCTCAAACGAGACAAAAATTTGTTTTAA
1 TGTCTCAAACGAGAC-AAAATTTGTTTTAA
594714 AATTCTCAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
35 24 0.29
36 51 0.61
37 8 0.10
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (36 bp):
TGTCTCAAACGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:596293 original size:12 final size:12
Alignment explanation
Indices: 596266--596313 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
596256 CTTTGTCCTC
596266 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
596278 TTTTTTCTTTGA
1 TTTTTTCTTTGA
* *
596290 TTTTTGCTTTTA
1 TTTTTTCTTTGA
596302 TTTTTTTCTTTG
1 -TTTTTTCTTTG
596314 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 14 0.47
13 9 0.30
ACGTcount: A:0.04, C:0.08, G:0.10, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:596306 original size:25 final size:23
Alignment explanation
Indices: 596267--596329 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
596257 TTTGTCCTCT
*
596267 TTTGTTCTTTGTTTTTTCTTTGATT
1 TTTGTT-TTT-TTTTTTCTTTGATC
*
596292 TTTGCTTTTATTTTTTTCTTTGCTC
1 TTTG-TTTT-TTTTTTTCTTTGATC
596317 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
596330 CTTTGGTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 22 0.65
26 3 0.09
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.78
Consensus pattern (23 bp):
TTTGTTTTTTTTTTTCTTTGATC
Found at i:596313 original size:18 final size:19
Alignment explanation
Indices: 596292--596327 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
596282 TTCTTTGATT
596292 TTTGCT-TTTATTTTTTTC
1 TTTGCTCTTTATTTTTTTC
*
596310 TTTGCTCTTTGTTTTTTT
1 TTTGCTCTTTATTTTTTT
596328 TTCTTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTGCTCTTTATTTTTTTC
Found at i:598419 original size:31 final size:32
Alignment explanation
Indices: 598359--598420 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
598349 TGACAAAATG
598359 ACACAAACAAAAGAGAAGAAAGAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAAGAAGTTAGTAT
*
598391 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAAGAAGTTAGTA
598421 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAAGAAGTTAGTAT
Found at i:599979 original size:22 final size:22
Alignment explanation
Indices: 599936--599979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
599926 AAATTTACAT
*
599936 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
599958 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
599980 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:601997 original size:13 final size:13
Alignment explanation
Indices: 601958--601997 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
601948 ATCTTCTGTT
601958 TTTTTTTATGTTTTC
1 TTTTTTT-T-TTTTC
*
601973 TTTTCTTTTTTTC
1 TTTTTTTTTTTTC
601986 TTTTTTTTTTTT
1 TTTTTTTTTTTT
601998 TTGAACCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 16 0.70
14 1 0.04
15 6 0.26
ACGTcount: A:0.03, C:0.07, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:602558 original size:3 final size:3
Alignment explanation
Indices: 602544--602595 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
602534 ATGTAAAATG
* **
602544 TAA TAT TAA TAA TAA -AA TAA CGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
602591 -AA TAA
1 TAA TAA
602596 CGGGAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:604247 original size:35 final size:34
Alignment explanation
Indices: 604188--604299 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
604178 AAAACATTCC
* * *
604188 TCAATTTCATTATAAATCCCAAATTTTAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTCTAAAATAAT
*
604223 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCTAAAATAAT
* *
604258 TCAATTACATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCTAAAATAAT
604293 TCAATTT
1 TCAATTT
604300 AAGGAGAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.04
35 61 0.91
36 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCTAAAATAAT
Found at i:605384 original size:36 final size:34
Alignment explanation
Indices: 605317--605430 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 34
605307 AAAAAAGACA
* *
605317 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
605352 GTAATTGAATTATTTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTA-TTTTGGAATTT-GGGTTTAGAAT
*
605388 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
605423 GAAATTGA
1 GAAATTGA
605431 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 1 0.01
35 38 0.54
36 29 0.41
37 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.23, T:0.43
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:623920 original size:13 final size:14
Alignment explanation
Indices: 623895--623969 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 14
623885 CCTCTTTTTT
623895 TTATTTATATTATA
1 TTATTTATATTATA
623909 TTATTT-TATTATA
1 TTATTTATATTATA
*
623922 -TATCTTATATCATTA
1 TTAT-TTATATTA-TA
*
623937 TATATATATATATATA
1 T-TATTTATAT-TATA
*
623953 TATATATATATATATA
1 T-TATTTATAT-TATA
623969 T
1 T
623970 GTATAGATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
12 3 0.06
13 9 0.17
14 10 0.19
15 2 0.04
16 24 0.46
17 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:623940 original size:2 final size:2
Alignment explanation
Indices: 623918--623974 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
623908 ATTATTTTAT
*
623918 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
*
623959 TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA
623975 GATGTATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:624028 original size:17 final size:17
Alignment explanation
Indices: 624006--624068 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
623996 TTACTATGTA
624006 TATATTTTTCTTAATAT
1 TATATTTTTCTTAATAT
**
624023 TATATTTTATACGTTTTTA-
1 TATATTTT-T-C-TTAATAT
624042 TATATATTTTCTTAATAT
1 TATAT-TTTTCTTAATAT
*
624060 TCTATTTTT
1 TATATTTTT
624069 GTTTTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 16 0.44
18 6 0.17
19 7 0.19
20 7 0.19
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (17 bp):
TATATTTTTCTTAATAT
Found at i:624082 original size:32 final size:36
Alignment explanation
Indices: 624004--624076 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
623994 ATTTACTATG
624004 TATATAT-TTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
624040 TATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATTTTCTTAATATTATATTTTATAGTTTT
624074 TAT
1 TAT
624077 TTATTTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 8 0.23
36 8 0.23
37 19 0.54
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:624097 original size:31 final size:29
Alignment explanation
Indices: 624056--624113 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
624046 TATTTTCTTA
* *
624056 ATATTCTATTTTTGTTTTTATTTATTTATAT
1 ATATTATATTTTT-ATTTTATTT-TTTATAT
624087 ATATTATATTTTTATTTTATTTTTTAT
1 ATATTATATTTTTATTTTATTTTTTAT
624114 TTTATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 8 0.32
31 12 0.48
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (29 bp):
ATATTATATTTTTATTTTATTTTTTATAT
Found at i:624108 original size:42 final size:42
Alignment explanation
Indices: 624038--624188 Score: 123
Period size: 42 Copynumber: 3.6 Consensus size: 42
624028 TTTATACGTT
* * ** *
624038 TTTATATATATTTTCTTAATATTCTATTTTTGTTTTTATTTA
1 TTTATATATATTATATTTTTATTTTATTTTTGTTTTTATTTA
*
624080 TTTATATATATTATATTTTTATTTTATTTTT-TATTTTATTTC
1 TTTATATATATTATATTTTTATTTTATTTTTGT-TTTTATTTA
* * * *
624122 TTAATATCATA-TGTATCTTTATTTT-TTCTTTG-TTTTACTTA
1 TTTATAT-ATATTATATTTTTATTTTATT-TTTGTTTTTATTTA
624163 GTATTATATAT-TTATTATTTTTATTT
1 -T-TTATATATATTA-TATTTTTATTT
624189 GTTTTAGTAA
Statistics
Matches: 87, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
41 10 0.11
42 59 0.68
43 18 0.21
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.69
Consensus pattern (42 bp):
TTTATATATATTATATTTTTATTTTATTTTTGTTTTTATTTA
Found at i:627646 original size:69 final size:69
Alignment explanation
Indices: 627527--627664 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
627517 GATTTAAACT
627527 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
627592 TCAA
66 TCAA
* * * * *
627596 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGTATCAC-TCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTC-ACTCGAAGATCATAGAGC
627660 ATCAA
65 ATCAA
627665 GAGAGAAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:628664 original size:32 final size:32
Alignment explanation
Indices: 628597--628709 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
628587 TGAGGGCATC
** *
628597 TTTGAAGATTCAACATCAAATGTTGGGACATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGTAGTT
* *
628630 TTTTAGATTTAACATCAAATGTTGGGGTAGTT
1 TTTGAGATTCAACATCAAATGTTGGGGTAGTT
* * * *
628662 TTTGATATTCAACATCGAATATTGGGGTA-TC
1 TTTGAGATTCAACATCAAATGTTGGGGTAGTT
*
628693 TTTGGGAATTCAACATC
1 TTTGAG-ATTCAACATC
628710 CTGATGCAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 5 0.08
32 58 0.88
33 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGTAGTT
Found at i:629487 original size:106 final size:106
Alignment explanation
Indices: 629334--629557 Score: 277
Period size: 106 Copynumber: 2.1 Consensus size: 106
629324 CGTGCCACTT
** * *
629334 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAACTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAATTTCCCAATC
*
629399 TCAGAGCCAATTTCAACTTCACAGCGAACGATATTGGACTC
66 CCAGAGCCAATTTCAACTTCACAGCGAACGATATTGGACTC
* * * * * * *
629440 GAGACAGCACAAACTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTCCTAGTC
1 GAGACAACACAAACTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAATTTCCCAATC
* ** * *
629505 CCAGAGCCAATTTTAACTTCATGGCGGAGGATATTGGACTC
66 CCAGAGCCAATTTCAACTTCACAGCGAACGATATTGGACTC
* *
629546 GAAACAATACAA
1 GAGACAACACAA
629558 CTTACTTGGA
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (106 bp):
GAGACAACACAAACTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAATTTCCCAATC
CCAGAGCCAATTTCAACTTCACAGCGAACGATATTGGACTC
Found at i:629867 original size:36 final size:37
Alignment explanation
Indices: 629827--629912 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
629817 ATTGAAAACA
* * *
629827 TTTCCCTTGAAATG-AATTTTATCTCGATTGAGATAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
* *
629863 TTTCCCTTGAAACGAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
*
629900 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
629913 ATAAATATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
Found at i:629881 original size:102 final size:101
Alignment explanation
Indices: 629775--630144 Score: 569
Period size: 102 Copynumber: 3.6 Consensus size: 101
629765 TTTTGGAACT
629775 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
*
629840 GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAAC
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * *
629876 GAAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAA
1 -AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
* * *
629941 TAAATTTTATCTCGCTTGGGGTAGTTTCCCTTGAAAC
65 TGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* *
629978 AAATTTTTGTCTCCCTTAAGATATTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAA
1 AAA-TTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
* *
630043 TGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
65 TGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
* * * *
630080 AAAATTTTGTTTCCCTTGAGATAGTTTCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 -AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
630145 CACAAAATAT
Statistics
Matches: 241, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
101 3 0.01
102 235 0.98
103 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (101 bp):
AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
Found at i:630098 original size:37 final size:37
Alignment explanation
Indices: 630045--630117 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
630035 CTTTGAAATG
*
630045 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
* *
630082 AATTTTGTTTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
630118 TAAACCTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:630232 original size:37 final size:37
Alignment explanation
Indices: 630182--630284 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
630172 AAAACGAGTT
630182 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
630219 TTGAGACGGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
630255 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
630285 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:630301 original size:102 final size:102
Alignment explanation
Indices: 630195--630381 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
630185 AGACAGTTTC
* **
630195 CCTTGAAACAAAATCTT-GTCTCTCTTGAGACGGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTT
1 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAATTT-CCTTGAGAACTAAATTTTGTCTCTCTT
630257 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
63 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * *
630297 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAATTTTGTCTCTCTTGAG
**
630362 ACAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
630382 TTTTGTCCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 6 0.08
101 23 0.31
102 45 0.61
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (102 bp):
CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:630360 original size:37 final size:36
Alignment explanation
Indices: 630299--630415 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 36
630289 TATCTTTTCC
* * *
630299 TTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
630335 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
630372 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
630408 TTGAAACA
1 TTGAAACA
630416 CAAAAAAACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 1 0.01
36 39 0.55
37 30 0.42
38 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:630444 original size:34 final size:37
Alignment explanation
Indices: 630401--630486 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 37
630391 TCTTGAGACA
*
630401 GTTTCTCTTGAAACACA-A-AAAAACCC-TCGAAATT
1 GTTTCTCTTGAAACACACACAAAAACCCTTCGAAAAT
*
630435 GTTTCTCTTGAAACACACACACAAAAACCCTTTGAAAAT
1 GTTTCTCTTG-AA-ACACACACAAAAACCCTTCGAAAAT
630474 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
630487 TACCAAACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 10 0.22
35 2 0.04
36 5 0.11
37 2 0.04
38 10 0.22
39 16 0.36
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.29
Consensus pattern (37 bp):
GTTTCTCTTGAAACACACACAAAAACCCTTCGAAAAT
Found at i:630635 original size:84 final size:85
Alignment explanation
Indices: 630493--630654 Score: 227
Period size: 84 Copynumber: 1.9 Consensus size: 85
630483 GAAATACCAA
* * *
630493 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAA
**
630558 GGGTTATCTGTCACCAAAAG
66 GGACTATCTGTCACCAAAAG
** * * *
630578 ACCTTCGAGTTCGACTATGCTCAGC-TCTAATGCACATCATTTACAGCATAGCTCAAGGCAAGAA
1 ACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAA
630642 GGACTATCTGTCA
66 GGACTATCTGTCA
630655 ATAAAATTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 45 0.67
85 22 0.33
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
ACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAA
GGACTATCTGTCACCAAAAG
Found at i:631680 original size:14 final size:15
Alignment explanation
Indices: 631666--631736 Score: 96
Period size: 14 Copynumber: 5.0 Consensus size: 15
631656 CTTTTTTATT
*
631666 TATATTATAT-TATT
1 TATATTATATATATA
*
631680 TTTATTATATATATA
1 TATATTATATATATA
631695 TATA-TATATATATA
1 TATATTATATATATA
631709 TATA-TATATATATA
1 TATATTATATATATA
631723 TATA-TATATATATA
1 TATATTATATATATA
631737 ATTTTTCTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
14 47 0.89
15 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:631683 original size:20 final size:22
Alignment explanation
Indices: 631658--631736 Score: 80
Period size: 20 Copynumber: 3.9 Consensus size: 22
631648 ATATTCCTCT
631658 TTTTTATT-TATAT-TATATTA
1 TTTTTATTATATATATATATTA
631678 TTTTTATTATATATATATA-TA
1 TTTTTATTATATATATATATTA
* *
631699 TATATA-TATATATATATA-TA
1 TTTTTATTATATATATATATTA
* *
631719 TATATA-TATATATATATA
1 TTTTTATTATATATATATA
631737 ATTTTTCTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 40 0.73
21 11 0.20
22 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTATTATATATATATATTA
Found at i:631692 original size:2 final size:2
Alignment explanation
Indices: 631685--631736 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
631675 TTATTTTTAT
631685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
631727 TA TA TA TA TA
1 TA TA TA TA TA
631737 ATTTTTCTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:631872 original size:16 final size:17
Alignment explanation
Indices: 631848--631890 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
631838 TATATATATA
*
631848 TATTATATTTTTACT-T
1 TATTTTATTTTTACTAT
*
631864 TATTTTATTTTTTCTAT
1 TATTTTATTTTTACTAT
631881 TATTTT-TTTT
1 TATTTTATTTT
631891 CTTAATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTTTATTTTTACTAT
Found at i:632114 original size:11 final size:11
Alignment explanation
Indices: 632098--632123 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
632088 ATTTTGTTTA
632098 TTTTTATTATT
1 TTTTTATTATT
632109 TTTTTATTATT
1 TTTTTATTATT
632120 TTTT
1 TTTT
632124 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:632121 original size:19 final size:20
Alignment explanation
Indices: 632079--632121 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
632069 ATTTTTTAAC
632079 ATTTTATTCATTTTGTTTAT
1 ATTTTATTCATTTTGTTTAT
632099 -TTTTATT-ATTTT-TTTATT
1 ATTTTATTCATTTTGTTTA-T
632117 ATTTT
1 ATTTT
632122 TTACGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
ATTTTATTCATTTTGTTTAT
Found at i:632163 original size:26 final size:28
Alignment explanation
Indices: 632104--632164 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
632094 TTTATTTTTA
*
632104 TTATTT-TTTTATTATTTTTTACGTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
* *
632131 TT-GTTATTTT-TCATTTTTT-CTTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
632156 TTATTTATT
1 TTATTTATT
632165 ATTCTCACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 7 0.25
26 15 0.54
27 6 0.21
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (28 bp):
TTATTTATTTTATCATTTTTTACGTGTT
Found at i:636288 original size:70 final size:70
Alignment explanation
Indices: 636200--636333 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
636190 TGTTCTGTGT
*
636200 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATTCTACCATTTGAATTTTACAT
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
636265 GATCC
66 GATCC
* *
636270 GCTTATTTCTATATGTATATTTGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
636334 CTGTTTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (70 bp):
GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
GATCC
Found at i:642994 original size:21 final size:22
Alignment explanation
Indices: 642957--642997 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
642947 ACACGTTTTA
*
642957 CTCTACTATTGTGGCATGTTTC
1 CTCTACTATTATGGCATGTTTC
642979 CTCTACT-TTATGGCATGTT
1 CTCTACTATTATGGCATGTT
642998 GTTCGCCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (22 bp):
CTCTACTATTATGGCATGTTTC
Found at i:655177 original size:15 final size:15
Alignment explanation
Indices: 655157--655187 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
655147 ATTCCAACTC
655157 TGCAATCTAATCGTA
1 TGCAATCTAATCGTA
655172 TGCAATCTAATCGTA
1 TGCAATCTAATCGTA
655187 T
1 T
655188 TGGGAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (15 bp):
TGCAATCTAATCGTA
Found at i:657860 original size:23 final size:23
Alignment explanation
Indices: 657830--657877 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
657820 GAGGTCTAAC
* * *
657830 TTTATTTTTATTTTATATATTTA
1 TTTATTTTAAGTTAATATATTTA
657853 TTTATTTTAAGTTAATATATTTA
1 TTTATTTTAAGTTAATATATTTA
657876 TT
1 TT
657878 ATTAACTAAT
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:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTAAGTTAATATATTTA
Done.