Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 5 of 17
Found at i:941375 original size:19 final size:19
Alignment explanation
Indices: 941353--941481 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
941343 AAAATCGCAA
941353 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
941372 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
941386 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
941405 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
941419 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
941438 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
941457 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
941477 TGCGA
1 TGCGA
941482 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:941395 original size:33 final size:33
Alignment explanation
Indices: 941353--941444 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
941343 AAAATCGCAA
941353 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
941386 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
941419 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
941445 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:941684 original size:93 final size:93
Alignment explanation
Indices: 941525--941904 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
941515 TTGAATGGAT
941525 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941590 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
941618 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941683 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
941711 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941775 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
941803 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941868 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
941896 AAATTTACT
1 AAATTTACT
941905 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:941838 original size:185 final size:186
Alignment explanation
Indices: 941525--941904 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
941515 TTGAATGGAT
941525 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941590 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
941655 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
941711 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
941775 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
941840 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
941896 AAATTTACT
1 AAATTTACT
941905 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:943628 original size:14 final size:14
Alignment explanation
Indices: 943609--943698 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
943599 TTGAAATGAA
943609 AATCGCAACGAGAG
1 AATCGCAACGAGAG
943623 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
943640 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
943656 AATCGCAACGCGAAATGG
1 AATCGCAA--CGAGA--G
943674 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
943689 AATCGCAACG
1 AATCGCAACG
943699 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 26 0.41
15 1 0.02
16 10 0.16
17 10 0.16
18 1 0.02
19 16 0.25
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:943646 original size:33 final size:33
Alignment explanation
Indices: 943601--943715 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
943591 TCTTTTGGTT
943601 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
943634 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
943667 GAAATGGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
943700 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
943716 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:943647 original size:19 final size:18
Alignment explanation
Indices: 943608--943720 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
943598 GTTGAAATGA
943608 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
943623 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
943640 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
943656 -AATCGCAACGCGAAATGG
1 AAATCGCAACGCGAGAT-G
943674 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
943689 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
943706 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
943721 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 14 0.18
17 11 0.14
18 1 0.01
19 28 0.35
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:943751 original size:14 final size:14
Alignment explanation
Indices: 943732--943786 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
943722 TTTGGTTTCG
943732 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
943746 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
943765 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
943779 CGTTGCGA
1 CGTTGCGA
943787 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:943949 original size:33 final size:33
Alignment explanation
Indices: 943907--943979 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
943897 AATACTAACT
*
943907 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
943940 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
943973 T-AAAATC
1 TGAAAATC
943980 TAAGTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 6 0.16
33 31 0.84
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:944211 original size:22 final size:22
Alignment explanation
Indices: 944159--944213 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
944149 TGGTTGTGAG
**
944159 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
944181 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
944203 GGATTTCTTCG
1 GGATTTCTTCG
944214 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:944384 original size:20 final size:20
Alignment explanation
Indices: 944359--944551 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
944349 CTTTAAATAT
944359 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
944379 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
944401 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
944420 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
944440 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
944460 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
944480 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
944500 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
944520 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
944540 CGCGTTGCGATT
1 CGCGTTGCGATT
944552 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:944546 original size:60 final size:60
Alignment explanation
Indices: 944359--944551 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
944349 CTTTAAATAT
**
944359 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
944420 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
944480 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
944540 CGCGTTGCGATT
1 CGCGTTGCGATT
944552 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:944632 original size:20 final size:20
Alignment explanation
Indices: 944607--944658 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
944597 AAGAATCGCG
*
944607 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
944627 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
944647 TTGCGATTCTGG
1 TTGCGATTCTGG
944659 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:944928 original size:14 final size:15
Alignment explanation
Indices: 944898--944927 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
944888 TTTTAATTCG
944898 ATTCGATTTGAAAAA
1 ATTCGATTTGAAAAA
944913 ATTCGATTTGAAAAA
1 ATTCGATTTGAAAAA
944928 TCTCGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
ATTCGATTTGAAAAA
Found at i:950706 original size:32 final size:32
Alignment explanation
Indices: 950665--950734 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
950655 GTATTTGGTT
950665 AGATGAAAGGAGTGTGTTGTGTAAAAGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAAAGATTGA
* *
950697 AGATGAAAGGAGTGTTTTGTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTGTGTAAAAGATTGA
950729 AGATGA
1 AGATGA
950735 TGTATACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTGTGTAAAAGATTGA
Found at i:950919 original size:2 final size:2
Alignment explanation
Indices: 950912--950948 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
950902 TATTAAAATA
950912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
950949 AACAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:959579 original size:37 final size:38
Alignment explanation
Indices: 959520--959629 Score: 136
Period size: 36 Copynumber: 3.0 Consensus size: 38
959510 GAGACGATAT
*
959520 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTG
1 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTA
* * **
959558 TTTCAAGA-AAACTGTCTCAAGTGAGA--CAAAATTTA
1 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTA
* *
959593 TTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTTT
1 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTT
959630 TTAGAGTAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
35 14 0.24
36 16 0.27
37 16 0.27
38 13 0.22
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (38 bp):
TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTA
Found at i:959610 original size:73 final size:70
Alignment explanation
Indices: 959520--959757 Score: 249
Period size: 70 Copynumber: 3.4 Consensus size: 70
959510 GAGACGATAT
*
959520 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTGTTTCAAGA-AAACTGTCTCAAGTGAGA
1 TTTCAAGAGAAAATATCTCAAGTGAGATG-AA-TTTTGTTTCAAGAGAAACTGTCTCAAGTGAGA
*
959584 CAAAATTTA
64 CAAAA--AA
* *
959593 TTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTT-TTT--AGAGTAACTATCTCTAAG-GAGA
1 TTTCAAGAGAAAATATCTCAAGTGAGATG-AATTTTGTTTCAAGAGAAACTGTCTC-AAGTGAGA
*
959654 CAAAAACG
64 CAAAAA-A
* * * *
959662 TTT-AAGGGAAAATATCTCAAGTGAGATGTAATTTTGTTTCAA-ATGAAGCTGTCCCGAGTGAGA
1 TTTCAAGAGAAAATATCTCAAGTGAGATG-AATTTTGTTTCAAGA-GAAACTGTCTCAAGTGAGA
959725 CAAAAAA
64 CAAAAAA
*
959732 TTTAAAG-GAAAATATCTCAAGTGAGA
1 TTTCAAGAGAAAATATCTCAAGTGAGA
959758 CTATCTTGTT
Statistics
Matches: 142, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
68 30 0.21
69 9 0.06
70 42 0.30
71 27 0.19
72 4 0.03
73 30 0.21
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (70 bp):
TTTCAAGAGAAAATATCTCAAGTGAGATGAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGACA
AAAAA
Found at i:959619 original size:36 final size:36
Alignment explanation
Indices: 959520--959687 Score: 141
Period size: 34 Copynumber: 4.8 Consensus size: 36
959510 GAGACGATAT
* **
959520 TTTCAAGACAAAATATCTCAAGTGAGATGCAATTTTTG
1 TTTCAAGAGAAAATATCTCAAGTGAGA--CAAAATTTG
* * *
959558 TTTCAAGA-AAACTGTCTCAAGTGAGACAAAATTTA
1 TTTCAAGAGAAAATATCTCAAGTGAGACAAAATTTG
**
959593 TTTCAAGAGAAAATATCTCAAGTGAGATGAAATTT-
1 TTTCAAGAGAAAATATCTCAAGTGAGACAAAATTTG
* * * **
959628 TTT-TAGAGTAACTATCTCTAAG-GAGACAAAA-ACG
1 TTTCAAGAGAAAATATCTC-AAGTGAGACAAAATTTG
*
959662 TTT-AAGGGAAAATATCTCAAGTGAGA
1 TTTCAAGAGAAAATATCTCAAGTGAGA
959688 TGTAATTTTG
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
33 3 0.03
34 37 0.35
35 20 0.19
36 22 0.21
37 16 0.15
38 8 0.08
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
TTTCAAGAGAAAATATCTCAAGTGAGACAAAATTTG
Found at i:960081 original size:19 final size:19
Alignment explanation
Indices: 960054--960102 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
960044 ATGACCAACA
* * *
960054 AATTAGCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
*
960073 AATTCGCAATGCGAACTCC
1 AATTCGCAACGCGAACTCC
960092 AATTTCGCAAC
1 AA-TTCGCAAC
960103 TCAGTTTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:960165 original size:21 final size:21
Alignment explanation
Indices: 960107--960182 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
960097 CGCAACTCAG
* *
960107 TTTCCAAATTCGCAATGCGAA
1 TTTCCAAATTCGCATTGCGAT
* **
960128 TATGTAAA-TCGCATTGCGAT
1 TTTCCAAATTCGCATTGCGAT
** *
960148 TTTCTGAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
960169 TTTCCAAATTCGCA
1 TTTCCAAATTCGCA
960183 ACGTGAATCT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:960221 original size:20 final size:20
Alignment explanation
Indices: 960175--960224 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
960165 CGATTTTCCA
960175 AATTCGCAACGTGAATCTGT
1 AATTCGCAACGTGAATCTGT
* *
960195 AAATCGCAACGTGAATTTGT
1 AATTCGCAACGTGAATCTGT
*
960215 ATTTCGCAAC
1 AATTCGCAAC
960225 ATAGAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
AATTCGCAACGTGAATCTGT
Found at i:962444 original size:21 final size:21
Alignment explanation
Indices: 962401--962445 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
962391 ATGAGTTCAA
* *
962401 TGCTTTACGTGAGGAAGTCGG
1 TGCTTTACGTGAAGAAATCGG
962422 TGCTTTACGTGAAGACAAT-GG
1 TGCTTTACGTGAAGA-AATCGG
962443 TGC
1 TGC
962446 ATGGCGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (21 bp):
TGCTTTACGTGAAGAAATCGG
Found at i:962474 original size:21 final size:21
Alignment explanation
Indices: 962450--962499 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
962440 TGGTGCATGG
*
962450 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGAGGT-TTTA
*
962471 CGTGGTGAGGTAGAGGTTTTA
1 CGTGATGAGGTAGAGGTTTTA
*
962492 CGCGATGA
1 CGTGATGA
962500 CAATGGTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (21 bp):
CGTGATGAGGTAGAGGTTTTA
Found at i:964026 original size:21 final size:20
Alignment explanation
Indices: 964002--964099 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 20
963992 CCTGTCATTA
964002 TTCAAGAGGCCTCTTCTATCG
1 TTCAAGAGGCC-CTTCTATCG
*
964023 TTCAAGAGGCCCCTATC-ATCC
1 TTCAAGAGG-CCCT-TCTATCG
* *
964044 TTCAAGAGGCCCTTCCCACCG
1 TTCAAGAGGCCCTT-CTATCG
*
964065 TTCAAGAGGCCCTTGTCATCG
1 TTCAAGAGGCCCTTCT-ATCG
964086 TTCAAGAGGTCCCT
1 TTCAAGAGG-CCCT
964100 CCCACTGTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 51 0.78
22 8 0.12
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (20 bp):
TTCAAGAGGCCCTTCTATCG
Found at i:964067 original size:42 final size:42
Alignment explanation
Indices: 964002--964109 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
963992 CCTGTCATTA
* *
964002 TTCAAGAGGCCTCTT-CTATCGTTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCC-CTTCCCACCGTTCAAGAGGCCCCTATCATCC
* * *
964044 TTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCTTGTCATCG
1 TTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCCTATCATCC
*
964086 TTCAAGAGGTCCC-TCCCACTGTTC
1 TTCAAGAGG-CCCTTCCCACCGTTC
964110 GAGATCCCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 3 0.05
42 52 0.90
43 3 0.05
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (42 bp):
TTCAAGAGGCCCTTCCCACCGTTCAAGAGGCCCCTATCATCC
Found at i:964109 original size:21 final size:21
Alignment explanation
Indices: 964044--964109 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
964034 CCTATCATCC
*
964044 TTCAAGAGGCCCTTCCCACCG
1 TTCAAGAGGCCCTTCCCACTG
**
964065 TTCAAGAGGCCCTTGTCA-TCG
1 TTCAAGAGGCCCTTCCCACT-G
964086 TTCAAGAGGTCCC-TCCCACTG
1 TTCAAGAGG-CCCTTCCCACTG
964107 TTC
1 TTC
964110 GAGATCCCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (21 bp):
TTCAAGAGGCCCTTCCCACTG
Found at i:965480 original size:17 final size:18
Alignment explanation
Indices: 965452--965488 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
965442 CTGCGTGAAA
965452 TTGATGTATTTGTAAAAG
1 TTGATGTATTTGTAAAAG
965470 TTGAT-TATTTGTAAAAG
1 TTGATGTATTTGTAAAAG
965487 TT
1 TT
965489 TATTTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (18 bp):
TTGATGTATTTGTAAAAG
Found at i:965547 original size:64 final size:64
Alignment explanation
Indices: 965476--965624 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
965466 AAAGTTGATT
*
965476 ATTTGTAAAAGTTTATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * *** *
965540 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTTCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
965604 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
965625 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:965748 original size:20 final size:20
Alignment explanation
Indices: 965720--965813 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
965710 TGCGATGGTT
*
965720 GCAATAGTCAAATTCGCAAC
1 GCAAAAGTCAAATTCGCAAC
*
965740 GCAAAAGTCAAATTCGCAAT
1 GCAAAAGTCAAATTCGCAAC
*
965760 GCGAAAGTCAAATTCGCAAC
1 GCAAAAGTCAAATTCGCAAC
*** *
965780 ATGAAAGTCAAATTCGCAAT
1 GCAAAAGTCAAATTCGCAAC
965800 G-AGAAAGTCAAATT
1 GCA-AAAGTCAAATT
965814 TGCGTTTCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (20 bp):
GCAAAAGTCAAATTCGCAAC
Found at i:965769 original size:40 final size:40
Alignment explanation
Indices: 965725--965813 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
965715 TGGTTGCAAT
* *
965725 AGTCAAATTCGCAACGCAAAAGTCAAATTCGCAATGCGAA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAATGAGAA
**
965765 AGTCAAATTCGCAACATGAAAGTCAAATTCGCAATGAGAA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAATGAGAA
965805 AGTCAAATT
1 AGTCAAATT
965814 TGCGTTTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (40 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAATGAGAA
Found at i:968330 original size:24 final size:24
Alignment explanation
Indices: 968296--968349 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
968286 CTAAAACATC
* *
968296 ATCAAAATCCGAGTATTCACCAAG
1 ATCAAAATCCGAGAATTAACCAAG
*
968320 ATCAAAGTCCGAGAATTAACCAAG
1 ATCAAAATCCGAGAATTAACCAAG
968344 ATCAAA
1 ATCAAA
968350 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCGAGAATTAACCAAG
Found at i:968496 original size:12 final size:12
Alignment explanation
Indices: 968475--968508 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
968465 GGTTGCGAGT
*
968475 TTTGAGATTGTG
1 TTTGATATTGTG
968487 TTTGATATTGTG
1 TTTGATATTGTG
*
968499 TTTGGTATTG
1 TTTGATATTG
968509 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:969318 original size:20 final size:22
Alignment explanation
Indices: 969293--969381 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 22
969283 AACTAAAACC
*
969293 TGTTGCGAAATT-AAAATTC-A
1 TGTTGCGAAATTCAAAAATCGA
969313 TGTTGCG-AATTCAAAAATCGA
1 TGTTGCGAAATTCAAAAATCGA
* **
969334 -GTTGCGAAA-ACAAATTTCG-
1 TGTTGCGAAATTCAAAAATCGA
* *
969353 CGTTGCG-AATTCAGAAATCGA
1 TGTTGCGAAATTCAAAAATCGA
969374 -GTTGCGAA
1 TGTTGCGAA
969382 TTTGAAATTC
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 6 0.11
20 44 0.81
21 4 0.07
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (22 bp):
TGTTGCGAAATTCAAAAATCGA
Found at i:969340 original size:40 final size:40
Alignment explanation
Indices: 969294--969404 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 40
969284 ACTAAAACCT
969294 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
1 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
** * ** *
969334 GTTGCGAAAACAAATTTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
* * *
969374 GTTGCGAATTTGAAATTCAGTATTGCGAATT
1 GTTGCGAAATTAAAATTCA-TGTTGCGAATT
969405 TGGAAATGGC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
40 47 0.84
41 9 0.16
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
Found at i:969382 original size:20 final size:19
Alignment explanation
Indices: 969314--969383 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
969304 TAAAATTCAT
969314 GTTGCGAATTCAAAAATCGA
1 GTTGCGAATTC-AAAATCGA
** * *
969334 GTTGCGAAAACAAATTTCGC
1 GTTGCGAATTCAAA-ATCGA
969354 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCA-AAATCGA
969374 GTTGCGAATT
1 GTTGCGAATT
969384 TGAAATTCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.08
20 35 0.88
21 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (19 bp):
GTTGCGAATTCAAAATCGA
Found at i:969437 original size:21 final size:21
Alignment explanation
Indices: 969398--969484 Score: 140
Period size: 21 Copynumber: 4.2 Consensus size: 21
969388 ATTCAGTATT
*
969398 GCGAATTTGG-AAATGGCAAC
1 GCGAATTTGGAAAATCGCAAC
969418 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
969439 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
* *
969460 GCGAATTTGGAAAATTGCAAT
1 GCGAATTTGGAAAATCGCAAC
969481 GCGA
1 GCGA
969485 TTTACATATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 10 0.16
21 53 0.84
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:971237 original size:27 final size:30
Alignment explanation
Indices: 971161--971228 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
971151 ATTGTAATAG
971161 GTTAAACTGTAACCAAATTATTATTAATGA
1 GTTAAACTGTAACCAAATTATTATTAATGA
971191 GTTAAACTGTAACCAAATTATTATTAATGA
1 GTTAAACTGTAACCAAATTATTATTAATGA
971221 -TT-AACTGT
1 GTTAAACTGT
971229 CAGAGATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 6 0.16
29 2 0.05
30 30 0.79
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (30 bp):
GTTAAACTGTAACCAAATTATTATTAATGA
Found at i:978444 original size:30 final size:30
Alignment explanation
Indices: 978405--978479 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
978395 GATGGCCTTG
*
978405 GTCCCTGTACTATTTAACATGGGTGGCCAA
1 GTCCCTGTACTATTTAACATGAGTGGCCAA
* ** *
978435 GTCCTTGTACTATTTGGCATTAGTGGCCAA
1 GTCCCTGTACTATTTAACATGAGTGGCCAA
*
978465 GTCCCTATACTATTT
1 GTCCCTGTACTATTT
978480 TGGTACTTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (30 bp):
GTCCCTGTACTATTTAACATGAGTGGCCAA
Found at i:979715 original size:2 final size:2
Alignment explanation
Indices: 979708--979745 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
979698 ACCTTTATTG
979708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- 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
979746 ATTACATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:985382 original size:3 final size:3
Alignment explanation
Indices: 985374--985404 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
985364 AATAGAAAAT
*
985374 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
985405 AGGTGGTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:995962 original size:13 final size:13
Alignment explanation
Indices: 995944--995969 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
995934 CACAACCCTT
995944 ATTCCATTTTTCC
1 ATTCCATTTTTCC
995957 ATTCCATTTTTCC
1 ATTCCATTTTTCC
995970 TCCAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTCCATTTTTCC
Found at i:1000906 original size:40 final size:40
Alignment explanation
Indices: 1000858--1000938 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1000848 AAATCATGAG
1000858 CCATCAGATCTGGGTCGATTTAGATGGTAAAATAATCATT
1 CCATCAGATCTGGGTCGATTTAGATGGTAAAATAATCATT
1000898 CCATCAGATCTGGGTCGATTTAGATGGTAAAATAATCATT
1 CCATCAGATCTGGGTCGATTTAGATGGTAAAATAATCATT
1000938 C
1 C
1000939 TTTACGCCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (40 bp):
CCATCAGATCTGGGTCGATTTAGATGGTAAAATAATCATT
Found at i:1002842 original size:26 final size:26
Alignment explanation
Indices: 1002813--1002863 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1002803 TCTATAATGT
*
1002813 GATTCATGTGTTTGCCTATTGAATAC
1 GATTCATGTGTTTACCTATTGAATAC
1002839 GATTCATGTGTTTACCTATTGAATA
1 GATTCATGTGTTTACCTATTGAATA
1002864 AATTCTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (26 bp):
GATTCATGTGTTTACCTATTGAATAC
Found at i:1004991 original size:15 final size:15
Alignment explanation
Indices: 1004971--1005001 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1004961 ATTATCGATG
1004971 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1004986 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1005001 A
1 A
1005002 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1010331 original size:33 final size:33
Alignment explanation
Indices: 1010289--1010357 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1010279 GCCAAGGCAA
1010289 TATTACTTAGTCCAGGAACCTAAGGGGGATTTT
1 TATTACTTAGTCCAGGAACCTAAGGGGGATTTT
1010322 TATTACTTAGTCCAGGAACCTAAGGGGGATTTT
1 TATTACTTAGTCCAGGAACCTAAGGGGGATTTT
1010355 TAT
1 TAT
1010358 GCATTATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (33 bp):
TATTACTTAGTCCAGGAACCTAAGGGGGATTTT
Found at i:1011277 original size:28 final size:28
Alignment explanation
Indices: 1011238--1011297 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1011228 AAATAAAAAA
* * *
1011238 TAAAAATTAT-AAATTATTATTTAATTT
1 TAAAAATTATAAAATAATTACTAAATTT
1011265 TAAAAAGTTATAAAATAATTACTAAATTT
1 TAAAAA-TTATAAAATAATTACTAAATTT
1011294 TAAA
1 TAAA
1011298 TTTTGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 4 0.14
29 18 0.64
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TAAAAATTATAAAATAATTACTAAATTT
Found at i:1011440 original size:9 final size:10
Alignment explanation
Indices: 1011428--1011492 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 10
1011418 TTTAAATAAT
1011428 AATT-TAAAA
1 AATTATAAAA
1011437 AATTATAAAAA
1 AATTAT-AAAA
*
1011448 TCAATTTTAAAA
1 --AATTATAAAA
1011460 AATTATAAAA
1 AATTATAAAA
*
1011470 CTCAATTTTAAAA
1 ---AATTATAAAA
1011483 AATTATAAAA
1 AATTATAAAA
1011493 GTAAACAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
9 4 0.09
10 19 0.42
11 4 0.09
12 4 0.09
13 14 0.31
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTATAAAA
Found at i:1011460 original size:23 final size:23
Alignment explanation
Indices: 1011430--1011492 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
1011420 TAAATAATAA
1011430 TTTAAAAAATTATAAAAATCAAT
1 TTTAAAAAATTATAAAAATCAAT
*
1011453 TTTAAAAAATTATAAAACTCAAT
1 TTTAAAAAATTATAAAAATCAAT
1011476 TTTAAAAAATTATAAAA
1 TTTAAAAAATTATAAAA
1011493 GTAAACAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (23 bp):
TTTAAAAAATTATAAAAATCAAT
Found at i:1011772 original size:48 final size:49
Alignment explanation
Indices: 1011705--1011800 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 49
1011695 ATATACCAAT
* **
1011705 TTTTTTACTAAACCTACCAAAAGATTGGTGTAATGATTATGTTTTTTCA
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
*
1011754 TTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATGTTTTTTC
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTC
1011801 TTTATATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 31 0.72
49 12 0.28
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (49 bp):
TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
Found at i:1014408 original size:73 final size:73
Alignment explanation
Indices: 1014321--1014466 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
1014311 TCATAATTAA
1014321 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1014386 TGTTTTAC
66 TGTTTTAC
1014394 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1014459 TGTTTTAC
66 TGTTTTAC
1014467 CTGCATCGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (73 bp):
ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
TGTTTTAC
Found at i:1015182 original size:5 final size:5
Alignment explanation
Indices: 1015164--1015230 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
1015154 TTCCTGCAAC
* * * * *
1015164 AAAAT -AAA- AAAAT AGAAT AAAAT ACATT TATAT AAAAT AAAAT AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
*
1015213 -ATAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
1015231 AATCAGACCC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
4 7 0.15
5 38 0.83
6 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:1015204 original size:20 final size:20
Alignment explanation
Indices: 1015192--1015230 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1015182 AAAATACATT
1015192 TATATAAAATAAAATAAAAG
1 TATATAAAATAAAATAAAAG
1015212 TATATAAAATAAAATAAAA
1 TATATAAAATAAAATAAAA
1015231 AATCAGACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TATATAAAATAAAATAAAAG
Found at i:1016470 original size:2 final size:2
Alignment explanation
Indices: 1016463--1016500 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1016453 GTCTCTAACA
1016463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1016501 CCTTTTCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1017572 original size:29 final size:29
Alignment explanation
Indices: 1017530--1017585 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1017520 GACAACCAGC
1017530 ATAGGTCGCCATGCACGCCCGACGTCCTT
1 ATAGGTCGCCATGCACGCCCGACGTCCTT
*
1017559 ATAGGTCGCCATGCACGCCCGGCGTCC
1 ATAGGTCGCCATGCACGCCCGACGTCC
1017586 AACGTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGACGTCCTT
Found at i:1017720 original size:61 final size:61
Alignment explanation
Indices: 1017634--1017753 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
1017624 TTGGTGCTAG
*
1017634 GCTTTGGTGTTATGCATGGGTCATGCACGGGGCATGGGATAGGTCGCCAAGAGCTTTGTCT
1 GCTTTGGTGTTATGCATGGGCCATGCACGGGGCATGGGATAGGTCGCCAAGAGCTTTGTCT
* *
1017695 GCTTTGGTGCTT-TGTATGGGCCATGCACGGGGCATGTGATAGGTCGCCAAGAGCTTTGT
1 GCTTTGGTG-TTATGCATGGGCCATGCACGGGGCATGGGATAGGTCGCCAAGAGCTTTGT
1017754 TCACGTGGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 53 0.96
62 2 0.04
ACGTcount: A:0.16, C:0.18, G:0.36, T:0.30
Consensus pattern (61 bp):
GCTTTGGTGTTATGCATGGGCCATGCACGGGGCATGGGATAGGTCGCCAAGAGCTTTGTCT
Found at i:1018261 original size:18 final size:18
Alignment explanation
Indices: 1018240--1018294 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1018230 AATAATTATT
1018240 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1018258 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1018270 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1018287 TAAATTAG
1 TAAATTAG
1018295 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:1018594 original size:29 final size:29
Alignment explanation
Indices: 1018557--1018634 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
1018547 TAGTAATAAA
1018557 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
1018587 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
1018617 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
1018635 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:1018603 original size:22 final size:22
Alignment explanation
Indices: 1018578--1018658 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
1018568 AATCATTTAT
1018578 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAAAA
*
1018600 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAG-----T--TTAA-GTTATATTAAAAAA
*
1018630 TAGTTAAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAAAA
1018652 TAGTTTA
1 TAGTTTA
1018659 TTAGTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
22 22 0.47
23 3 0.06
25 1 0.02
27 1 0.02
29 4 0.09
30 16 0.34
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAAAA
Found at i:1019968 original size:23 final size:23
Alignment explanation
Indices: 1019940--1019984 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1019930 TTTAATTATT
*
1019940 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
1019963 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
1019985 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:1019984 original size:18 final size:20
Alignment explanation
Indices: 1019934--1019984 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
1019924 GTTATTTTTA
1019934 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
1019955 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
1019975 TTTATTATTT
1 ATTATTATTT
1019985 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:1020926 original size:21 final size:21
Alignment explanation
Indices: 1020902--1020986 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
1020892 TAATTTCATT
*
1020902 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
1020923 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
1020944 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
1020962 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
1020983 ATTA
1 ATTA
1020987 TTATAATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
20 6 0.13
21 17 0.36
22 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:1020940 original size:60 final size:60
Alignment explanation
Indices: 1020872--1021287 Score: 396
Period size: 60 Copynumber: 6.8 Consensus size: 60
1020862 AATCATTACT
1020872 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
1020932 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATTAT-
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
* * * * ** * * * * ** *
1020991 AATTTCATTACTAGTTATGTAACGAA-AATATGGTGAATTGAACCAAACATT-GTTCATTATTCA
1 AA-ATCATTA--A-ATAT-TAA-TAATAATTTCAT-TATT--ACTAATCATTACTAAATCATT-A
*
1021054 A-GTC
56 ATATC
* * * * * * * * *
1021058 GTAAATCATT-ACTATTAAATCATTAAATATTAATAATAAATTATTATTACT-AATCATTACTAT
1 --AAATCATTAAATATT-AAT-AAT-AAT-TTCATTATTACTAATCATTACTAAATCATTAATAT
*
1021121 G
60 C
1021122 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
1021182 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATTATC
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
*
1021242 AAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTA
1 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
1021288 TCAAATCATT
Statistics
Matches: 287, Mismatches: 47, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
59 38 0.13
60 162 0.56
61 2 0.01
62 12 0.04
63 10 0.03
64 25 0.09
65 7 0.02
66 13 0.05
67 11 0.04
68 5 0.02
69 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (60 bp):
AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
Found at i:1021078 original size:14 final size:14
Alignment explanation
Indices: 1021059--1021130 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
1021049 ATTCAAGTCG
1021059 TAAATCATTACTAT
1 TAAATCATTACTAT
*
1021073 TAAATCATTAAATAT
1 TAAATCATT-ACTAT
* *
1021088 TAATAATAAATTATTAT
1 T-A-AAT-CATTACTAT
1021105 TACTAATCATTACTAT
1 TA--AATCATTACTAT
*
1021121 GAAATCATTA
1 TAAATCATTA
1021131 AATATTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
14 17 0.36
15 5 0.11
16 10 0.21
17 12 0.26
18 3 0.06
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (14 bp):
TAAATCATTACTAT
Found at i:1021097 original size:21 final size:22
Alignment explanation
Indices: 1021059--1021144 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 22
1021049 ATTCAAGTCG
* *
1021059 TAAATCATTACTATTAAATCAT
1 TAAATCATTAATAATAAATCAT
*
1021081 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTAATAAT-AA--ATCAT
*
1021105 TACTAATCATTACT-ATGAAATCAT
1 TA--AATCATTAATAAT-AAATCAT
1021129 TAAAT-ATTAATAATAA
1 TAAATCATTAATAATAA
1021145 TTTCATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
21 14 0.28
22 12 0.24
24 12 0.24
26 7 0.14
27 5 0.10
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:1021120 original size:48 final size:49
Alignment explanation
Indices: 1021061--1021168 Score: 191
Period size: 48 Copynumber: 2.2 Consensus size: 49
1021051 TCAAGTCGTA
*
1021061 AATCATTACTATTAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTATGAAATCATTAAATATTAATAATAAATTCATTATTACT
*
1021109 AATCATTACTATGAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTATGAAATCATTAAATATTAATAATAAATTCATTATTACT
1021158 AATCATTACTA
1 AATCATTACTA
1021169 AATCATTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 37 0.65
49 20 0.35
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (49 bp):
AATCATTACTATGAAATCATTAAATATTAATAATAAATTCATTATTACT
Found at i:1021176 original size:21 final size:21
Alignment explanation
Indices: 1021152--1021236 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
1021142 TAATTTCATT
*
1021152 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
1021173 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
1021194 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
1021212 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
1021233 ATTA
1 ATTA
1021237 TTATCAAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
20 6 0.13
21 17 0.36
22 10 0.21
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:1021284 original size:48 final size:48
Alignment explanation
Indices: 1021222--1021384 Score: 274
Period size: 48 Copynumber: 3.4 Consensus size: 48
1021212 ATTACTAATC
*
1021222 ATTACTAAATCATTATTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1021271 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
*
1021319 ATTACTAATCATTACTATCAAATCATTACAA-ATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTA-AATATTAATAATAAATT-ATT
1021368 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1021385 AATCATTAAT
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
48 82 0.75
49 28 0.25
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:1021300 original size:216 final size:216
Alignment explanation
Indices: 1021059--1021553 Score: 757
Period size: 216 Copynumber: 2.3 Consensus size: 216
1021049 ATTCAAGTCG
*
1021059 TAAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATGAA
1 TAAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1021124 ATCATTA-AATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCA
66 ATCATTACAA-ATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCA
* * *
1021188 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATC-ATTATTATCAAATC-ATTA
130 TTAAATACTAATAATAATTTCATTATTACTAATCATTACT--ATCAATCATTA-CAAATCAATAA
* *
1021251 -AATATTAATAATAAATTATTATTAC
192 TAAT-TTAATAATAAATAATCATTAC
*
1021276 T-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1 TAAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1021340 ATCATTACAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCAT
66 ATCATTACAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCAT
*
1021405 TAAATACTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTACAAATTAATAATAA
131 TAAATACTAATAATAATTTCATTATTACTAATCATTACTATC-AATCATTACAAATCAATAATAA
* * * *
1021470 TTTCATTATTACTAATCATTAC
195 TTTAATAATAAATAATCATTAC
* * *
1021492 TAAATCATTAATATTAAATCATTAAATACTAATAATAATTTCATTATTACTAATCATTACTA
1 TAAATCATTACTATTAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTA
1021554 AATCATTACT
Statistics
Matches: 255, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
214 3 0.01
215 5 0.02
216 186 0.73
217 41 0.16
218 20 0.08
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (216 bp):
TAAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
ATCATTACAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCAT
TAAATACTAATAATAATTTCATTATTACTAATCATTACTATCAATCATTACAAATCAATAATAAT
TTAATAATAAATAATCATTAC
Found at i:1021398 original size:60 final size:60
Alignment explanation
Indices: 1021319--1021444 Score: 211
Period size: 60 Copynumber: 2.1 Consensus size: 60
1021309 ATAAATTATT
* *
1021319 ATTACT-AATCATTACTATCAAATCATTACAA-ATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTA-AATACTAATAATAATTTCATTATTACTAATC
1021378 ATTACTAAATCATTAATATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
1021438 ATTACTA
1 ATTACTA
1021445 TCAAATCATT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
59 8 0.13
60 55 0.87
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
Found at i:1021467 original size:109 final size:109
Alignment explanation
Indices: 1021059--1021553 Score: 727
Period size: 109 Copynumber: 4.6 Consensus size: 109
1021049 ATTCAAGTCG
* * * *
1021059 TAAATCATTACTATTAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTATGA
1 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
1021123 AATCATTA-AATATTAATAATAATTTCATTATTACTAATCATTAC
66 AATCATTACAA-ATTAATAATAATTTCATTATTACTAATCATTAC
1021167 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA--A
1 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
* * * * * * * * *
1021230 ATCATTATTATCAAA-TCATTA-AATATTAATAATAAATTATTATTAC
66 A--ATCATTA-CAAATTAATAATAAT-TTCATTATTACTAATCATTAC
* *
1021276 T-AATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTATCA
1 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
1021339 AATCATTACAAATTAATAATAATTTCATTATTACTAATCATTAC
66 AATCATTACAAATTAATAATAATTTCATTATTACTAATCATTAC
*
1021383 TAAATCATTAATATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATCATTACTATCA
1 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
1021448 AATCATTACAAATTAATAATAATTTCATTATTACTAATCATTAC
66 AATCATTACAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
1021492 TAAATCATTAATATTAAATCATTAAATACTAATAATAATTTCATTATTACTAATCATTACTA
1 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
1021554 AATCATTACT
Statistics
Matches: 348, Mismatches: 27, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
106 4 0.01
107 48 0.14
108 117 0.34
109 176 0.51
110 1 0.00
111 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (109 bp):
TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
AATCATTACAAATTAATAATAATTTCATTATTACTAATCATTAC
Found at i:1021491 original size:49 final size:49
Alignment explanation
Indices: 1021378--1021493 Score: 189
Period size: 49 Copynumber: 2.3 Consensus size: 49
1021368 ATTACTAATC
*
1021378 ATTACTAAATCATTAATATCAAATCATTAAATACTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATACTAATAATAATTTCATT
*
1021428 ATTACTAATCATTACTATCAAATCATTACAA-ATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTA-AATACTAATAATAATTTCATT
1021477 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1021494 AATCATTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
49 55 0.87
50 8 0.13
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATACTAATAATAATTTCATT
Found at i:1021498 original size:60 final size:60
Alignment explanation
Indices: 1021428--1021575 Score: 246
Period size: 60 Copynumber: 2.5 Consensus size: 60
1021418 TAATTTCATT
*
1021428 ATTACT-AATCATTACTATCAAATCATTACAA-ATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AATACTAATAATAATTTCATTATTACTAATC
* *
1021487 ATTACTAAATCATTAATATTAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
1021547 ATTACTAAATCATTACTATCAAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA
1021576 TTATAATAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
59 8 0.10
60 74 0.90
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATACTAATAATAATTTCATTATTACTAATC
Found at i:1021619 original size:26 final size:26
Alignment explanation
Indices: 1021547--1021639 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 26
1021537 ATTACTAATC
* * *
1021547 ATTACTAAATCATTACTATCAA--ATC
1 ATTATTAAATCATTATTAT-AATGATT
* *
1021572 ATTATTATAATAATTTTTATAATGATT
1 ATTATTA-AATCATTATTATAATGATT
*
1021599 TTTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
1021625 ATTATTAAATCATTA
1 ATTATTAAATCATTA
1021640 CTAAATCATC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
25 8 0.14
26 40 0.71
27 8 0.14
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATGATT
Found at i:1021672 original size:61 final size:60
Alignment explanation
Indices: 1021601--1021809 Score: 256
Period size: 61 Copynumber: 3.6 Consensus size: 60
1021591 TAATGATTTT
1021601 TATTAAATCATTATTATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAA
1 TATTAAATCATTATTATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAA
* *
1021661 TATTTAAATCATTATTATAATGATTATTATTAAATCATTA-T---T-AT--AATGATT-AT
1 TA-TTAAATCATTATTATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAA
* * * *
1021714 TATCAAATTATTATTATAATGATTATTATCATATCATTACTAAATCATCAAATCATTAAA
1 TATTAAATCATTATTATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAA
* *
1021774 TATTAAATTCATTATTA-AATCATTATAATTCAAATC
1 TATTAAA-TCATTATTATAATGATTATTATT-AAATC
1021810 TATTCAAGTC
Statistics
Matches: 124, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
52 33 0.27
53 4 0.03
54 6 0.05
56 3 0.02
57 3 0.02
59 6 0.05
60 20 0.16
61 49 0.40
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (60 bp):
TATTAAATCATTATTATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAA
Found at i:1021696 original size:26 final size:26
Alignment explanation
Indices: 1021666--1021752 Score: 147
Period size: 26 Copynumber: 3.3 Consensus size: 26
1021656 TTAAATATTT
*
1021666 AAATCATTATTATAATGATTATTATT
1 AAATCATTATTATAATGATTATTATC
1021692 AAATCATTATTATAATGATTATTATC
1 AAATCATTATTATAATGATTATTATC
*
1021718 AAATTATTATTATAATGATTATTATC
1 AAATCATTATTATAATGATTATTATC
*
1021744 ATATCATTA
1 AAATCATTA
1021753 CTAAATCATC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (26 bp):
AAATCATTATTATAATGATTATTATC
Found at i:1021705 original size:113 final size:112
Alignment explanation
Indices: 1021567--1021809 Score: 357
Period size: 113 Copynumber: 2.2 Consensus size: 112
1021557 CATTACTATC
* * * *
1021567 AAATCATTATTA-T-AATAATTTTTATAATGATTTTTATTAAATCATTATTATAATGATTATTAT
1 AAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTAT
*
1021630 TAAATCATTACTAAATCATCAAATCATTAAATATTTAAA-TCATTATT
66 CAAATCATTACTAAATCATCAAATCATTAAATA-TTAAATTCATTATT
* *
1021677 ATAATGATTATTATTAAATCATTATTATAATGATTATTATCAAATTATTATTATAATGATTATTA
1 A-AATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTA
*
1021742 TCATATCATTACTAAATCATCAAATCATTAAATATTAAATTCATTATT
65 TCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCATTATT
*
1021790 AAATCATTATAATTCAAATC
1 AAATCATTATTATT-AAATC
1021810 TATTCAAGTC
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
110 1 0.01
111 10 0.08
112 17 0.14
113 90 0.76
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (112 bp):
AAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGATTATTAT
CAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCATTATT
Found at i:1021778 original size:52 final size:52
Alignment explanation
Indices: 1021650--1021778 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
1021640 CTAAATCATC
* *
1021650 AAATCATTAAAT-ATTTAAATCATTATTATAATGATTATTATTAAATCATTATT
1 AAATCATTAAATCA-TTAAAT-ATTATTATAATGATTATTATCAAATCATTACT
* * * *
1021703 ATAATGATTATTATCA--AATTATTATTATAATGATTATTATCATATCATTACT
1 A-AATCATTA-AATCATTAAATATTATTATAATGATTATTATCAAATCATTACT
*
1021755 AAATCATCAAATCATTAAATATTA
1 AAATCATTAAATCATTAAATATTA
1021779 AATTCATTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
50 4 0.07
51 6 0.10
52 37 0.61
53 4 0.07
54 7 0.11
55 2 0.03
56 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (52 bp):
AAATCATTAAATCATTAAATATTATTATAATGATTATTATCAAATCATTACT
Found at i:1021969 original size:17 final size:18
Alignment explanation
Indices: 1021949--1022038 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 18
1021939 TATTAGTAAA
1021949 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
1021966 TCATTATTATTAATAATTACT
1 TCATTATTATTAATAA-T--T
* *
1021987 AATCATTACTATCAAATAA-T
1 --TCATTATTAT-TAATAATT
* * *
1022007 TAAATATTAATAATAATT
1 TCATTATTATTAATAATT
1022025 TCATTATTATTAAT
1 TCATTATTATTAAT
1022039 CATTACTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
17 16 0.29
18 22 0.40
19 1 0.02
20 1 0.02
21 1 0.02
23 9 0.16
24 5 0.09
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:1025063 original size:26 final size:24
Alignment explanation
Indices: 1025003--1025063 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
1024993 TACTAATATT
*
1025003 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
1025027 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
1025054 ATTTAATAAT
1 A-TTAATAAT
1025064 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:1025138 original size:20 final size:21
Alignment explanation
Indices: 1025110--1025154 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1025100 TATAAATATT
* *
1025110 TAATGATTTAG-ATTTAATAC
1 TAATCATTTAGTAATTAATAC
*
1025130 TAATCATTTAGTAATTATTAC
1 TAATCATTTAGTAATTAATAC
1025151 TAAT
1 TAAT
1025155 AATCATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TAATCATTTAGTAATTAATAC
Found at i:1025352 original size:17 final size:17
Alignment explanation
Indices: 1025299--1025358 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
1025289 AATATAAATA
*
1025299 AAACAAAATATTTTTTT
1 AAACACAATATTTTTTT
* *
1025316 AAAACAACACTAAATATTTTT
1 -AAAC-ACA--ATATTTTTTT
1025337 AAACACAATATTTTTTT
1 AAACACAATATTTTTTT
1025354 AAACA
1 AAACA
1025359 AAAATTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 5 0.15
20 4 0.12
21 8 0.24
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AAACACAATATTTTTTT
Found at i:1025826 original size:8 final size:8
Alignment explanation
Indices: 1025815--1025839 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1025805 TTTAATAACT
1025815 TAAACTAA
1 TAAACTAA
1025823 TAAACTAA
1 TAAACTAA
1025831 TAAACTAA
1 TAAACTAA
1025839 T
1 T
1025840 TTTTATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAACTAA
Found at i:1025891 original size:21 final size:21
Alignment explanation
Indices: 1025858--1025906 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1025848 AATATAATAT
1025858 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1025879 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1025900 ATTAACT
1 A-TAACT
1025907 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1026091 original size:6 final size:6
Alignment explanation
Indices: 1026061--1026103 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1026051 AGTTTATATG
* * * *
1026061 TGCTTA TGCTTA TGCTCC TGGTTC TGCTTC TGCTTC TGCTTC T
1 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC T
1026104 ACCCTAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.05, C:0.28, G:0.19, T:0.49
Consensus pattern (6 bp):
TGCTTC
Found at i:1026570 original size:36 final size:36
Alignment explanation
Indices: 1026523--1026677 Score: 184
Period size: 36 Copynumber: 4.0 Consensus size: 36
1026513 TCCCCAATCT
1026523 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
* * *
1026559 CCCCATGCATGAACCGATCCTTGGTCGTGCACGATCTCCCCAATCT
1 CCCCATGCATGAACCGATCCTT-G--GT---CG--C-CCCGAGT-G
*
1026605 CCCCATGCATGAACCGATCCTTGGTCACCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1026641 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1026677 C
1 C
1026678 ATGGCACGAT
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 58 0.57
37 6 0.06
38 1 0.01
39 2 0.02
40 1 0.01
42 2 0.02
43 2 0.02
44 1 0.01
45 6 0.06
46 22 0.22
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.21
Consensus pattern (36 bp):
CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
Found at i:1026644 original size:82 final size:86
Alignment explanation
Indices: 1026507--1026735 Score: 340
Period size: 82 Copynumber: 2.6 Consensus size: 86
1026497 CGACCTACAA
1026507 ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGCCCCATGCATGAA
1 ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGCCCCATGCATGAA
1026572 CCGATCCTTGGT-C-G-T-GC
66 CCGATCCTTGGTCCGGATGGC
*
1026589 ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCACCCCGAGTGCCCCATGCATGAA
1 ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGCCCCATGCATGAA
1026654 CCGATCCTTGGTCGCCCCGAGTGCATGGC
66 CCGATCCTTGGT----CC--G-G-ATGGC
*
1026683 ACGATCTCCCCAATCTCCCCATACATGAACCGATCCTTGGTCGCCCCGAGTGC
1 ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGC
1026736 ATGGCGACCT
Statistics
Matches: 132, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
82 76 0.58
87 1 0.01
91 1 0.01
93 1 0.01
94 53 0.40
ACGTcount: A:0.19, C:0.40, G:0.20, T:0.21
Consensus pattern (86 bp):
ACGATCTCCCCAATCTCCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTGCCCCATGCATGAA
CCGATCCTTGGTCCGGATGGC
Found at i:1026680 original size:29 final size:29
Alignment explanation
Indices: 1026646--1026738 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
1026636 GAGTGCCCCA
1026646 TGCATGAACCGATCCTTGGTCGCCCCGAG
1 TGCATGAACCGATCCTTGGTCGCCCCGAG
* **** *
1026675 TGCATG-GCACGATCTCCCCAATCTCCCC-A-
1 TGCATGAAC-CGA--TCCTTGGTCGCCCCGAG
*
1026704 TACATGAACCGATCCTTGGTCGCCCCGAG
1 TGCATGAACCGATCCTTGGTCGCCCCGAG
1026733 TGCATG
1 TGCATG
1026739 GCGACCTCCT
Statistics
Matches: 44, Mismatches: 14, Indels: 12
0.63 0.20 0.17
Matches are distributed among these distances:
27 9 0.20
28 2 0.05
29 22 0.50
30 2 0.05
31 9 0.20
ACGTcount: A:0.19, C:0.37, G:0.23, T:0.22
Consensus pattern (29 bp):
TGCATGAACCGATCCTTGGTCGCCCCGAG
Found at i:1026768 original size:29 final size:29
Alignment explanation
Indices: 1026732--1026811 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
1026722 GTCGCCCCGA
*
1026732 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
* *
1026761 GTGTATGGCGACCTCTTTGGTCGTTGGGT
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
1026790 GTGCATGGCGACCTCTTTGGTC
1 GTGCATGGCGACCTCTTTGGTC
1026812 ACTGTACAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.07, C:0.24, G:0.36, T:0.33
Consensus pattern (29 bp):
GTGCATGGCGACCTCTTTGGTCGTTGGGC
Found at i:1028144 original size:2 final size:2
Alignment explanation
Indices: 1028137--1028163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1028127 CAAGCATCGT
1028137 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 T
1028164 CTATGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1028729 original size:2 final size:2
Alignment explanation
Indices: 1028724--1028794 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
1028714 AATTGATTTG
1028724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1028766 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1028795 TTTTGAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1029669 original size:17 final size:18
Alignment explanation
Indices: 1029647--1029682 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1029637 ACGTTTTGTC
1029647 ATTTTAAATAAAA-AACA
1 ATTTTAAATAAAACAACA
*
1029664 ATTTTAATTAAAACAACA
1 ATTTTAAATAAAACAACA
1029682 A
1 A
1029683 ATTAAGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTTTAAATAAAACAACA
Found at i:1030532 original size:6 final size:6
Alignment explanation
Indices: 1030519--1030557 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1030509 TTTTTAAACT
* *
1030519 AAAATA ATAATA ATAA-A AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1030558 ACCTCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:1030556 original size:17 final size:18
Alignment explanation
Indices: 1030513--1030556 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1030503 ACAAGATTTT
*
1030513 TAAACTAAAATAATAATAA
1 TAAA-TAAAATAAAAATAA
1030532 TAAA-AAAATAAAAATAA
1 TAAATAAAATAAAAATAA
1030549 -AAATAAAA
1 TAAATAAAA
1030557 AACCTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
19 4 0.17
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAATAAAATAAAAATAA
Found at i:1030558 original size:14 final size:14
Alignment explanation
Indices: 1030518--1030551 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1030508 ATTTTTAAAC
* *
1030518 TAAAATAATAATAA
1 TAAAAAAATAAAAA
1030532 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
1030546 TAAAAA
1 TAAAAA
1030552 TAAAAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:1030988 original size:17 final size:17
Alignment explanation
Indices: 1030968--1031003 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1030958 TAAGATATAT
1030968 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
*
1030985 ATATTAAACTAATCCTA
1 ATATTAAACTAAACCTA
1031002 AT
1 AT
1031004 CTACTTCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTAAACTAAACCTA
Found at i:1032201 original size:53 final size:53
Alignment explanation
Indices: 1032134--1032364 Score: 293
Period size: 53 Copynumber: 4.4 Consensus size: 53
1032124 AGGGATTAAG
**** * * *
1032134 GAACTCGAACAATCTTCTAAAAATGGGTTCGTTCCCTATTTCTTCAGGGAGTA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
* ** * *
1032187 GAACTCGAATAATCTTCTGTTTACGGGTTCGCTCCCTCTTACTTCAGGGGGTA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
* *
1032240 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAAGGAGTA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
* *
1032293 AAACTCGAACAATCTTCTGCCTACGGGTTCACTCCCT-TTTGCTTCAGGGAGTA
1 GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTT-CTTCAGGGAGTA
*
1032346 GAACTTGAACAATCTTCTG
1 GAACTCGAACAATCTTCTG
1032365 GTGTGATTCT
Statistics
Matches: 155, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 2 0.01
53 153 0.99
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (53 bp):
GAACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
Found at i:1032810 original size:42 final size:41
Alignment explanation
Indices: 1032735--1032821 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
1032725 TCCGAGAAGG
* * *
1032735 CTTA-AAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAAATGACCCGAAAGACTTATCATCATGCTCGAAAGA
*
1032775 CTTACAAATGACCCGAAAGATTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAAGACTT-ATCATCATGCTCGAAAGA
1032817 CTTAC
1 CTTAC
1032822 TGATGGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 4 0.10
41 15 0.37
42 22 0.54
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (41 bp):
CTTACAAATGACCCGAAAGACTTATCATCATGCTCGAAAGA
Found at i:1032913 original size:80 final size:80
Alignment explanation
Indices: 1032775--1032987 Score: 354
Period size: 80 Copynumber: 2.7 Consensus size: 80
1032765 GCTCGAAAGA
* * *
1032775 CTTACAAATGACCCGAAAGATTTCATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
**
1032840 ACTCTTCGGTGAAGG
66 ACTCTTCCATGAAGG
*
1032855 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
1032920 ACTCTTCCATGAAGG
66 ACTCTTCCATGAAGG
* *
1032935 CTTACAAATTTCCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1032988 CCCGAAGGAC
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 125 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (80 bp):
CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACT
ACTCTTCCATGAAGG
Found at i:1032996 original size:42 final size:42
Alignment explanation
Indices: 1032949--1033173 Score: 173
Period size: 42 Copynumber: 5.1 Consensus size: 42
1032939 CAAATTTCCT
1032949 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
* *
1032991 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTAC
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC-C---C
* * ** * * * ** **
1033037 TGATGGGTTTGCTTCATTACT-CTTCCGTGAAGGCTTACAAATTACCC
1 -GAAGGATTT-AATCATCA-TGC-T-CG-AAAGACTTACTGATGGCCC
* * *
1033084 TAATGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
* * * *
1033126 TAAAGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCC
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1033168 GAAGGA
1 GAAGGA
1033174 CTTACTAAGT
Statistics
Matches: 139, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
42 93 0.67
43 3 0.02
44 2 0.01
45 6 0.04
46 5 0.04
47 7 0.05
48 7 0.05
49 2 0.01
50 3 0.02
51 11 0.08
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (42 bp):
GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
Found at i:1032998 original size:20 final size:20
Alignment explanation
Indices: 1032970--1033030 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1032960 TCATCATGCT
1032970 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
1032990 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
1033012 CGAAAGACTTACTGATGGC
1 CGAAAGACTTACTGATGGC
1033031 ACTTACTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 2 0.06
22 12 0.38
23 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:1033020 original size:22 final size:21
Alignment explanation
Indices: 1032959--1033022 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1032949 GAAGGATTTA
1032959 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1032980 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1033000 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1033022 A
1 A
1033023 CTGATGGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1033036 original size:13 final size:13
Alignment explanation
Indices: 1033018--1033042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1033008 TGCTCGAAAG
1033018 ACTTACTGATGGC
1 ACTTACTGATGGC
1033031 ACTTACTGATGG
1 ACTTACTGATGG
1033043 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1033142 original size:135 final size:135
Alignment explanation
Indices: 1032896--1033165 Score: 425
Period size: 135 Copynumber: 2.0 Consensus size: 135
1032886 TGCTCGAAAG
* *
1032896 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTTCCTGAAGGATTTAAT
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTCCCTGAAGGACTTAAT
* * *
1032961 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTAAGCATCATGCTCGAAAGACTTACTG
1033026 ATGGC
131 ATGGC
* * *
1033031 ACTTACTGATGGGTTTGCTTCATTACTCTTCCGTGAAGGCTTACAAATTACCCT-AATGACTTAA
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATT-CCCTGAAGGACTTAA
* * *
1033095 TCATCATGCTCGAAAGACTTACTGATGGCCCTAAAGATTTAAGCATCATGCTCGAAAGACTTATT
65 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTAAGCATCATGCTCGAAAGACTTACT
1033160 GATGGC
130 GATGGC
1033166 CCGAAGGACT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
135 120 0.98
136 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (135 bp):
ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTCCCTGAAGGACTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTAAGCATCATGCTCGAAAGACTTACTG
ATGGC
Found at i:1039475 original size:6 final size:6
Alignment explanation
Indices: 1039460--1039495 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1039450 AGCTAATAAG
*
1039460 AATGCA AATGCG AATGCA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
1039496 CAAGGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:1042044 original size:11 final size:12
Alignment explanation
Indices: 1042022--1042054 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1042012 TTTTTAAACT
*
1042022 AAAATAATAATA
1 AAAATAAAAATA
1042034 AAAA-AAAAATA
1 AAAATAAAAATA
1042045 AAAATAAAAA
1 AAAATAAAAA
1042055 ACCTCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:1042044 original size:17 final size:17
Alignment explanation
Indices: 1042022--1042055 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1042012 TTTTTAAACT
*
1042022 AAAATAATAATAAAAAA
1 AAAATAAAAATAAAAAA
1042039 AAAATAAAAATAAAAAA
1 AAAATAAAAATAAAAAA
1042056 CCTCATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATAAAAAA
Found at i:1042489 original size:17 final size:17
Alignment explanation
Indices: 1042467--1042502 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1042457 AGATATATAT
1042467 ATATTAAACTAAACCTA
1 ATATTAAACTAAACCTA
*
1042484 ATATTAAACTAATCCTA
1 ATATTAAACTAAACCTA
1042501 AT
1 AT
1042503 CTACTTCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTAAACTAAACCTA
Found at i:1043638 original size:25 final size:25
Alignment explanation
Indices: 1043601--1043648 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1043591 GTTTTATTAA
1043601 AAATTATAAGAGGTGCGAAATTATT
1 AAATTATAAGAGGTGCGAAATTATT
* * *
1043626 AAATTTTAGGAGGTGTGAAATTA
1 AAATTATAAGAGGTGCGAAATTA
1043649 GATAATCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (25 bp):
AAATTATAAGAGGTGCGAAATTATT
Found at i:1044480 original size:21 final size:21
Alignment explanation
Indices: 1044454--1044493 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1044444 GGCTAGGCTT
*
1044454 TCAGGTTGTTCATTTGGTCCA
1 TCAGGTTGTTCATTCGGTCCA
1044475 TCAGGTTGTTCATTCGGTC
1 TCAGGTTGTTCATTCGGTC
1044494 TCAGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.42
Consensus pattern (21 bp):
TCAGGTTGTTCATTCGGTCCA
Found at i:1045152 original size:32 final size:32
Alignment explanation
Indices: 1045116--1045192 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
1045106 ACAAAGTTTA
*
1045116 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
1045148 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
1045181 CGATAATTGAAA
1 CGATAATTGAAA
1045193 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:1045206 original size:21 final size:21
Alignment explanation
Indices: 1045181--1045222 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1045171 CTTCCAAGTT
1045181 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1045202 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1045223 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1049697 original size:27 final size:27
Alignment explanation
Indices: 1049663--1049714 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1049653 TCCAACCATA
1049663 TTGACATTCTGATGGAGCCTTGAATAT
1 TTGACATTCTGATGGAGCCTTGAATAT
1049690 TTGACATTCTGATGGAGCCTTGAAT
1 TTGACATTCTGATGGAGCCTTGAAT
1049715 CAACCTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (27 bp):
TTGACATTCTGATGGAGCCTTGAATAT
Found at i:1059920 original size:18 final size:17
Alignment explanation
Indices: 1059899--1059952 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1059889 AAAGTCAGCA
*
1059899 AGTTCATTAAATAAAGTT
1 AGTTCATTAAATAAA-CT
* *
1059917 AGTTCATTGATTAAACT
1 AGTTCATTAAATAAACT
1059934 AGTTCATT-AATCAAACT
1 AGTTCATTAAAT-AAACT
1059951 AG
1 AG
1059953 CTCTTATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 2 0.06
17 16 0.52
18 13 0.42
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
AGTTCATTAAATAAACT
Found at i:1063818 original size:33 final size:33
Alignment explanation
Indices: 1063764--1063841 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1063754 CGAAATTCCC
1063764 AACTTATAAAAG--TTTTTTTTTTTGGATAAAT
1 AACTTATAAAAGTTTTTTTTTTTTTGGATAAAT
1063795 AACTTATAAAAGTTTTTTTTTTTTTGGATAAAT
1 AACTTATAAAAGTTTTTTTTTTTTTGGATAAAT
1063828 AACTTATAAAAGTT
1 AACTTATAAAAGTT
1063842 GCTGGCGCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 12 0.27
33 33 0.73
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (33 bp):
AACTTATAAAAGTTTTTTTTTTTTTGGATAAAT
Found at i:1067869 original size:21 final size:22
Alignment explanation
Indices: 1067843--1067894 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1067833 AATTCAGAAC
1067843 TTTAAAATTCCTC-TTATAAT-T
1 TTTAAAATTCCTCATTA-AATCT
*
1067864 TTTAAAATTTCTCATTAAATCT
1 TTTAAAATTCCTCATTAAATCT
*
1067886 CTTAAAATT
1 TTTAAAATT
1067895 TTAGTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAAATTCCTCATTAAATCT
Found at i:1069149 original size:18 final size:16
Alignment explanation
Indices: 1069116--1069166 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 16
1069106 GAAAAAAACG
1069116 AAATAAAAACAATTAAAT
1 AAAT-AAAA-AATTAAAT
1069134 ATATATAAAAAATTAAAT
1 A-A-ATAAAAAATTAAAT
1069152 AAAT-AAAAATTAAAT
1 AAATAAAAAATTAAAT
1069167 TTTGAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 1 0.03
18 10 0.32
19 5 0.16
20 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAAAAATTAAAT
Found at i:1072094 original size:84 final size:84
Alignment explanation
Indices: 1071153--1072094 Score: 1068
Period size: 84 Copynumber: 11.3 Consensus size: 84
1071143 CTGAATGAAA
* * * * * * * *
1071153 TCGAACTCGAAGGTC-TTTGATGACAAATAACCCTTCTCGCCTTGAGTTATGTTGTAAATAATGC
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * * ** *
1071217 ACATTTGAGATGAATGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * ** * * *
1071236 TCGAACTCGAAGATCTTTGGTTGGCAGATAACCCTTATAATCTTGAGTTATGCTACAAATAATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
1071301 GCCTTTGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
1071320 TCAAACCCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGATATGTTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * *
1071385 TCCTTGGAGTTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
1071404 TCAAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
1071469 GCCTTGGAGCTGAGCGTGG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
1071488 TCGAACTCGAAGGTCTTTTGGTGGCAGATAGCTCTTCTAGCCTTGAGCTAT-TTTCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
1071552 GCCTTGGTGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
1071571 TCGAACTCGAAGGTCTTTTGTTGGTATATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * *
1071636 GACTTTGAGCTGAGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * * *
1071655 TCGAACTGGAAGGTC---T-TTGGTAGATAACCCTTCTAGCCTTGAGCTAAGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
1071716 GCCTTGTAGCTAAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * *
1071735 TCAAACTTGAAGGTCTTTTGTTGGTAGATAACCCTTCTAGCCTTAAGTTATGTTGCAAATAATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
1071800 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * ** * *
1071819 TCAAACTTGAAGGTCTTTTGTTGGCAAATAACCTTTCTTTCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
1071884 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
1071903 TCAAACTCGAAGGTCTTTTGTCGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
*
1071968 GCCTTGGAGCTGAGTGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
1071987 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCAAGCCTTGAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
1072052 GCCTTTGAGTTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
1072071 TCGAACTCGAAAGTATTTTGTTGG
1 TCGAACTCGAAGGTCTTTTGTTGG
1072095 AAAATATCCC
Statistics
Matches: 725, Mismatches: 128, Indels: 11
0.84 0.15 0.01
Matches are distributed among these distances:
80 68 0.09
81 1 0.00
83 87 0.12
84 569 0.78
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:1072385 original size:124 final size:124
Alignment explanation
Indices: 1072140--1072649 Score: 678
Period size: 124 Copynumber: 4.2 Consensus size: 124
1072130 ATATCATTCG
* *
1072140 TCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATGGGATATCCTTC
1 TCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
* ** ** * *
1072205 GTCATGAAGTTGAAATCCAATCCGAAGATGAATGTTACTGGTGGGCACGATACCCTTCA
66 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
* **
1072264 TCGTGAATTTGAAACCGTGGATGGCCCATTTTTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
1 TCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
* * * *
1072329 GTCGTGAAGTTGAAATCCAATCTAAAGATGATTGTTGTTGATGAGCAAGATTCCCTTCG
66 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
* * * * * *
1072388 TCGTGAAGTTTAAACCGTGGAT-GACCTTTCGTTATGAAGTTGAGCCTTGAATTGAATATCATTC
1 TCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
1072452 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
66 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
* * *
1072511 TTGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTT
1 TCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
* * * *
1072576 ATCGTGAAGTTGAAAT-C---C---A-ATGAATGTTGCTGGTGAGCACAATTCCCTTCG
66 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
**
1072627 TCGTGAAGTTGAAATTGTGGATG
1 TCGTGAAGTTGAAACCGTGGATG
1072650 TGGGTACAAT
Statistics
Matches: 340, Mismatches: 45, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
116 49 0.14
117 1 0.00
120 1 0.00
123 111 0.33
124 178 0.52
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (124 bp):
TCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTC
GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCA
Found at i:1072573 original size:247 final size:248
Alignment explanation
Indices: 1072136--1072596 Score: 726
Period size: 247 Copynumber: 1.9 Consensus size: 248
1072126 CATGATATCA
* * *
1072136 TTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATGGGATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGCCTTGAATGGAATATC
* * *
1072201 CTTCGTCATGAAGTTGAAATCCAATCCGAAGATGAATGTTACTGGTGGGCACGATACCCTTCATC
66 ATTCGTCATGAAGTTGAAATCCAATCCAAAGATGAATGTTACTGGTGAGCACGATACCCTTCATC
* ** * *
1072266 GTGAATTTGAAACCGTGGATGGCCCATTTTTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT
131 GTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTCAT
1072331 CGTGAAGTTGAAATCCAATCTAAAGATGATTGTTGTTGATGAGCAAGATTCCC
196 CGTGAAGTTGAAATCCAATCTAAAGATGATTGTTGTTGATGAGCAAGATTCCC
* * *
1072384 TTCGTCGTGAAGTTTAAACCGTGGAT-GACCTTTCGTTATGAAGTTGAGCCTTGAATTGAATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGCCTTGAATGGAATATC
* * ** * *
1072448 ATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGAGCACGATTCCCTTCATT
66 ATTCGTCATGAAGTTGAAATCCAATCCAAAGATGAATGTTACTGGTGAGCACGATACCCTTCATC
*
1072513 GTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTTAT
131 GTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTCAT
1072578 CGTGAAGTTGAAATCCAAT
196 CGTGAAGTTGAAATCCAAT
1072597 GAATGTTGCT
Statistics
Matches: 192, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
247 167 0.87
248 25 0.13
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (248 bp):
TTCGTCGTGAAGTTGAAACCGTGGATGGACCCTTCGTTATGAAGTTGAGCCTTGAATGGAATATC
ATTCGTCATGAAGTTGAAATCCAATCCAAAGATGAATGTTACTGGTGAGCACGATACCCTTCATC
GTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTAAGCCTTGAATTGGATATCCTTCAT
CGTGAAGTTGAAATCCAATCTAAAGATGATTGTTGTTGATGAGCAAGATTCCC
Done.