Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008206.1 Hibiscus syriacus cultivar Beakdansim tig00110828_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: 1504526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1035780 original size:12 final size:12
Alignment explanation
Indices: 1035763--1035787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1035753 ATATAATCCT
1035763 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1035775 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1035787 G
1 G
1035788 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1038155 original size:19 final size:19
Alignment explanation
Indices: 1038115--1038179 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
1038105 GATTCTCTCG
1038115 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1038135 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1038154 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1038173 TTGCGAT
1 TTGCGAT
1038180 AGTCAATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1038307 original size:14 final size:14
Alignment explanation
Indices: 1038288--1038322 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1038278 TCAATTACAG
1038288 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
1038302 AAATCATCTTTTAC
1 AAATCAACTTTTAC
1038316 AAATCAA
1 AAATCAA
1038323 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:1040324 original size:33 final size:33
Alignment explanation
Indices: 1040278--1040370 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1040268 GCGAAACCAA
* *
1040278 AATCGCAACGCGAAATGAAAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1040311 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1040344 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1040371 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1040335 original size:19 final size:19
Alignment explanation
Indices: 1040241--1040375 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1040231 TAGTTTACTT
* *
1040241 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1040261 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1040280 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1040299 TCGCAA--CGACAT---AA
1 TCGCAACGCGAAATGAAAA
*
1040313 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1040332 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1040346 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1040365 TCGCAATGCGA
1 TCGCAACGCGA
1040376 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1040349 original size:14 final size:14
Alignment explanation
Indices: 1040297--1040353 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1040287 GCGAAATGAA
* *
1040297 AATCGCAACGACAT
1 AATCGCAACGAAAG
1040311 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1040328 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1040344 AATCGCAACG
1 AATCGCAACG
1040354 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1040393 original size:19 final size:19
Alignment explanation
Indices: 1040371--1040499 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
1040361 AAAATCGCAA
1040371 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1040390 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
1040404 TGCGATTATGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1040423 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1040437 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1040456 TGTGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1040475 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1040495 TGCGA
1 TGCGA
1040500 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1040416 original size:33 final size:33
Alignment explanation
Indices: 1040371--1040462 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
1040361 AAAATCGCAA
1040371 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
1040404 TGCGATTATGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1040437 TGCGATTTTCATTTCGCGTTGTGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1040463 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 51 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1040702 original size:93 final size:93
Alignment explanation
Indices: 1040543--1040923 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
1040533 TTGAATGGAT
1040543 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1040608 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1040636 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1040701 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1040729 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1040794 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1040822 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
1040887 AGTTTAGCAGAATTAGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1040915 AAATTTACT
1 AAATTTACT
1040924 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1042644 original size:14 final size:14
Alignment explanation
Indices: 1042625--1042714 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1042615 TTGAAATGAA
1042625 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1042639 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1042656 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1042672 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1042691 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1042705 AATCGCAACG
1 AATCGCAACG
1042715 CGAAATAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1042662 original size:33 final size:33
Alignment explanation
Indices: 1042617--1042731 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1042607 TCTTTTGGTT
1042617 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1042650 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1042683 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1042716 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
1042732 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1042663 original size:19 final size:18
Alignment explanation
Indices: 1042624--1042736 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
1042614 GTTGAAATGA
1042624 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1042639 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1042656 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1042672 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1042689 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
1042705 -AATCGCAACGCGAAATAA
1 AAATCGCAACGCGAGAT-G
*
1042723 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1042737 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
14 24 0.31
16 15 0.19
17 11 0.14
19 28 0.36
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1042805 original size:20 final size:19
Alignment explanation
Indices: 1042755--1042807 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
1042745 TCGCGTTGCG
**
1042755 ATTCTCTCGTTGCGATTTC
1 ATTCTCTCGTTGCGAAGTC
*
1042774 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGA-AGTC
1042793 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
1042808 TTTTCATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 10 0.36
19 8 0.29
20 10 0.36
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (19 bp):
ATTCTCTCGTTGCGAAGTC
Found at i:1042814 original size:20 final size:19
Alignment explanation
Indices: 1042755--1042828 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1042745 TCGCGTTGCG
1042755 ATTCTCTCGTTGCGATTTC
1 ATTCTCTCGTTGCGATTTC
* **
1042774 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGA-TTTC
1042793 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGA-TTTC
*
1042813 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1042829 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 10 0.23
19 8 0.18
20 13 0.30
21 13 0.30
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
ATTCTCTCGTTGCGATTTC
Found at i:1042950 original size:33 final size:33
Alignment explanation
Indices: 1042908--1042978 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1042898 AATACTAACT
1042908 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1042941 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1042974 TGAAA
1 TGAAA
1042979 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1043211 original size:22 final size:22
Alignment explanation
Indices: 1043159--1043213 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1043149 TGGTTGTGAG
**
1043159 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1043181 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1043203 GGATTTCTTCG
1 GGATTTCTTCG
1043214 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:1043384 original size:20 final size:20
Alignment explanation
Indices: 1043359--1043552 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1043349 CTTTAAATAT
1043359 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1043379 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1043401 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1043420 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1043440 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1043460 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1043480 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1043500 CGCGTTGTGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1043520 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1043540 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1043553 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1043546 original size:60 final size:60
Alignment explanation
Indices: 1043359--1043552 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1043349 CTTTAAATAT
**
1043359 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1043420 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
1043480 CACGTTGCGATTTACGGATACGCGTTGTGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1043540 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1043553 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 22, 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:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1043569 original size:21 final size:21
Alignment explanation
Indices: 1043539--1043621 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1043529 ATTTTCATAT
*
1043539 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1043560 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1043581 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
1043602 TCGCGTTGTGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1043622 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1056056 original size:57 final size:58
Alignment explanation
Indices: 1055989--1056097 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 58
1055979 CTAGTGGAAA
1055989 TACCTAATTTTCCAATATTCAATGAGCA-TTACCT-ATTTTCCAATATTCAATGAGTAT
1 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATA-TCAATGAGTAT
*
1056046 TACCTAATTTTTCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAAT
1 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAAT
1056098 ATTCAATGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
57 27 0.55
58 11 0.22
59 11 0.22
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (58 bp):
TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAATGAGTAT
Found at i:1056065 original size:29 final size:29
Alignment explanation
Indices: 1055989--1056097 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
1055979 CTAGTGGAAA
1055989 TACCTAATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
1056018 TACCT-ATTTTCCAATATTCAATGAGTAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
1056046 TACCTAATTTTTCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
1056076 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
1056098 ATTCAATGAA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
28 27 0.36
29 30 0.41
30 17 0.23
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:1056691 original size:31 final size:31
Alignment explanation
Indices: 1056656--1056714 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1056646 AATTCGGTGA
1056656 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
*
1056687 ATTCAATATGTCCTTCTCACTAGGAACT
1 ATTCAATATGTCATTCTCACTAGGAACT
1056715 TCTTGGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:1061398 original size:57 final size:58
Alignment explanation
Indices: 1061334--1061467 Score: 218
Period size: 57 Copynumber: 2.3 Consensus size: 58
1061324 CTAGTGGAAA
*
1061334 TACCTAATTTTCCAATATTAAATGAGCATTACC-AATTTTCCAATATTCAATGA-ATAT
1 TACCTAATTTTCCAATATTAAATGAACATTACCTAATTTTCCAATATTCAATGACAT-T
*
1061391 TACCTAATTTTCCAATATTCAATGAACATTACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTAAATGAACATTACCTAATTTTCCAATATTCAATGA-CATT
1061450 TACCTAATTTTCCAATAT
1 TACCTAATTTTCCAATAT
1061468 CAATATTCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
57 31 0.43
58 20 0.28
59 19 0.26
60 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (58 bp):
TACCTAATTTTCCAATATTAAATGAACATTACCTAATTTTCCAATATTCAATGACATT
Found at i:1061408 original size:29 final size:29
Alignment explanation
Indices: 1061334--1061471 Score: 217
Period size: 29 Copynumber: 4.8 Consensus size: 29
1061324 CTAGTGGAAA
* *
1061334 TACCTAATTTTCCAATATTAAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAACAT
*
1061363 TACC-AATTTTCCAATATTCAATGAATAT
1 TACCTAATTTTCCAATATTCAATGAACAT
1061391 TACCTAATTTTCCAATATTCAATGAACAT
1 TACCTAATTTTCCAATATTCAATGAACAT
*
1061420 TACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAACA-T
1061450 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
1061472 ATTCAATGAG
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
28 25 0.25
29 59 0.58
30 18 0.18
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAACAT
Found at i:1062382 original size:27 final size:28
Alignment explanation
Indices: 1062326--1062389 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1062316 TAGATTTAAA
*
1062326 ATAAATAAAAATAAAATTAACATAATTTT
1 ATAAA-AAAAATAAAATTAACATAACTTT
*
1062355 ATAAAAAAAA-AATATTAACACT-ACTTT
1 ATAAAAAAAATAAAATTAACA-TAACTTT
*
1062382 AGAAAAAA
1 ATAAAAAA
1062390 TTAACATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 20 0.65
28 6 0.19
29 5 0.16
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (28 bp):
ATAAAAAAAATAAAATTAACATAACTTT
Found at i:1065980 original size:2 final size:2
Alignment explanation
Indices: 1065973--1066016 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1065963 ACTTAAAATA
1065973 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
1066015 AT
1 AT
1066017 TCCAAAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1067614 original size:18 final size:19
Alignment explanation
Indices: 1067571--1067625 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
1067561 GGATATACAA
1067571 TGGTCCTTCGGGACATACACAG
1 TGGTCCTTCGGGACAT--A-AG
1067593 TGGTCCTTCGGGACAT-AG
1 TGGTCCTTCGGGACATAAG
*
1067611 TGGTCTTTCGGGACA
1 TGGTCCTTCGGGACA
1067626 AATATTCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (19 bp):
TGGTCCTTCGGGACATAAG
Found at i:1068280 original size:10 final size:10
Alignment explanation
Indices: 1068248--1068298 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 10
1068238 ACTGTAGCAC
1068248 TGTTCATTAT
1 TGTTCATTAT
*
1068258 TGTTTATGGTAT
1 TGTTCAT--TAT
1068270 TGTTCATTAT
1 TGTTCATTAT
1068280 TGTTCACATTAT
1 TGTT--CATTAT
1068292 TGTTCAT
1 TGTTCAT
1068299 ACCTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 16 0.46
12 19 0.54
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (10 bp):
TGTTCATTAT
Found at i:1068292 original size:22 final size:22
Alignment explanation
Indices: 1068248--1068298 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1068238 ACTGTAGCAC
* **
1068248 TGTTCATTATTGTTTATGGTAT
1 TGTTCATTATTGTTCACAGTAT
*
1068270 TGTTCATTATTGTTCACATTAT
1 TGTTCATTATTGTTCACAGTAT
1068292 TGTTCAT
1 TGTTCAT
1068299 ACCTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (22 bp):
TGTTCATTATTGTTCACAGTAT
Found at i:1069237 original size:12 final size:12
Alignment explanation
Indices: 1069205--1069239 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1069195 GTAAGACTTT
*
1069205 TTCTTTCTCTTC
1 TTCTTTCTTTTC
1069217 TTCTTTCTTTTC
1 TTCTTTCTTTTC
*
1069229 TTTTTTCTTTT
1 TTCTTTCTTTT
1069240 ACCCTGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTCTTTTC
Found at i:1069509 original size:2 final size:2
Alignment explanation
Indices: 1069502--1069665 Score: 328
Period size: 2 Copynumber: 82.0 Consensus size: 2
1069492 AAAAGATAAC
1069502 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1069544 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1069586 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1069628 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1069666 ATGTATGTAT
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 162 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1085308 original size:34 final size:34
Alignment explanation
Indices: 1085265--1085334 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1085255 GCATCCAAAC
*
1085265 AATGTAATTGGTTTTCTGGAATTTGTTTTTCAGA
1 AATGTAATTGGTTTTCTGGAATTGGTTTTTCAGA
1085299 AATGTAATTGGTTTTCTGGAATTGGTTTTTCAGA
1 AATGTAATTGGTTTTCTGGAATTGGTTTTTCAGA
1085333 AA
1 AA
1085335 ATCAATTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (34 bp):
AATGTAATTGGTTTTCTGGAATTGGTTTTTCAGA
Found at i:1086196 original size:136 final size:135
Alignment explanation
Indices: 1085936--1086210 Score: 505
Period size: 136 Copynumber: 2.0 Consensus size: 135
1085926 TTTGAACACT
1085936 TATTTTTTACTTTAAACCTTAAATTAATTTTATTAATTGCCACTGCAATTCTTCCATAAGATGTT
1 TATTTTTTACTTTAAACCTTAAATTAATTTTATTAATTGCCACTGCAATTCTTCCATAAGATGTT
1086001 AATAATAATTAGATTAATTGATATCATTTCATAATTTAGAGATTGGAAAAATTAAAAAAAATGAC
66 AATAATAATTAGATTAATTGATATCATTTCATAATTTAGAGATTGGAAAAATT-AAAAAAATGAC
1086066 GGTAAA
130 GGTAAA
1086072 TATTTTTTACTTTAAACCTTAAATTAATTTTATTAATTGCCACTGCAATTCTTCCATAAGATGTT
1 TATTTTTTACTTTAAACCTTAAATTAATTTTATTAATTGCCACTGCAATTCTTCCATAAGATGTT
1086137 AATAATAATTAGATTAATTGATATCATTTCAATAATTTAGAGGATTGGAAAAATTAAAAAAAAAT
66 AATAATAATTAGATTAATTGATATCATTTC-ATAATTTAGA-GATTGGAAAAATT--AAAAAAAT
1086202 GACGGTAAA
127 GACGGTAAA
1086211 GATTATAATC
Statistics
Matches: 136, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
136 95 0.70
137 10 0.07
138 13 0.10
139 18 0.13
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (135 bp):
TATTTTTTACTTTAAACCTTAAATTAATTTTATTAATTGCCACTGCAATTCTTCCATAAGATGTT
AATAATAATTAGATTAATTGATATCATTTCATAATTTAGAGATTGGAAAAATTAAAAAAATGACG
GTAAA
Found at i:1087817 original size:2 final size:2
Alignment explanation
Indices: 1087810--1087848 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1087800 ATATTATGAA
1087810 AT 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 AT A
1087849 GAAGCAACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1096305 original size:151 final size:146
Alignment explanation
Indices: 1096021--1096312 Score: 530
Period size: 151 Copynumber: 2.0 Consensus size: 146
1096011 GGATACTTAT
1096021 GCGAGCGATGAAGTGAAAGCTTGCATCCCACCCCACCTTAGTGGGTCATTAGAGGTATGGATGGT
1 GCGAGCGATGAAGTGAAAGCTTGCATCCCACCCCACCTTAGTGGGTCATTAGAGGTATGGATGGT
*
1096086 ATACTCTTATATGTATGCTATTATTGAGTGGCATCCAGTTGATCGCGTGCTCCGTCAGTATGGTT
66 ATACCCTTATATGTATGCTATTATTGAGTGGCATCCAGTTGATCGCGTGCTCCGTCAGTATGGTT
1096151 GTACGCAATATTCCTG
131 GTACGCAATATTCCTG
1096167 GCGAGCGATGAAGTGAAAGCTTGCATCCCACCCCACCTTAGTGGGTCATTAGAGGTATGGATATC
1 GCGAGCGATGAAGTGAAAGCTTGCATCCCACCCCACCTTAGTGGGTCATTAGAGGTATGG--AT-
1096232 GGTTATACCCTTATATGTTATGCTATTATTGAGTGGCATCCAGTTGATCGCGTGCTCCGTCAGTA
63 GG-TATACCCTTATATG-TATGCTATTATTGAGTGGCATCCAGTTGATCGCGTGCTCCGTCAGTA
1096297 TGGTTGTACGCAATAT
126 TGGTTGTACGCAATAT
1096313 ATTCCTGGAG
Statistics
Matches: 140, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
146 60 0.43
148 2 0.01
149 2 0.01
150 13 0.09
151 63 0.45
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (146 bp):
GCGAGCGATGAAGTGAAAGCTTGCATCCCACCCCACCTTAGTGGGTCATTAGAGGTATGGATGGT
ATACCCTTATATGTATGCTATTATTGAGTGGCATCCAGTTGATCGCGTGCTCCGTCAGTATGGTT
GTACGCAATATTCCTG
Found at i:1096760 original size:21 final size:21
Alignment explanation
Indices: 1096734--1096827 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1096724 TATGCCATCT
* *
1096734 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
1096755 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1096776 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1096797 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1096818 CCGCAGGGTT
1 CCGCAGGGTT
1096828 TTACCATATG
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1097401 original size:33 final size:34
Alignment explanation
Indices: 1097342--1097438 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1097332 AAATGTTTTT
*
1097342 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1097376 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1097409 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1097439 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1097445 original size:34 final size:33
Alignment explanation
Indices: 1097340--1097445 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1097330 ATAAATGTTT
*
1097340 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1097374 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1097406 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1097441 TTAAA
1 TTAAA
1097446 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1098053 original size:128 final size:128
Alignment explanation
Indices: 1097822--1098201 Score: 670
Period size: 128 Copynumber: 3.0 Consensus size: 128
1097812 AGTTATTCAA
* *
1097822 ACTGATATATTTAGTGTCCCCGAGGGACATGAGTGACATAATAGAGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
**
1097887 GACGAAATAATGGAAGGCGCACCCCCGGGAACATGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
1097950 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
1098015 GACGAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGGT
66 GACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
* *
1098078 ACTGATATATCTAGTGTCCCCGAGGGACATAAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
1098143 GACGAAATAATGGAAAGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAAT
66 GACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAAT
1098202 GGAAGTCGAT
Statistics
Matches: 241, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 241 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:1105688 original size:35 final size:39
Alignment explanation
Indices: 1105636--1105715 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 39
1105626 TATAATTTTA
1105636 AATACAACAAACTTACAATAA-G-TATTAAATGGTAAAT
1 AATACAACAAACTTACAATAACGATATTAAATGGTAAAT
1105673 AATA-AACAAA-TTACAATAACTGATATTAAATGGT-AAT
1 AATACAACAAACTTACAATAAC-GATATTAAATGGTAAAT
1105710 AA-ACAA
1 AATACAA
1105716 AATTAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
35 9 0.23
36 7 0.18
37 12 0.31
38 11 0.28
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (39 bp):
AATACAACAAACTTACAATAACGATATTAAATGGTAAAT
Found at i:1105719 original size:35 final size:33
Alignment explanation
Indices: 1105634--1105720 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 33
1105624 AATATAATTT
*
1105634 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATA-AACAAAATTACAATAAGTATTAAATGG
*
1105668 TAAATAATAAACAAATTACAATAACTGATATTAAATGG
1 TAAATAA-ACA-AAATTACAATAA--G-TATTAAATGG
1105706 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
1105721 ACAAAATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
33 1 0.02
34 8 0.18
35 17 0.38
36 2 0.04
37 6 0.13
38 11 0.24
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (33 bp):
TAAATAAACAAAATTACAATAAGTATTAAATGG
Found at i:1105725 original size:9 final size:9
Alignment explanation
Indices: 1105711--1105770 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
1105701 AATGGTAATA
1105711 AACAAAATT
1 AACAAAATT
1105720 AACAAAATT
1 AACAAAATT
1105729 AACAAAA-T
1 AACAAAATT
1105737 ----AAATT
1 AACAAAATT
1105742 AACAAAAATT
1 AAC-AAAATT
1105752 CCAACAAAATT
1 --AACAAAATT
1105763 AACAAAAT
1 AACAAAAT
1105771 AAATTAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
4 3 0.07
5 1 0.02
8 1 0.02
9 24 0.56
10 5 0.12
11 6 0.14
12 3 0.07
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (9 bp):
AACAAAATT
Found at i:1105742 original size:13 final size:12
Alignment explanation
Indices: 1105723--1105777 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 12
1105713 CAAAATTAAC
1105723 AAAATTAACAAA
1 AAAATTAACAAA
1105735 ATAAATTAAC--A
1 A-AAATTAACAAA
* *
1105746 AAAATT-CCAAC
1 AAAATTAACAAA
1105757 AAAATTAACAAA
1 AAAATTAACAAA
1105769 ATAAATTAA
1 A-AAATTAA
1105778 GTATTAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
9 1 0.03
10 5 0.15
11 8 0.24
12 5 0.15
13 15 0.44
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATTAACAAA
Found at i:1106000 original size:3 final size:3
Alignment explanation
Indices: 1105951--1105982 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1105941 CTCCTCACTG
*
1105951 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1105983 GTCGTCGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:1108089 original size:17 final size:18
Alignment explanation
Indices: 1108057--1108090 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1108047 TAGTTAAATA
1108057 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
1108075 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
1108091 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:1109100 original size:48 final size:49
Alignment explanation
Indices: 1109047--1109145 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
1109037 AACAATTAAC
1109047 TCAATTAACACTATAATT-T-TAAAAAAATGTACCTAATCATCATTCAAT
1 TCAATTAACACTAT-ATTGTATAAAAAAATGTACCTAATCATCATTCAAT
** * * *
1109095 TCAATTAACACTATATTGTATTTAAAAATTTACTTAATTATCATTCAAT
1 TCAATTAACACTATATTGTATAAAAAAATGTACCTAATCATCATTCAAT
1109144 TC
1 TC
1109146 GATAGAAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
47 3 0.07
48 15 0.34
49 26 0.59
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.40
Consensus pattern (49 bp):
TCAATTAACACTATATTGTATAAAAAAATGTACCTAATCATCATTCAAT
Found at i:1113786 original size:23 final size:23
Alignment explanation
Indices: 1113760--1113808 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1113750 TTCATTTAGC
1113760 GTTCGTTTAATGA-TCACGAACGT
1 GTTCGTTTAAT-ATTCACGAACGT
*
1113783 GTTCGTTTAATATTCACGAATGT
1 GTTCGTTTAATATTCACGAACGT
1113806 GTT
1 GTT
1113809 TATAAATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (23 bp):
GTTCGTTTAATATTCACGAACGT
Found at i:1113881 original size:22 final size:22
Alignment explanation
Indices: 1113816--1113875 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1113806 GTTTATAAAT
*
1113816 ATGTTCGTTTAGCGTT-CATATA
1 ATGTTCGTTTAGCGTTGC-TTTA
*
1113838 GTGTTCGTTTAGCGTTGCTTTA
1 ATGTTCGTTTAGCGTTGCTTTA
* *
1113860 ATGTTTGTTTATCGTT
1 ATGTTCGTTTAGCGTT
1113876 TGTTTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.15, C:0.12, G:0.22, T:0.52
Consensus pattern (22 bp):
ATGTTCGTTTAGCGTTGCTTTA
Found at i:1114114 original size:28 final size:28
Alignment explanation
Indices: 1114079--1114143 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
1114069 TGTTCATGAA
*
1114079 CATAAATGAACGAGTTGATAAACGAGCT
1 CATAAATGAACGAGTTGATAAACGAACT
1114107 CATAAATGAACGAGTTGATAAACGAACT
1 CATAAATGAACGAGTTGATAAACGAACT
1114135 CATAAATGA
1 CATAAATGA
1114144 GCTTGTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (28 bp):
CATAAATGAACGAGTTGATAAACGAACT
Found at i:1114127 original size:16 final size:16
Alignment explanation
Indices: 1114080--1114133 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1114070 GTTCATGAAC
1114080 ATAAATGAACGAGTTG
1 ATAAATGAACGAGTTG
* *
1114096 AT--A--AACGAGCTC
1 ATAAATGAACGAGTTG
1114108 ATAAATGAACGAGTTG
1 ATAAATGAACGAGTTG
*
1114124 ATAAACGAAC
1 ATAAATGAAC
1114134 TCATAAATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 9 0.31
14 2 0.07
16 18 0.62
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.20
Consensus pattern (16 bp):
ATAAATGAACGAGTTG
Found at i:1122415 original size:259 final size:258
Alignment explanation
Indices: 1121905--1122486 Score: 805
Period size: 259 Copynumber: 2.2 Consensus size: 258
1121895 ATTTTTATTT
* * ***
1121905 AATATATAAATTAGAAACCCGA-CAGATATAAAATAATAAAAAAATTATTTTTATTCAATAAAAA
1 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAA-TATTTTTATTCAATAAAAA
* * *
1121969 TATTGACTTAATTGAAAAAATTTATATATAGAGGGGTATTATTGTAATTATTCATAAATCTATAA
65 TAGTGACTTAATTGAAAAAATTTATATAGAGAGGGGTATTATTGTAATTATTCATAAATATATAA
* *
1122034 GGTAAAATTATAAAAGAAAAATTTGAGTCGGTTCGGTTTTTTTCACCCTAAACCCAAACTCAACC
130 GGTAAAATTAT---A-AAAAATTT--GTCGGGTCGGTATTTTTCACCCTAAACCCAAACTCAACC
* * * *
1122099 CAACTCGAATATCACACTTAAAAAACCCGACCTAACCCGAACAAAATAAAGTTTCACCCGACCCG
189 CAACCCGAATATCACACTTAAAAAAACCGACCCAACCCGAACAAAATAAAATTTCACCCGACCCG
1122164 ACCCG
254 ACCCG
* * *
1122169 AATATATGAATTAGTAATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAAT
1 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATAAAAAT
1122234 AGTGACTTAATT-AAAAATATATATATATAGAGAGGGGTATTATTGTAATTATTCATAAATATAT
66 AGTGACTTAATTGAAAAA-AT-T-TATATAGAGAGGGGTATTATTGTAATTATTCATAAATATAT
* * * *
1122298 AAGGTAAAATTAT-ATATATTT-TCGGGTCAGGTATTTTTCACCTTAAACCCAAACTCAACCCGA
128 AAGGTAAAATTATAAAAAATTTGTCGGGTC-GGTATTTTTCACCCTAAACCCAAACTCAACCCAA
* ** *
1122361 CCCGAATATCACACTTAAAAAAACCGACCCGACCCGGCCAAAATAAAATTTCACCCGACTCGACC
192 CCCGAATATCACACTTAAAAAAACCGACCCAACCCGAACAAAATAAAATTTCACCCGACCCGACC
1122426 CG
257 CG
1122428 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATA-TTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATA
1122487 TATAAATAAG
Statistics
Matches: 285, Mismatches: 28, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
258 18 0.06
259 134 0.47
261 6 0.02
263 5 0.02
264 52 0.18
265 18 0.06
266 52 0.18
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (258 bp):
AATATATGAATTAGAAACCCGACCCGACCCAAAATAATAAAAAAATATTTTTATTCAATAAAAAT
AGTGACTTAATTGAAAAAATTTATATAGAGAGGGGTATTATTGTAATTATTCATAAATATATAAG
GTAAAATTATAAAAAATTTGTCGGGTCGGTATTTTTCACCCTAAACCCAAACTCAACCCAACCCG
AATATCACACTTAAAAAAACCGACCCAACCCGAACAAAATAAAATTTCACCCGACCCGACCCG
Found at i:1123931 original size:17 final size:17
Alignment explanation
Indices: 1123898--1123945 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1123888 ACCACCCGAT
*
1123898 TAAAAATAAATTT-CCC
1 TAAAAATCAATTTCCCC
*
1123914 TAAAAATCAGTTTCCCC
1 TAAAAATCAATTTCCCC
*
1123931 TAAAACTCAATTTCC
1 TAAAAATCAATTTCC
1123946 TTTAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAAATCAATTTCCCC
Found at i:1124164 original size:3 final size:3
Alignment explanation
Indices: 1124158--1124195 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1124148 TTCTTAAGAA
1124158 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1124196 TAAAGCATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1124884 original size:12 final size:12
Alignment explanation
Indices: 1124867--1124891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1124857 AAAAATAATT
1124867 TTTTTGTTATAA
1 TTTTTGTTATAA
1124879 TTTTTGTTATAA
1 TTTTTGTTATAA
1124891 T
1 T
1124892 GATTAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTTGTTATAA
Found at i:1125554 original size:15 final size:15
Alignment explanation
Indices: 1125534--1125563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1125524 ACTATTAATG
*
1125534 ACAAAATTAATTTTA
1 ACAAAATTAAATTTA
1125549 ACAAAATTAAATTTA
1 ACAAAATTAAATTTA
1125564 TCACAATACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
ACAAAATTAAATTTA
Found at i:1128626 original size:20 final size:20
Alignment explanation
Indices: 1128601--1128638 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1128591 TATCAACCAT
*
1128601 CATGGACCGCCACGTCAGCA
1 CATGGACCACCACGTCAGCA
*
1128621 CATGGACCATCACGTCAG
1 CATGGACCACCACGTCAG
1128639 TAAAGTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.24, T:0.13
Consensus pattern (20 bp):
CATGGACCACCACGTCAGCA
Found at i:1134396 original size:64 final size:65
Alignment explanation
Indices: 1134328--1134488 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
1134318 TTGTTTGAAT
* * ** *
1134328 GTGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAAATAGAAACATCAAATGCA-ATT
1 GTGCACCGATGCATAGGTAGTGCATCGATGCATCCCAGTGAAAATA-AAACATCAAATGCATATT
1134391 A
65 A
* * * * * *
1134392 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTGATAATACAACATCGAATGCATTTT
1 GTGCACCGATGCAT-AGGTAGTGCATCGATGCATCCCAGTGAAAATAAAACATCAAATGCATATT
1134456 A
65 A
1134457 -TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 GTGCACCGATGCAT-AGGTAGTGCATCGATGCAT
1134489 ACTTTCATTG
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
63 2 0.03
64 63 0.80
65 14 0.18
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (65 bp):
GTGCACCGATGCATAGGTAGTGCATCGATGCATCCCAGTGAAAATAAAACATCAAATGCATATTA
Found at i:1135184 original size:31 final size:31
Alignment explanation
Indices: 1135146--1135208 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1135136 AGGGTCGAGG
* *
1135146 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTAGGTTCTTCGGAATATATGGACT
*
1135177 GTTTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTAGGTTCTTCGGAATATATGGACT
1135208 G
1 G
1135209 GTCATTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGAATATATGGACT
Found at i:1139197 original size:31 final size:31
Alignment explanation
Indices: 1139159--1139283 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
1139149 AGGGTCGAGG
1139159 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1139190 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1139221 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1139252 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1139283 G
1 G
1139284 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1145045 original size:44 final size:44
Alignment explanation
Indices: 1144983--1145111 Score: 179
Period size: 44 Copynumber: 3.0 Consensus size: 44
1144973 AGTCAGATTC
* * *
1144983 ACAGCTAATCAACATGCTTATATAATGGTCTTGTCTTATTTAGA
1 ACAGCTGATCAACATGCTTATATAACGGTCTTGTCGTATTTAGA
**
1145027 ACAGCTGATCAATGTGCTTATATAACGGTCTTGTCGTATTTAGA
1 ACAGCTGATCAACATGCTTATATAACGGTCTTGTCGTATTTAGA
* * *
1145071 ACATCCGATCAACATGCTTATATGACGGTCTTGT-GTATTTA
1 ACAGCTGATCAACATGCTTATATAACGGTCTTGTCGTATTTA
1145112 CGTTAATGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 7 0.09
44 68 0.91
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (44 bp):
ACAGCTGATCAACATGCTTATATAACGGTCTTGTCGTATTTAGA
Found at i:1149667 original size:23 final size:23
Alignment explanation
Indices: 1149640--1149720 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
1149630 TGAATTCAAC
*
1149640 TGCATTATTGCAACACTTATTGT
1 TGCATTATTGCAACCCTTATTGT
* *
1149663 TGCATTATTGCAGCCCTTATTGC
1 TGCATTATTGCAACCCTTATTGT
*
1149686 TGCATTATTTCAACCCTTATTGT
1 TGCATTATTGCAACCCTTATTGT
1149709 TGCATTATTGCA
1 TGCATTATTGCA
1149721 GTCCTTCAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (23 bp):
TGCATTATTGCAACCCTTATTGT
Found at i:1149692 original size:46 final size:46
Alignment explanation
Indices: 1149639--1149726 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
1149629 GTGAATTCAA
1149639 CTGCATTATTGCAACACTTATTGTTGCATTATTGCAGCCCTTATTG
1 CTGCATTATTGCAACACTTATTGTTGCATTATTGCAGCCCTTATTG
* * *
1149685 CTGCATTATTTCAACCCTTATTGTTGCATTATTGCAGTCCTT
1 CTGCATTATTGCAACACTTATTGTTGCATTATTGCAGCCCTT
1149727 CAGCTCACGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
CTGCATTATTGCAACACTTATTGTTGCATTATTGCAGCCCTTATTG
Found at i:1149963 original size:39 final size:38
Alignment explanation
Indices: 1149920--1150067 Score: 190
Period size: 39 Copynumber: 3.8 Consensus size: 38
1149910 TTATTATTTT
** *
1149920 AAATTATTAGTTTGTTAGTTTATGGTTTAAGGTAAAACA
1 AAATT-TTAGTTAATTAGTTTATAGTTTAAGGTAAAACA
*
1149959 AAATTTTAGTTAATTAG-TTAGTTAGCTTAAGGTAAAACA
1 AAATTTTAGTTAATTAGTTTA--TAGTTTAAGGTAAAACA
*
1149998 AAATTTTAGTTAATTAGTTTGTTAGTTTAAGGTAAAACA
1 AAATTTTAGTTAATTAGTTT-ATAGTTTAAGGTAAAACA
*
1150037 AAATTTTAGTTAATTAGTTTGTTAGTTTAAG
1 AAATTTTAGTTAATTAGTTT-ATAGTTTAAG
1150068 TTTTATTATT
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
37 3 0.03
38 10 0.10
39 84 0.85
40 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (38 bp):
AAATTTTAGTTAATTAGTTTATAGTTTAAGGTAAAACA
Found at i:1150188 original size:28 final size:27
Alignment explanation
Indices: 1150149--1150201 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1150139 TATATTAAAA
1150149 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1150177 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1150202 TAACTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1150301 original size:28 final size:29
Alignment explanation
Indices: 1150270--1150329 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1150260 AGTTTATTAG
*
1150270 TAGTTTA-AGTTTTA-TTATAATAAAAAAA
1 TAGTTTATAGTTTAAGTTAT-ATAAAAAAA
1150298 TAGTTTATTAGTTTAAGTTATATAAAAAAA
1 TAGTTTA-TAGTTTAAGTTATATAAAAAAA
1150328 TA
1 TA
1150330 ATTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.25
30 17 0.61
31 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (29 bp):
TAGTTTATAGTTTAAGTTATATAAAAAAA
Found at i:1150565 original size:18 final size:18
Alignment explanation
Indices: 1150542--1150596 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1150532 AATAATTATT
1150542 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1150560 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1150572 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1150589 TAAATTAG
1 TAAATTAG
1150597 GGTAAACAAA
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:1150644 original size:21 final size:21
Alignment explanation
Indices: 1150620--1150659 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1150610 TATAATGAGT
1150620 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
1150641 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
1150660 CATATAGAAA
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:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:1150896 original size:30 final size:30
Alignment explanation
Indices: 1150829--1150932 Score: 129
Period size: 30 Copynumber: 3.4 Consensus size: 30
1150819 TTTAGTTAAT
* * *
1150829 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAGAA
*
1150860 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAGAA
*
1150890 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAGTTTATTAGTTTAAGTTATATTAAAGAA
*
1150920 TAATTTATTAGTT
1 TAGTTTATTAGTT
1150933 GTTTAAGGGA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 6 0.09
30 49 0.75
31 10 0.15
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAGAA
Found at i:1150898 original size:15 final size:16
Alignment explanation
Indices: 1150875--1150921 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
1150865 TATTAGTTTA
1150875 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
***
1150891 AGTT-TATTAGTTAA-
1 AGTTATATTAAAGAAT
1150905 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
1150921 A
1 A
1150922 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:1153233 original size:17 final size:17
Alignment explanation
Indices: 1153213--1153254 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1153203 ATTAGTATCA
1153213 AATAATTAAATATTAAT
1 AATAATTAAATATTAAT
* * *
1153230 AATAAATCATTATTAAT
1 AATAATTAAATATTAAT
1153247 AATAATTA
1 AATAATTA
1153255 GTAAATCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAAATATTAAT
Found at i:1153319 original size:59 final size:58
Alignment explanation
Indices: 1153195--1153303 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 58
1153185 ATTTCATTAC
*
1153195 TAGT-AATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTATTAATAATAAT
1 TAGTAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTATAAATAATAAT
1153253 TAGTAAATCATTAGTATCAAATAATTAAATATT-TAA-AAATCATTAATAAAT
1 TAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-ATAAAT
1153304 TCGACTATGT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
56 8 0.17
57 8 0.17
58 4 0.08
59 28 0.58
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (58 bp):
TAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTATAAATAATAAT
Found at i:1153401 original size:14 final size:14
Alignment explanation
Indices: 1153382--1153410 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1153372 ATTAGTAATA
1153382 ATTATTAAATCATT
1 ATTATTAAATCATT
1153396 ATTATTAAATCATT
1 ATTATTAAATCATT
1153410 A
1 A
1153411 CTAAATCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1153410 original size:8 final size:8
Alignment explanation
Indices: 1153385--1153472 Score: 58
Period size: 8 Copynumber: 10.5 Consensus size: 8
1153375 AGTAATAATT
1153385 ATTAAATC
1 ATTAAATC
*
1153393 ATT--ATT
1 ATTAAATC
1153399 ATTAAATC
1 ATTAAATC
1153407 ATTACTAAATC
1 A-T--TAAATC
*
1153418 ATCAAATC
1 ATTAAATC
1153426 ATTAAAT-
1 ATTAAATC
1153433 ATTAAAATC
1 ATT-AAATC
1153442 ATTATCAAATC
1 A-T-T-AAATC
1153453 ATTAAAT-
1 ATTAAATC
1153460 ATTAAAATC
1 ATT-AAATC
1153469 ATTA
1 ATTA
1153473 TTAAATCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
6 5 0.08
7 6 0.09
8 30 0.47
9 6 0.09
10 3 0.05
11 14 0.22
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTAAATC
Found at i:1153445 original size:35 final size:34
Alignment explanation
Indices: 1153388--1153465 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
1153378 AATAATTATT
*
1153388 AAATCATT-ATTATTAAATCATTA-CTAAATCATC
1 AAATCATTAAATATTAAATCATTATC-AAATCATC
*
1153421 AAATCATTAAATATTAAAATCATTATCAAATCATT
1 AAATCATTAAATATT-AAATCATTATCAAATCATC
1153456 AAAT-ATTAAA
1 AAATCATTAAA
1153466 ATCATTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 8 0.20
34 11 0.28
35 20 0.50
36 1 0.03
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (34 bp):
AAATCATTAAATATTAAATCATTATCAAATCATC
Found at i:1153448 original size:27 final size:27
Alignment explanation
Indices: 1153418--1153482 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1153408 TTACTAAATC
1153418 ATCAAATCATTAAATATTAAAATCATT
1 ATCAAATCATTAAATATTAAAATCATT
1153445 ATCAAATCATTAAATATTAAAATCATT
1 ATCAAATCATTAAATATTAAAATCATT
*
1153472 ATTAAATCATT
1 ATCAAATCATT
1153483 TTTATAGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (27 bp):
ATCAAATCATTAAATATTAAAATCATT
Found at i:1153787 original size:18 final size:17
Alignment explanation
Indices: 1153714--1153877 Score: 71
Period size: 18 Copynumber: 10.2 Consensus size: 17
1153704 CTATCAAATC
1153714 ATTAAATATTAATAATA
1 ATTAAATATTAATAATA
* * *
1153731 ATT-ATTATTACT-ATC
1 ATTAAATATTAATAATA
* * *
1153746 ATT-ACTA-TCA-AATC
1 ATTAAATATTAATAATA
1153760 ATTAAATATTAATAATA
1 ATTAAATATTAATAATA
* * *
1153777 ATTTAATTATTACTAATC
1 A-TTAAATATTAATAATA
* *
1153795 ATT-ACTACT-A-AATA
1 ATTAAATATTAATAATA
1153809 ATTAAATATTAATAATA
1 ATTAAATATTAATAATA
* * * *
1153826 ATTTCATTATTACTAATC
1 A-TTAAATATTAATAATA
* * *
1153844 ATT-ACTACT-A-AATC
1 ATTAAATATTAATAATA
1153858 ATTAAATATTAATAATA
1 ATTAAATATTAATAATA
1153875 ATT
1 ATT
1153878 TTATTATAAT
Statistics
Matches: 107, Mismatches: 28, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
14 20 0.19
15 19 0.18
16 19 0.18
17 22 0.21
18 27 0.25
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAAATATTAATAATA
Found at i:1153798 original size:49 final size:47
Alignment explanation
Indices: 1153689--1153944 Score: 376
Period size: 49 Copynumber: 5.4 Consensus size: 47
1153679 ATTACTAATA
1153689 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA-TTATT
1 ATTACT-AATCATTACTA-CAAATCATTAAATATTAATAATAATTTATT
1153737 ATTACT-ATCATTACTATCAAATCATTAAATATTAATAATAATTTAATT
1 ATTACTAATCATTACTA-CAAATCATTAAATATTAATAATAATTT-ATT
*
1153785 ATTACTAATCATTACTACTAAATAATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTAC-AAATCATTAAATATTAATAATAATTT-ATT
1153834 ATTACTAATCATTACTACTAAATCATTAAATATTAATAATAATTTTATT
1 ATTACTAATCATTACTAC-AAATCATTAAATATTAATAATAA-TTTATT
* * *
1153883 ATAATTAATCATTACTACCAATCATTAAATATTAATAAT--TTTATT
1 ATTACTAATCATTACTACAAATCATTAAATATTAATAATAATTTATT
1153928 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1153945 AATAATTATT
Statistics
Matches: 195, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
45 21 0.11
46 35 0.18
47 2 0.01
48 36 0.18
49 98 0.50
50 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (47 bp):
ATTACTAATCATTACTACAAATCATTAAATATTAATAATAATTTATT
Found at i:1153847 original size:13 final size:13
Alignment explanation
Indices: 1153782--1153861 Score: 53
Period size: 13 Copynumber: 6.3 Consensus size: 13
1153772 TAATAATTTA
1153782 ATTATTACTAATC
1 ATTATTACTAATC
*
1153795 ATTACTACTAA--
1 ATTATTACTAATC
*
1153806 ATAATTA--AAT-
1 ATTATTACTAATC
* *
1153816 ATTAATAATAATTTC
1 ATTATTACTAA--TC
1153831 ATTATTACTAATC
1 ATTATTACTAATC
*
1153844 ATTACTACTAAATC
1 ATTATTACT-AATC
1153858 ATTA
1 ATTA
1153862 AATATTAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 5 0.10
12 2 0.04
13 20 0.38
14 9 0.17
15 9 0.17
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTATTACTAATC
Found at i:1157702 original size:46 final size:48
Alignment explanation
Indices: 1157629--1157732 Score: 133
Period size: 50 Copynumber: 2.2 Consensus size: 48
1157619 GATACTAACA
* * *
1157629 AATTAATAATTTTTTT-TTATAT-TTA-ATAACTTAAACTAAGAAACT
1 AATTAATAATTTTTTTATAATATAATATATAACTTAAACTAACAAACT
1157674 AATTAACTAATTTTTTATATAATATAATATATAACTTAAACTAACAAACT
1 AATTAA-TAATTTTTT-TATAATATAATATATAACTTAAACTAACAAACT
1157724 AATATAATA
1 AAT-TAATA
1157733 TAACTTAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
45 6 0.12
46 9 0.18
47 1 0.02
48 5 0.10
49 2 0.04
50 24 0.48
51 3 0.06
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (48 bp):
AATTAATAATTTTTTTATAATATAATATATAACTTAAACTAACAAACT
Found at i:1157733 original size:28 final size:30
Alignment explanation
Indices: 1157693--1157754 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
1157683 ATTTTTTATA
1157693 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1157723 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1157751 TAAT
1 TAAT
1157755 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1158344 original size:32 final size:32
Alignment explanation
Indices: 1158301--1158365 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1158291 GGCCATGCAC
*
1158301 TGCTCCCTGGATAGCTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
1158333 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
1 TGCTCCATGGATAGCTCGCACTCACTCCTTGG
1158365 T
1 T
1158366 CGCCCGGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (32 bp):
TGCTCCATGGATAGCTCGCACTCACTCCTTGG
Found at i:1158403 original size:29 final size:29
Alignment explanation
Indices: 1158361--1158416 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1158351 CACTCACTCC
*
1158361 TTGGTCGCCCGGAGTGCATGGCAACCTCT
1 TTGGTCACCCGGAGTGCATGGCAACCTCT
*
1158390 TTGGTCACCCGGAGTGCATGGCGACCT
1 TTGGTCACCCGGAGTGCATGGCAACCT
1158417 ACGACTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.32, T:0.23
Consensus pattern (29 bp):
TTGGTCACCCGGAGTGCATGGCAACCTCT
Found at i:1159413 original size:3 final size:3
Alignment explanation
Indices: 1159407--1159435 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1159397 TAATATACTA
1159407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1159436 GGATAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1160012 original size:58 final size:58
Alignment explanation
Indices: 1159888--1160009 Score: 156
Period size: 58 Copynumber: 2.1 Consensus size: 58
1159878 GTCAAATTAA
* * *
1159888 CATTTTGTAACTTTTAATAGTTGGGTACCCAACAAAATAGTGCCTATAATTAATGGAC
1 CATTTTGTAACTTTTAATAGTTGGGGACCCAACAAAATAGTGCCCATAATTAAGGGAC
* * **
1159946 CATTTTGTAAC-TTTAATAGTTGAGGGACTCAACAAAATAGTGCCCCATAGTTGGGGGAC
1 CATTTTGTAACTTTTAATAGTTG-GGGACCCAACAAAATAGTG-CCCATAATTAAGGGAC
1160005 CATTT
1 CATTT
1160010 GTATATTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
57 11 0.20
58 28 0.51
59 16 0.29
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (58 bp):
CATTTTGTAACTTTTAATAGTTGGGGACCCAACAAAATAGTGCCCATAATTAAGGGAC
Found at i:1160383 original size:22 final size:22
Alignment explanation
Indices: 1160357--1160399 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1160347 TAATAAATTA
1160357 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1160379 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1160400 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1160408 original size:22 final size:22
Alignment explanation
Indices: 1160359--1160407 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1160349 ATAAATTATT
**
1160359 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1160381 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1160404 TAAA
1 TAAA
1160408 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1160411 original size:54 final size:54
Alignment explanation
Indices: 1160347--1160924 Score: 417
Period size: 54 Copynumber: 10.8 Consensus size: 54
1160337 ACAACTACAA
1160347 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
***
1160401 TAATAAATTATTT-AAATAAATCAATCCATACAACTACATAATAAATCAATCC-TA-
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTA-A-AATAAATCAATCCATAC
** * * * * *
1160455 TTTTAAA--A--T-AAATCAATCCATGCAAATAAATTATTTAAATAAATCAATCCATGC
1 TAATAAATTATTTAAAATAAATCAAT-C-CAT--ATT-TTAAAATAAATCAATCCATAC
** *
1160509 -AATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTAAAATAAAT-CAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A-T-AAATCAATCCATAC
* * * *
1160565 -CAT--A-T-TTTAAAATAAATCAATCCATA--CTAATAAT-TAT-AA--AATA-
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAA-AATAAATCAATCCATAC
** * ** *
1160608 -AATCCA-TATTTTAAATAAATCAATCCATACTAATAAATTATTTAAATAAAT-CA-A-
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--TAAATCAATCCATAC
* * * *
1160662 TCATACAACTA--CAATAATAAATC-ATCCATATTTTAAAATAAATAAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1160715 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1160769 TAATAAATTATTTAAAATAGATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
1160823 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
*
1160881 TAATAAATTATTTAAAATAAATCAATCCATATTTTATAATAAAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
1160925 TATTTTAAAA
Statistics
Matches: 422, Mismatches: 53, Indels: 98
0.74 0.09 0.17
Matches are distributed among these distances:
43 4 0.01
44 2 0.00
45 4 0.01
46 20 0.05
47 1 0.00
48 2 0.00
49 6 0.01
50 22 0.05
51 3 0.01
52 44 0.10
53 38 0.09
54 153 0.36
55 19 0.05
56 28 0.07
57 12 0.03
58 64 0.15
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1160465 original size:77 final size:77
Alignment explanation
Indices: 1160362--1160767 Score: 424
Period size: 77 Copynumber: 5.2 Consensus size: 77
1160352 AATTATTTAA
1160362 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATC
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATC
1160427 CATACAACTACAT
66 CATACAA-TACAT
* *
1160440 AATAAATCAATCC-TATTTTAAAATAAATCAATCCATGCAAATAAATTATTTAAATAAATCAATC
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATC
* *
1160504 CATGCAATAAATTATTT
66 CATACAAT--A-CA--T
** * * *
1160521 AAAATAAATCAATCCATACTAATAAATTATTAAAATAAAT-CAT-C-CAT--ATT-TTAAAATAA
1 --AATAAATCAATCCATA-TTTTAAA--A-T-AAATCAATCCATACTAATAAATTATTTAAATAA
1160580 ATCAATCCATACTAATA-AT
59 ATCAATCCATAC-AATACAT
* *
1160599 TATAAAATAAATCCATATTTT-AAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAAT
1 AAT-AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAAT
1160663 -CATACAACTACAAT
65 CCATACAA-TAC-AT
*
1160677 AATAAATC-ATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AAATAAATCAAT
***
1160741 CCATATTTTA-A-
65 CCATACAATACAT
1160752 AATAAATCAATCCATA
1 AATAAATCAATCCATA
1160768 CTAATAAATT
Statistics
Matches: 277, Mismatches: 23, Indels: 58
0.77 0.06 0.16
Matches are distributed among these distances:
71 7 0.03
72 4 0.01
73 2 0.01
74 2 0.01
75 12 0.04
76 34 0.12
77 115 0.42
78 33 0.12
79 5 0.02
80 1 0.00
81 1 0.00
82 1 0.00
83 32 0.12
84 8 0.03
85 5 0.02
86 2 0.01
87 2 0.01
88 4 0.01
89 7 0.03
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (77 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAATC
CATACAATACAT
Found at i:1160496 original size:31 final size:30
Alignment explanation
Indices: 1160460--1160567 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 30
1160450 TCCTATTTTA
1160460 AAATAAATCAATCCATGCAAATAAATTATTT
1 AAATAAATCAATCCATGC-AATAAATTATTT
1160491 AAATAAATCAATCCATGCAATAAATTATTT
1 AAATAAATCAATCCATGCAATAAATTATTT
* *
1160521 AAAATAAATCAATCCATACTAATAAATTATTA
1 -AAATAAATCAATCCATGC-AATAAATTATTT
1160553 AAATAAATC-ATCCAT
1 AAATAAATCAATCCAT
1160568 ATTTTAAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
30 18 0.25
31 44 0.60
32 11 0.15
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATAAATCAATCCATGCAATAAATTATTT
Found at i:1160550 original size:32 final size:32
Alignment explanation
Indices: 1160456--1160939 Score: 239
Period size: 32 Copynumber: 16.4 Consensus size: 32
1160446 TCAATCCTAT
* *
1160456 TTTAAAATAAATCAATCCATGCAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1160488 TTT-AAATAAATCAATCCATGC-AATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160518 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160550 -TTAAAATAAATC-AT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160570 TTTAAAATAAATCAATCCATACTAAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* ** *
1160601 --TAAAATAAATCCAT--ATTTTAAATAAATCAA
1 TTTAAAATAAATCAATCCATACT-AATAAAT-TA
** * * * * * *
1160631 TCCATACT-AATAAAT-TAT-TTAAATAAATCAA
1 TTTAAAATAAATCAATCCATACT-AATAAAT-TA
* * * * **
1160662 TCATACAACTACAAT-AAT--A-AATCATCCATAT-
1 T-TTA-AAATA-AATCAATCCATACTAATAAAT-TA
*
1160693 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160725 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160747 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1160779 TTTAAAATAGATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1160801 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1160833 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
1160863 --T--AATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1160891 TTTAAAATAAATCAATCCATATTTTATAATAAATTA
1 TTTAAAATAAATCAATCCATA----CTAATAAATTA
1160927 TTTTAAAATAAAT
1 -TTTAAAATAAAT
1160940 TATTTTATAG
Statistics
Matches: 359, Mismatches: 31, Indels: 119
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.04
22 31 0.09
23 5 0.01
24 4 0.01
26 29 0.08
27 9 0.03
28 17 0.05
29 25 0.07
30 22 0.06
31 75 0.21
32 96 0.27
33 5 0.01
34 3 0.01
35 3 0.01
36 10 0.03
37 12 0.03
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1160574 original size:21 final size:22
Alignment explanation
Indices: 1160550--1160636 Score: 97
Period size: 21 Copynumber: 3.9 Consensus size: 22
1160540 TAATAAATTA
1160550 TTAAAATAAATC-ATCCATATT
1 TTAAAATAAATCAATCCATATT
*
1160571 TTAAAATAAATCAATCCATACTA
1 TTAAAATAAATCAATCCATA-TT
* * *
1160594 ATAATTATAAAATAAATCCATATT
1 TTAA-AAT-AAATCAATCCATATT
1160618 TT-AAATAAATCAATCCATA
1 TTAAAATAAATCAATCCATA
1160637 CTAATAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
21 24 0.44
22 9 0.17
23 5 0.09
24 4 0.07
25 12 0.22
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (22 bp):
TTAAAATAAATCAATCCATATT
Found at i:1160705 original size:98 final size:98
Alignment explanation
Indices: 1160516--1160713 Score: 244
Period size: 98 Copynumber: 2.0 Consensus size: 98
1160506 TGCAATAAAT
* **
1160516 TATTTAAAATAAATCAATCCATACTAATAAATTATTAAAATAAATCATCCATATTTTAAAATAAA
1 TATTTAAAATAAATCAATCCATACTAATAAATTATTAAAATAAATCATCCATACTACAAAATAAA
*
1160581 TCAATCCATACTAATAATTATAAAATAAATCCA
66 TCAATCCATACTAATAATAATAAAATAAATCCA
* *
1160614 TATTTTAAATAAATCAATCCATACTAATAAATTATTTAAATAAATCAAT-CATACAACTACAATA
1 TATTTAAAATAAATCAATCCATACTAATAAATTATTAAAATAAATC-ATCCAT---ACTACAA-A
**
1160678 ATAAATC-ATCCATA-TTTTAA-AAT-AAATAAATCCA
61 ATAAATCAATCCATACTAATAATAATAAAATAAATCCA
1160712 TA
1 TA
1160714 CTAATAAATT
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
98 60 0.69
99 4 0.05
100 4 0.05
101 11 0.13
102 8 0.09
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (98 bp):
TATTTAAAATAAATCAATCCATACTAATAAATTATTAAAATAAATCATCCATACTACAAAATAAA
TCAATCCATACTAATAATAATAAAATAAATCCA
Found at i:1160751 original size:22 final size:22
Alignment explanation
Indices: 1160725--1160767 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1160715 TAATAAATTA
1160725 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1160747 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1160768 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1160776 original size:22 final size:22
Alignment explanation
Indices: 1160727--1160775 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1160717 ATAAATTATT
**
1160727 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1160749 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1160772 TAAA
1 TAAA
1160776 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1160930 original size:15 final size:15
Alignment explanation
Indices: 1160910--1161059 Score: 237
Period size: 15 Copynumber: 10.0 Consensus size: 15
1160900 AATCAATCCA
*
1160910 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1160925 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
* *
1160940 TATTTTATAGTAAAT
1 TATTTTAAAATAAAT
* *
1160955 TATTTTATAATAATT
1 TATTTTAAAATAAAT
1160970 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
1160985 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1161000 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
1161015 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1161030 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1161045 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1161060 AACCTTATTA
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 124 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:1161883 original size:252 final size:254
Alignment explanation
Indices: 1161576--1162081 Score: 989
Period size: 252 Copynumber: 2.0 Consensus size: 254
1161566 AAAATTAGAA
1161576 GCATATATGATTGAAAGGTTATATTATTTAATCAATGATAATTTTTATTTTTTAAAAGATTGACA
1 GCATATATGATTGAAAGGTTATATTATTTAATCAATGATAATTTTTATTTTTTAAAAGATTGACA
*
1161641 AAAATTTTAAATGTATAAAATTAAAAAATCATTTTTACTTTTTAAAAATTTTCATGCCAGTAATT
66 AAAATTATAAATGTATAAAATTAAAAAATCATTTTTACTTTTTAAAAATTTTCATGCCAGTAATT
1161706 ATCGATG-AAATGAATCAAAATTAAGGAAGAAAAATATTTTCAAGTAAAAATAATATAAACACTC
131 ATCGATGAAAATGAATCAAAATTAAGGAAGAAAAATATTTTCAAGTAAAAATAATATAAACACTC
1161770 -ATGTTATAAAATTAAAATATATAATTTGAATTTTAAATTCTAAAACATTATAGACATG
196 AATGTTATAAAATTAAAATATATAATTTGAATTTTAAATTCTAAAACATTATAGACATG
1161828 GCATATATGATTGAAAGGTTATATTATTTAATCAATGATAATTTTTATTTTTTAAAAGATTGACA
1 GCATATATGATTGAAAGGTTATATTATTTAATCAATGATAATTTTTATTTTTTAAAAGATTGACA
1161893 AAAATTATAAATGTATAAAATTAAAAAATCATTTTTACTTTTTAAAAATTTTCATGCCAGTAATT
66 AAAATTATAAATGTATAAAATTAAAAAATCATTTTTACTTTTTAAAAATTTTCATGCCAGTAATT
1161958 ATCGATGAAAATGAATCAAAATTAAGGAAGAAAAATATTTTCAAGTAAAAATAATATAAACACTC
131 ATCGATGAAAATGAATCAAAATTAAGGAAGAAAAATATTTTCAAGTAAAAATAATATAAACACTC
1162023 AATGTTATAAAATTAAAATATATAATTTGAATTTTAAATTCTAAAACATTATAGACATG
196 AATGTTATAAAATTAAAATATATAATTTGAATTTTAAATTCTAAAACATTATAGACATG
1162082 ATGTATTTAA
Statistics
Matches: 251, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
252 136 0.54
253 57 0.23
254 58 0.23
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (254 bp):
GCATATATGATTGAAAGGTTATATTATTTAATCAATGATAATTTTTATTTTTTAAAAGATTGACA
AAAATTATAAATGTATAAAATTAAAAAATCATTTTTACTTTTTAAAAATTTTCATGCCAGTAATT
ATCGATGAAAATGAATCAAAATTAAGGAAGAAAAATATTTTCAAGTAAAAATAATATAAACACTC
AATGTTATAAAATTAAAATATATAATTTGAATTTTAAATTCTAAAACATTATAGACATG
Found at i:1165496 original size:31 final size:31
Alignment explanation
Indices: 1165458--1165528 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
1165448 AGGGTCGAGG
1165458 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTATTCGGGACATATGGACT
*
1165489 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTATTCGGGACATATGGACT
*
1165520 GATTACCTA
1 GTTTACCTA
1165529 GGCTCTTCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTATTCGGGACATATGGACT
Found at i:1165536 original size:31 final size:31
Alignment explanation
Indices: 1165472--1165538 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1165462 ACCTATGTTA
* * *
1165472 TTCGGGACATATGGACTGTTTACCTATGTTC
1 TTCGGGACATATGGACTGATTACCTAGGCTC
1165503 TTCGGGACATATGGACTGATTACCTAGGCTC
1 TTCGGGACATATGGACTGATTACCTAGGCTC
1165534 TTCGG
1 TTCGG
1165539 AATCTATGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (31 bp):
TTCGGGACATATGGACTGATTACCTAGGCTC
Found at i:1165547 original size:31 final size:31
Alignment explanation
Indices: 1165472--1165548 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1165462 ACCTATGTTA
* * * *
1165472 TTCGGGACATATGGACTGTTTACCTATGTTC
1 TTCGGAACATATGGACTGATTACCTAGGCTC
*
1165503 TTCGGGACATATGGACTGATTACCTAGGCTC
1 TTCGGAACATATGGACTGATTACCTAGGCTC
1165534 TTCGGAATC-TATGGA
1 TTCGGAA-CATATGGA
1165549 TTGGTCCTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (31 bp):
TTCGGAACATATGGACTGATTACCTAGGCTC
Found at i:1166712 original size:17 final size:17
Alignment explanation
Indices: 1166692--1166726 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1166682 TTTCTTTCAG
*
1166692 TGTACTGTTTCTTTTTC
1 TGTACTGCTTCTTTTTC
1166709 TGTACTGCTTCTTTTTC
1 TGTACTGCTTCTTTTTC
1166726 T
1 T
1166727 ATAATGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.20, G:0.11, T:0.63
Consensus pattern (17 bp):
TGTACTGCTTCTTTTTC
Found at i:1169771 original size:13 final size:13
Alignment explanation
Indices: 1169753--1169777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1169743 TAATAAGGGG
1169753 AAAATAAAAATAA
1 AAAATAAAAATAA
1169766 AAAATAAAAATA
1 AAAATAAAAATA
1169778 TATATGTATA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:1170094 original size:19 final size:19
Alignment explanation
Indices: 1170072--1170120 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1170062 CCACAATATT
1170072 AATAATAAAACAAATAA-TA
1 AATAATAAAAC-AATAAGTA
* *
1170091 AATAGTAAAACAGTAAGTA
1 AATAATAAAACAATAAGTA
1170110 AATAAATAAAA
1 AAT-AATAAAA
1170121 TTAGAAACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (19 bp):
AATAATAAAACAATAAGTA
Found at i:1171941 original size:253 final size:253
Alignment explanation
Indices: 1171488--1172012 Score: 917
Period size: 253 Copynumber: 2.1 Consensus size: 253
1171478 TGAAATGACT
* **
1171488 CCCTT-GTCGTGAGGTTGAGTTGAAACTGGAAAGCTCTGAGCATGATATCCTTTGTCGTGAAGTT
1 CCCTTCGTCGTGAAGTTGAGTTGAAACTGGAAAGCTCTGAGCATGATATCCTTCCTCGTGAAGTT
* * *
1171552 GAAACCAAACTCAAAGCTTTTGACAAGTGGCCTCTAAATCATCTTCTAGCTCAAGATACTTTGTC
66 GAAACCAAACTCAAAGCTTTTGAAAAGTGACCTCTAAATCATCTTCTAGCTCAAGATACTTCGTC
* *
1171617 GTGAAGGTGAAACTTGACTGGAAGACTTTGGTGTTGATGTGTTACATATGACTCATTCGTCGTGA
131 GTGAAGGTGAAACTTGACCGGAAGACTTTGGTGTTGATGTGTTACAGATGACTCATTCGTCGTGA
* *
1171682 AGTTGGGTCAACCTGTTAGGGTACGATACCCTTCGTTGTGAAGTTTGAATTGTATGGC
196 AGTTGGGTCAACCTGTTAGGGTACGATACCCTTCGTTGTGAAGTTGGAATTATATGGC
1171740 CCCTTCGTCGTGAAGTTGAGTTGAAACTGGAAAGCTCTGAGCATGATATCCTTCCTCGTGAAGTT
1 CCCTTCGTCGTGAAGTTGAGTTGAAACTGGAAAGCTCTGAGCATGATATCCTTCCTCGTGAAGTT
* *
1171805 GAAACCAAACTCAAAGCTTTTGAAAAGTGACCTCTGAATCGTCTTCTAGCTCAAGATACTTCGTC
66 GAAACCAAACTCAAAGCTTTTGAAAAGTGACCTCTAAATCATCTTCTAGCTCAAGATACTTCGTC
*
1171870 GTGAAGGTGAAACTTGACCGGAAGACTTTGGTGTTGATGTGTTACAGATGACTCCTTCGTCGTGA
131 GTGAAGGTGAAACTTGACCGGAAGACTTTGGTGTTGATGTGTTACAGATGACTCATTCGTCGTGA
*
1171935 AGTTGGGTCAACCTGTTAGGGTACGATACCCTTCGTTGTGAAGTTGGAATTATATGGG
196 AGTTGGGTCAACCTGTTAGGGTACGATACCCTTCGTTGTGAAGTTGGAATTATATGGC
1171993 CCCTTCGTCGTGAAGTTGAG
1 CCCTTCGTCGTGAAGTTGAG
1172013 CCCCGAAATT
Statistics
Matches: 258, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
252 5 0.02
253 253 0.98
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (253 bp):
CCCTTCGTCGTGAAGTTGAGTTGAAACTGGAAAGCTCTGAGCATGATATCCTTCCTCGTGAAGTT
GAAACCAAACTCAAAGCTTTTGAAAAGTGACCTCTAAATCATCTTCTAGCTCAAGATACTTCGTC
GTGAAGGTGAAACTTGACCGGAAGACTTTGGTGTTGATGTGTTACAGATGACTCATTCGTCGTGA
AGTTGGGTCAACCTGTTAGGGTACGATACCCTTCGTTGTGAAGTTGGAATTATATGGC
Found at i:1173718 original size:8 final size:8
Alignment explanation
Indices: 1173697--1173764 Score: 61
Period size: 8 Copynumber: 8.8 Consensus size: 8
1173687 CCCACCTTAT
1173697 TTTTCTTTC
1 TTTT-TTTC
*
1173706 ATTTTTTC
1 TTTTTTTC
*
1173714 -TTTTTGC
1 TTTTTTTC
*
1173721 TTTTGTTC
1 TTTTTTTC
*
1173729 TTTTGTTC
1 TTTTTTTC
1173737 -TTTTTTC
1 TTTTTTTC
*
1173744 TTTTGTTC
1 TTTTTTTC
1173752 -TTTTTTC
1 TTTTTTTC
1173759 TTTTTT
1 TTTTTT
1173765 CAATTTAGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
7 18 0.37
8 28 0.57
9 3 0.06
ACGTcount: A:0.01, C:0.13, G:0.06, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1173731 original size:15 final size:15
Alignment explanation
Indices: 1173707--1173762 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
1173697 TTTTCTTTCA
*
1173707 TTTTTTCTTTT-TGC
1 TTTTTTCTTTTGTTC
1173721 TTTTGTTCTTTTGTTC
1 TTTT-TTCTTTTGTTC
1173737 TTTTTTCTTTTGTTC
1 TTTTTTCTTTTGTTC
1173752 TTTTTTCTTTT
1 TTTTTTCTTTT
1173763 TTCAATTTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
14 4 0.10
15 29 0.74
16 6 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTGTTC
Found at i:1173764 original size:23 final size:22
Alignment explanation
Indices: 1173707--1173763 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 22
1173697 TTTTCTTTCA
1173707 TTTTTTCTTTTTGCTTTTGTTC
1 TTTTTTCTTTTTGCTTTTGTTC
*
1173729 TTTTGTTCTTTTTTCTTTTGTTC
1 TTTT-TTCTTTTTGCTTTTGTTC
1173752 TTTTTTCTTTTT
1 TTTTTTCTTTTT
1173764 TCAATTTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (22 bp):
TTTTTTCTTTTTGCTTTTGTTC
Found at i:1175258 original size:21 final size:21
Alignment explanation
Indices: 1175232--1175277 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1175222 GAATGCGGCT
1175232 GCCAAGGTAGCTAAAGCGTCA
1 GCCAAGGTAGCTAAAGCGTCA
1175253 GCCAAGGTAGCTAAAGCGTCA
1 GCCAAGGTAGCTAAAGCGTCA
1175274 GCCA
1 GCCA
1175278 TTTGATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (21 bp):
GCCAAGGTAGCTAAAGCGTCA
Found at i:1180840 original size:25 final size:27
Alignment explanation
Indices: 1180800--1180850 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
1180790 ACGAATGTAA
1180800 AAACATGGAAAATATAAAATAAAAAAC
1 AAACATGGAAAATATAAAATAAAAAAC
*
1180827 AAACAT-G-AAATATAAAATGAAAAA
1 AAACATGGAAAATATAAAATAAAAAA
1180851 TATGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.70
26 1 0.04
27 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.16
Consensus pattern (27 bp):
AAACATGGAAAATATAAAATAAAAAAC
Found at i:1187098 original size:20 final size:20
Alignment explanation
Indices: 1187035--1187098 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1187025 AACCAAAGAT
* *
1187035 AAATAGAGAGAGAA-AAAATA
1 AAATAAAGAGATAAGAAAA-A
*
1187055 AAATAAA-ATAT-AGAATAAA
1 AAATAAAGAGATAAGAA-AAA
1187074 GAAATAAAGAGATAAGAAAAA
1 -AAATAAAGAGATAAGAAAAA
1187095 AAAT
1 AAAT
1187099 GAAACACGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 19 0.54
21 6 0.17
22 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (20 bp):
AAATAAAGAGATAAGAAAAA
Found at i:1187228 original size:13 final size:13
Alignment explanation
Indices: 1187210--1187234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1187200 AATAAGGGGG
1187210 AAAATAAAAATAA
1 AAAATAAAAATAA
1187223 AAAATAAAAATA
1 AAAATAAAAATA
1187235 TATATGTATA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:1187351 original size:19 final size:19
Alignment explanation
Indices: 1187313--1187351 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1187303 AAGAATAATG
**
1187313 ATATAAAAAATAAACGAAA
1 ATATAAAAAATAAAAAAAA
*
1187332 ATATTAAAAATAAAAAAAA
1 ATATAAAAAATAAAAAAAA
1187351 A
1 A
1187352 ACTAATAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
ATATAAAAAATAAAAAAAA
Found at i:1188735 original size:2 final size:2
Alignment explanation
Indices: 1188728--1188776 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
1188718 CACAAACATA
*
1188728 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT GT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1188769 AT A- AT AT A
1 AT AT AT AT A
1188777 GTTAGCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.90
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1190121 original size:74 final size:76
Alignment explanation
Indices: 1189939--1190146 Score: 251
Period size: 75 Copynumber: 2.8 Consensus size: 76
1189929 CAAAGCCAAA
* * * * * **
1189939 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCTTAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1190003 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* *
1190015 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
1190079 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
1190090 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
1190147 GTTCAACGGT
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
74 20 0.18
75 63 0.55
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:1195951 original size:23 final size:23
Alignment explanation
Indices: 1195921--1195982 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
1195911 CCCCCCCTGA
1195921 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1195944 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1195967 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
1195983 CACAGGGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1195991 original size:21 final size:21
Alignment explanation
Indices: 1195921--1196004 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 21
1195911 CCCCCCCTGA
*
1195921 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
*
1195944 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
1195967 GGGAACCGATTCCCCC-CACAG
1 GGGAACCGATTCCCCCTCA-AG
* *
1195988 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
1196005 GGGGTTCTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
23 39 0.70
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTCAAG
Found at i:1197989 original size:16 final size:16
Alignment explanation
Indices: 1197948--1197989 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1197938 TGTTTCAACA
* *
1197948 TTTTGAATTGTTTGAT
1 TTTTGGATTGTTGGAT
1197964 TTTGTGGATTGTTGGAT
1 TTT-TGGATTGTTGGAT
1197981 TTTTGGATT
1 TTTTGGATT
1197990 TATGGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (16 bp):
TTTTGGATTGTTGGAT
Found at i:1198741 original size:21 final size:21
Alignment explanation
Indices: 1198687--1198743 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1198677 ATGCTCGGAG
*
1198687 GGAACCGATTCCACCATAGGA
1 GGAACCGATTCCCCCATAGGA
1198708 GGAACCGATTCCCCCATAGGA
1 GGAACCGATTCCCCCATAGGA
1198729 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
1198744 CTAAACATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.35, G:0.23, T:0.14
Consensus pattern (21 bp):
GGAACCGATTCCCCCATAGGA
Found at i:1198777 original size:96 final size:96
Alignment explanation
Indices: 1198611--1198818 Score: 265
Period size: 96 Copynumber: 2.2 Consensus size: 96
1198601 TTGCTCAGAG
* * ** *
1198611 GGAACCGATTCCCCCCTTAGGAGGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTCCAG
1 GGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAG
*
1198676 AATGCTCGGAGGGAACCGAT-TCCACCATAGGA
65 AATGCTCGGAGGGAACCGATCCCCACCA-AGGA
* *** *
1198708 GGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTTTTTTTCCGAGAATTCCAGT
1 GGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGA
* *
1198773 ATGCTCGGAGGGAACCGATCCCCCCCAAGGG
66 ATGCTCGGAGGGAACCGATCCCCACCAAGGA
*
1198804 GGTACCGATTCCCCC
1 GGAACCGATTCCCCC
1198819 CTGTTCAACG
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 81 0.84
97 15 0.16
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (96 bp):
GGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGA
ATGCTCGGAGGGAACCGATCCCCACCAAGGA
Found at i:1201486 original size:16 final size:15
Alignment explanation
Indices: 1201467--1201518 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1201457 AAAAATAATT
1201467 TTAAAAGTTAGAGTAA
1 TTAAAAGTTA-AGTAA
*
1201483 TT-AAATTATAAGTAA
1 TTAAAAGT-TAAGTAA
*
1201498 TTTAAAAGTGAAGTAA
1 -TTAAAAGTTAAGTAA
1201514 TTAAA
1 TTAAA
1201519 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 14 0.47
16 12 0.40
17 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
TTAAAAGTTAAGTAA
Found at i:1205071 original size:81 final size:76
Alignment explanation
Indices: 1204909--1205136 Score: 242
Period size: 81 Copynumber: 2.9 Consensus size: 76
1204899 TGCGTCTAAT
* * * ** *
1204909 AATGTTATGGTTCACTAAGAAACATGTTGCGATATGTAATCTTAATATTTTTATTAATAAAATAA
1 AATGTCATGGTTCACTAAGAAATAAGTTGTTATATGTAATGTTAATA-TTTTATTAATAAAATAA
* * *
1204974 GTTACGCCCAAT
65 GTTGCACCCAAG
* *
1204986 AATGTTATGGTTCACTAAGAAAATAAGTTGTGATCTGTAATGTAATGTTAATATTTT-TTAATAA
1 AATGTCATGGTTCACTAAG-AAATAAG-T-TG-T-TAT-ATGTAATGTTAATATTTTATTAATAA
1205050 AATAAGTTGCACCCAAG
60 AATAAGTTGCACCCAAG
* * * *
1205067 AATGTCATGGTTCATTAAGAAATATGTTGTTATATGTTATGTTAATATTATTATTAATAAAATAG
1 AATGTCATGGTTCACTAAGAAATAAGTTGTTATATGTAATGTTAATATT-TTATTAATAAAATAA
1205132 GTTGC
65 GTTGC
1205137 GCCAAAAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
75 15 0.12
76 4 0.03
77 36 0.28
78 7 0.05
79 2 0.02
80 8 0.06
81 38 0.30
82 5 0.04
83 13 0.10
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (76 bp):
AATGTCATGGTTCACTAAGAAATAAGTTGTTATATGTAATGTTAATATTTTATTAATAAAATAAG
TTGCACCCAAG
Done.