Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:265745 original size:19 final size:19
Alignment explanation
Indices: 265705--265853 Score: 194
Period size: 19 Copynumber: 8.4 Consensus size: 19
265695 GATTCTCCCG
265705 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
265725 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265744 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
265758 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265777 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265796 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
265810 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265829 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265847 TTGCGAT
1 TTGCGAT
265854 AGTCAATTTT
Statistics
Matches: 114, Mismatches: 4, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.11
16 14 0.12
17 14 0.12
18 18 0.16
19 41 0.36
20 15 0.13
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:265799 original size:52 final size:52
Alignment explanation
Indices: 265686--265853 Score: 311
Period size: 52 Copynumber: 3.2 Consensus size: 52
265676 GAAATTAAAA
*
265686 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
265739 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
265791 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
265842 TCGCATTGCGAT
1 TCGCATTGCGAT
265854 AGTCAATTTT
Statistics
Matches: 114, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
51 19 0.17
52 62 0.54
53 33 0.29
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:265814 original size:33 final size:33
Alignment explanation
Indices: 265686--265836 Score: 137
Period size: 33 Copynumber: 4.4 Consensus size: 33
265676 GAAATTAAAA
*
265686 TCGCATTGCGATTCTCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
265719 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 T-CGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATT
* * * *
265760 GCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
265791 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
265824 TCGCATTGCGATT
1 TCGCATTGCGATT
265837 TCATTTCGCA
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
31 9 0.10
32 5 0.05
33 39 0.42
34 10 0.11
35 2 0.02
36 3 0.03
37 5 0.05
39 10 0.11
40 6 0.06
41 4 0.04
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:265995 original size:14 final size:14
Alignment explanation
Indices: 265959--265995 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
265949 CATCAATTAC
*
265959 ACAAATCAACTTTT
1 ACAAATCATCTTTT
265973 ACAAATCATCTTTT
1 ACAAATCATCTTTT
265987 ACAAATCAT
1 ACAAATCAT
265996 TAAACAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:267504 original size:21 final size:21
Alignment explanation
Indices: 267465--267505 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
267455 ACTCTCGAGG
* *
267465 AATGATAGGGGGGGCCTCTTC
1 AATGATAGGAGGGGACTCTTC
*
267486 AATGATAGGAGTGGACTCTT
1 AATGATAGGAGGGGACTCTT
267506 GAGGGATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (21 bp):
AATGATAGGAGGGGACTCTTC
Found at i:267986 original size:14 final size:14
Alignment explanation
Indices: 267967--268023 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
267957 GCGAAATGAA
*
267967 AATCGCAACGACAG
1 AATCGCAACGAAAG
267981 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
267998 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
268014 AATCGCAACG
1 AATCGCAACG
268024 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:267994 original size:33 final size:33
Alignment explanation
Indices: 267948--268040 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
267938 GCGAAACCAA
*
267948 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
267981 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
268014 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
268041 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:268005 original size:19 final size:19
Alignment explanation
Indices: 267911--268045 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
267901 TAGTTTACTT
* *
267911 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
267931 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
267950 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
267969 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
267983 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
268002 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
268016 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
268035 TCGCAATGCGA
1 TCGCAACGCGA
268046 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:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:268063 original size:19 final size:19
Alignment explanation
Indices: 268041--268169 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
268031 AAAATCGCAA
268041 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
268060 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
268074 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
268093 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
268107 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
268126 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
268145 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
268165 TGCGA
1 TGCGA
268170 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:268083 original size:33 final size:33
Alignment explanation
Indices: 268041--268132 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
268031 AAAATCGCAA
268041 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
268074 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
268107 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
268133 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:268333 original size:93 final size:93
Alignment explanation
Indices: 268217--268591 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
268207 ATGGATTGCA
268217 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
268281 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
268309 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
268374 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
268402 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
268467 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
268495 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
268560 TAGCAGAATTGGCAGC-ACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
268587 TTACT
1 TTACT
268592 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 19 0.07
93 262 0.93
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:270334 original size:33 final size:33
Alignment explanation
Indices: 270289--270403 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
270279 TCTTTTGGTT
*
270289 GAAATGAAAATCGCAACGAGAGAATTGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
270322 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
270355 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
270388 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
270404 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:270339 original size:19 final size:19
Alignment explanation
Indices: 270315--270408 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
270305 CGAGAGAATT
*
270315 GCAACGCGAAATGACAATC
1 GCAACGCGAAATGAAAATC
*
270334 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
270348 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
270367 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
270381 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
270400 GCAATGCGA
1 GCAACGCGA
270409 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:270349 original size:14 final size:14
Alignment explanation
Indices: 270297--270386 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
270287 TTGAAATGAA
270297 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
270311 AATTGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
270330 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
270344 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
270363 AATCGCAACGAGAG
1 AATCGCAACGAGAG
270377 AATCGCAACG
1 AATCGCAACG
270387 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.32
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:270437 original size:19 final size:19
Alignment explanation
Indices: 270404--270494 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
270394 AAAATCGCAA
**
270404 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
270423 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
270442 TGCGATTGTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*** *
270461 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCGCGT
270481 TGCGATTTTCATTT
1 TGCGATTTTCATTT
270495 ATCTCGTTGC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 47 0.76
20 15 0.24
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:270628 original size:32 final size:32
Alignment explanation
Indices: 270589--270657 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
270579 ACTAACTTGA
*
270589 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
270621 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
270653 AAATC
1 AAATC
270658 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:270631 original size:18 final size:18
Alignment explanation
Indices: 270608--270657 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
270598 CGAGAGAATA
270608 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
270626 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
270640 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
270658 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:270886 original size:22 final size:22
Alignment explanation
Indices: 270834--270888 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
270824 TGGTTGTGAG
**
270834 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
270856 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
270878 GGATTTCTTCG
1 GGATTTCTTCG
270889 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:271060 original size:20 final size:20
Alignment explanation
Indices: 271035--271147 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
271025 CTTTAAATAT
271035 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
271055 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
271075 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
271095 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
271115 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
271135 CGCGTTGCGATTT
1 CGCGTTGCGATTT
271148 TGGAAAATCG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
20 80 0.99
21 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:271164 original size:21 final size:21
Alignment explanation
Indices: 271134--271216 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
271124 ATTTTCATAT
*
271134 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
271155 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
271176 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
271197 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
271217 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:271207 original size:42 final size:43
Alignment explanation
Indices: 271114--271212 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
271104 ATTTATGTGT
* *
271114 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
271155 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
271197 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
271213 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:275080 original size:6 final size:6
Alignment explanation
Indices: 275069--275106 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
275059 TTATCACAAA
275069 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TG
275107 AGAAAGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
TGGGAT
Found at i:279802 original size:42 final size:41
Alignment explanation
Indices: 279747--279863 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 41
279737 TCCCGAATTT
* * *
279747 CCGTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAT-GTTTC
*
279789 CCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATGTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTC
*
279830 CTCGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 C-CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
279864 CGTAATTCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
41 5 0.07
42 64 0.93
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTC
Found at i:280084 original size:22 final size:23
Alignment explanation
Indices: 280054--280097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
280044 TTTATTTAGT
280054 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
280077 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
280098 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:280193 original size:59 final size:58
Alignment explanation
Indices: 280065--280223 Score: 148
Period size: 59 Copynumber: 2.7 Consensus size: 58
280055 ATTAATATTT
* * *
280065 ATAATAATATAATA-TTATATTTTTAATATTATATAA-AATAATCAATTATATTATAATA
1 ATAATAATATTATATTTATA-TTTTAATAATATATAATAA-AATAAATTATATTATAATA
* *
280123 AT-ATAAGATATTATATTTTTATTTTAATAATATATAATAAAA-AAATTATATATTTAATA
1 ATAAT-A-ATATTATATTTATATTTTAATAATATATAATAAAATAAATTATAT-TATAATA
* *
280182 ATGAATAATATTAT-TTATATATTTAAATAATATTTTAATAAA
1 AT-AATAATATTATATT-TATATTTTAATAATA-TATAATAAA
280224 GATATTTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
57 2 0.02
58 13 0.15
59 52 0.62
60 15 0.18
61 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (58 bp):
ATAATAATATTATATTTATATTTTAATAATATATAATAAAATAAATTATATTATAATA
Found at i:280243 original size:23 final size:23
Alignment explanation
Indices: 280217--280261 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
280207 AATAATATTT
280217 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
280240 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
280262 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:280580 original size:14 final size:14
Alignment explanation
Indices: 280561--280601 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
280551 AAATGTAATT
*
280561 CATTTTACAGAAAA
1 CATTTTTCAGAAAA
*
280575 CATTTTTCGGAAAA
1 CATTTTTCAGAAAA
280589 CATTTTTCAGAAA
1 CATTTTTCAGAAA
280602 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (14 bp):
CATTTTTCAGAAAA
Found at i:280645 original size:15 final size:15
Alignment explanation
Indices: 280603--280648 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
280593 TTTCAGAAAT
280603 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
280618 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
280632 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
280647 GT
1 GT
280649 TCCAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:280666 original size:21 final size:21
Alignment explanation
Indices: 280627--280669 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
280617 AGAATTCAAA
* **
280627 TTCCAGTAATTTATTTTCCAG
1 TTCCAGTAATTCAAATTCCAG
280648 TTCCAGTAATTCAAATTCCAG
1 TTCCAGTAATTCAAATTCCAG
280669 T
1 T
280670 AATTCATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:286461 original size:3 final size:3
Alignment explanation
Indices: 286453--286506 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
286443 GAGCCACGTG
286453 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
286501 TAT TAT
1 TAT TAT
286507 GTTGAAGGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:297242 original size:29 final size:29
Alignment explanation
Indices: 297215--297332 Score: 177
Period size: 29 Copynumber: 4.1 Consensus size: 29
297205 TGATATTTTT
*
297215 GTAAATATTTTTAAAAGGGTGTTATTTTC
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
*
297244 GTAAATA-TTTTAAAA-GGCGTTAGTTTC
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
* *
297271 ATAAATATTTTTAAAAGGGTGTTAGTTTT
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
*
297300 GTAAGTATTTTTAAAAGGGTGTTAGTTTC
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
297329 GTAA
1 GTAA
297333 TTAGTTTCTG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
27 16 0.20
28 16 0.20
29 47 0.59
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (29 bp):
GTAAATATTTTTAAAAGGGTGTTAGTTTC
Found at i:297282 original size:56 final size:58
Alignment explanation
Indices: 297216--297328 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 58
297206 GATATTTTTG
297216 TAAATATTTTTAAAAGGGTGTTA-TTTTCGTAAATA-TTTTAAAA-GGCGTTAGTTTCA
1 TAAATATTTTTAAAAGGGTGTTAGTTTT-GTAAATATTTTTAAAAGGGCGTTAGTTTCA
* *
297272 TAAATATTTTTAAAAGGGTGTTAGTTTTGTAAGTATTTTTAAAAGGGTGTTAGTTTC
1 TAAATATTTTTAAAAGGGTGTTAGTTTTGTAAATATTTTTAAAAGGGCGTTAGTTTC
297329 GTAATTAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 29 0.56
57 12 0.23
58 11 0.21
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.46
Consensus pattern (58 bp):
TAAATATTTTTAAAAGGGTGTTAGTTTTGTAAATATTTTTAAAAGGGCGTTAGTTTCA
Found at i:311536 original size:19 final size:20
Alignment explanation
Indices: 311512--311554 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
311502 TATATATCAA
311512 AAAAAAT-TCAATTAATACC
1 AAAAAATGTCAATTAATACC
* *
311531 AAAAAATGTTAATTAATATC
1 AAAAAATGTCAATTAATACC
311551 AAAA
1 AAAA
311555 GTAGTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAATGTCAATTAATACC
Found at i:312291 original size:30 final size:30
Alignment explanation
Indices: 312250--312319 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
312240 TAAAATTAAC
* * *
312250 TTTGAAGTTTATAATACCATTTTTCAATAT
1 TTTGGAGTTTATAATACAATCTTTCAATAT
*
312280 TTTGGAGTTTATAATATAATCTTTCAATAT
1 TTTGGAGTTTATAATACAATCTTTCAATAT
312310 TTTGGAGTTT
1 TTTGGAGTTT
312320 GAATTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.51
Consensus pattern (30 bp):
TTTGGAGTTTATAATACAATCTTTCAATAT
Found at i:316709 original size:20 final size:20
Alignment explanation
Indices: 316684--316734 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
316674 TCCTATGAGG
*
316684 GTTTGTGAAGGATACTAGAA
1 GTTTGTTAAGGATACTAGAA
*
316704 GTTTGTTAAGTATACTAGAA
1 GTTTGTTAAGGATACTAGAA
316724 GTTTGTTAAGG
1 GTTTGTTAAGG
316735 GAATCATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTTGTTAAGGATACTAGAA
Found at i:318308 original size:19 final size:19
Alignment explanation
Indices: 318286--318325 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
318276 ATAAATTCAA
* *
318286 AATAAATTAATTAAATTTT
1 AATAAATGAATCAAATTTT
*
318305 AATAAATGAATCATATTTT
1 AATAAATGAATCAAATTTT
318324 AA
1 AA
318326 CTTTACATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
AATAAATGAATCAAATTTT
Found at i:318998 original size:18 final size:18
Alignment explanation
Indices: 318972--319006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
318962 TCGAAATGAC
*
318972 TGAAATAAATTATAAGAT
1 TGAAATAAATAATAAGAT
*
318990 TGAATTAAATAATAAGA
1 TGAAATAAATAATAAGA
319007 CATGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
TGAAATAAATAATAAGAT
Found at i:320318 original size:24 final size:24
Alignment explanation
Indices: 320226--320327 Score: 73
Period size: 24 Copynumber: 4.2 Consensus size: 24
320216 GAATATTTTA
* * *
320226 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
320250 TTTGACATCTGATCTGAAATCTAT
1 TCTGATATCTGATCTGAATTATGT
*
320274 TCTGAT-TCCT-ATCCTGGATTATGT
1 TCTGATAT-CTGAT-CTGAATTATGT
*
320298 TCTGATATCTTATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
*
320322 TTTGAT
1 TCTGAT
320328 TTCCTATATC
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 54 0.90
25 3 0.05
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:324606 original size:10 final size:10
Alignment explanation
Indices: 324593--324622 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
324583 AAAACAAAAA
324593 TCCCGGTTTT
1 TCCCGGTTTT
324603 TCCCGGTTTT
1 TCCCGGTTTT
*
324613 TTCCGGTTTT
1 TCCCGGTTTT
324623 CAGCCGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.20, T:0.53
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:325234 original size:14 final size:14
Alignment explanation
Indices: 325215--325242 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
325205 GGTCATTAAG
325215 AATATCATAATCAT
1 AATATCATAATCAT
325229 AATATCATAATCAT
1 AATATCATAATCAT
325243 GCAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATCATAATCAT
Found at i:330175 original size:26 final size:26
Alignment explanation
Indices: 330146--330205 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
330136 CATTGGGCAT
330146 ATGAATGC-AAGAACCCGAAACTGAGG
1 ATGAA-GCAAAGAACCCGAAACTGAGG
*
330172 ATGAAGCATAAGAACCCGAAACTGGGG
1 ATGAAGCA-AAGAACCCGAAACTGAGG
330199 ATGAAGC
1 ATGAAGC
330206 TTTCCATCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 2 0.06
26 5 0.16
27 24 0.77
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (26 bp):
ATGAAGCAAAGAACCCGAAACTGAGG
Found at i:330185 original size:27 final size:27
Alignment explanation
Indices: 330154--330205 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
330144 ATATGAATGC
330154 AAGAACCCGAAACTGAGGATGAAGCAT
1 AAGAACCCGAAACTGAGGATGAAGCAT
*
330181 AAGAACCCGAAACTGGGGATGAAGC
1 AAGAACCCGAAACTGAGGATGAAGC
330206 TTTCCATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (27 bp):
AAGAACCCGAAACTGAGGATGAAGCAT
Found at i:335331 original size:106 final size:106
Alignment explanation
Indices: 335196--335388 Score: 341
Period size: 106 Copynumber: 1.8 Consensus size: 106
335186 CAAACGCAAA
* * *
335196 AGCAAAATAGTGATAGGTGTATTTGAAAGAGAAAGAAAAACATACAACTAAGTTTGTGAACACAG
1 AGCAAAATAGTGATAGATGTATTTGAAAGAGAAAGAAAAACATACAAATAAGTATGTGAACACAG
335261 TGAAATAACTTAACAGTAAAGCACATTTGAAATAACTTAAC
66 TGAAATAACTTAACAGTAAAGCACATTTGAAATAACTTAAC
* *
335302 AGCAAAATAGTGATAGATGTGTTTGAAAGAGAGAGAAAAACATACAAATAAGTATGTGAACACAG
1 AGCAAAATAGTGATAGATGTATTTGAAAGAGAAAGAAAAACATACAAATAAGTATGTGAACACAG
335367 TGAAATAACTTAACAGTAAAGC
66 TGAAATAACTTAACAGTAAAGC
335389 GCACCTCCTG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (106 bp):
AGCAAAATAGTGATAGATGTATTTGAAAGAGAAAGAAAAACATACAAATAAGTATGTGAACACAG
TGAAATAACTTAACAGTAAAGCACATTTGAAATAACTTAAC
Found at i:339688 original size:2 final size:2
Alignment explanation
Indices: 339681--339710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
339671 AATCTTGCCC
339681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
339711 GCATTGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:339858 original size:2 final size:2
Alignment explanation
Indices: 339851--339877 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
339841 GATATTATCT
339851 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
339878 TAGCATTAAG
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:341434 original size:262 final size:262
Alignment explanation
Indices: 340969--341492 Score: 1030
Period size: 262 Copynumber: 2.0 Consensus size: 262
340959 AGTGTTTATG
340969 AAATTAGCACCATGACATAAAAAGGATTCACATCATCAATAGTCTAGGAAAAAAGAACAAAGTGT
1 AAATTAGCACCATGACATAAAAAGGATTCACATCATCAATAGTCTAGGAAAAAAGAACAAAGTGT
* *
341034 AAAGGAACCGCAAATAAGAGCTGAGAATAAGATTTTATTAAGTAAATTGTCACTCGAATTCTACG
66 AAAGAAACCGCAAATAAGAGCTGAGAATAAGATTTTATGAAGTAAATTGTCACTCGAATTCTACG
341099 GGTTTGAAATCCACATAAACTTACACTAATTTGCAAAACCATGTGTTCTGTGATATTTTGTCTTT
131 GGTTTGAAATCCACATAAACTTACACTAATTTGCAAAACCATGTGTTCTGTGATATTTTGTCTTT
341164 GGCTTTAATGTCTATCCAATAAAATGATAGTGTAGCTTCTCCTTTTATTCTCTTACATTAGCATA
196 GGCTTTAATGTCTATCCAATAAAATGATAGTGTAGCTTCTCCTTTTATTCTCTTACATTAGCATA
341229 AC
261 AC
341231 AAATTAGCACCATGACATAAAAAGGATTCACATCATCAATAGTCTAGGAAAAAAGAACAAAGTGT
1 AAATTAGCACCATGACATAAAAAGGATTCACATCATCAATAGTCTAGGAAAAAAGAACAAAGTGT
341296 AAAGAAACCGCAAATAAGAGCTGAGAATAAGATTTTATGAAGTAAATTGTCACTCGAATTCTACG
66 AAAGAAACCGCAAATAAGAGCTGAGAATAAGATTTTATGAAGTAAATTGTCACTCGAATTCTACG
341361 GGTTTGAAATCCACATAAACTTACACTAATTTGCAAAACCATGTGTTCTGTGATATTTTGTCTTT
131 GGTTTGAAATCCACATAAACTTACACTAATTTGCAAAACCATGTGTTCTGTGATATTTTGTCTTT
341426 GGCTTTAATGTCTATCCAATAAAATGATAGTGTAGCTTCTCCTTTTATTCTCTTACATTAGCATA
196 GGCTTTAATGTCTATCCAATAAAATGATAGTGTAGCTTCTCCTTTTATTCTCTTACATTAGCATA
341491 AC
261 AC
341493 CATTGACACT
Statistics
Matches: 260, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
262 260 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (262 bp):
AAATTAGCACCATGACATAAAAAGGATTCACATCATCAATAGTCTAGGAAAAAAGAACAAAGTGT
AAAGAAACCGCAAATAAGAGCTGAGAATAAGATTTTATGAAGTAAATTGTCACTCGAATTCTACG
GGTTTGAAATCCACATAAACTTACACTAATTTGCAAAACCATGTGTTCTGTGATATTTTGTCTTT
GGCTTTAATGTCTATCCAATAAAATGATAGTGTAGCTTCTCCTTTTATTCTCTTACATTAGCATA
AC
Found at i:347051 original size:16 final size:15
Alignment explanation
Indices: 347026--347057 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
347016 TCAATTTTAT
347026 TATTTATTATTTACG
1 TATTTATTATTTACG
347041 TATTATATTATTTACG
1 TATT-TATTATTTACG
347057 T
1 T
347058 TACATATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
TATTTATTATTTACG
Found at i:348852 original size:21 final size:21
Alignment explanation
Indices: 348804--348846 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
348794 GCTTCTTTGA
* *
348804 AAATTTAACATTATGATACAT
1 AAATTTTATATTATGATACAT
348825 AAATTTTATATTATGATACAT
1 AAATTTTATATTATGATACAT
348846 A
1 A
348847 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
AAATTTTATATTATGATACAT
Found at i:356417 original size:24 final size:23
Alignment explanation
Indices: 356377--356437 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
356367 ATGATAGATG
*
356377 TTAAATAGTCATTTGAATATTTAAAT
1 TTAAATA-T-ATTTGAAT-TTGAAAT
*
356403 TTAAATATATTTGAATTTGATAT
1 TTAAATATATTTGAATTTGAAAT
356426 TTAAATTATATT
1 TTAAA-TATATT
356438 CTTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.31
24 14 0.44
25 1 0.03
26 7 0.22
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (23 bp):
TTAAATATATTTGAATTTGAAAT
Found at i:362083 original size:31 final size:30
Alignment explanation
Indices: 362046--362123 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
362036 CTCAGTATTC
*
362046 TAAGCTTTGCTAAGCTTTACTTAATTCT-CTCA
1 TAAGCTTTGCTAAGCTTT-C--AATCCTACTCA
* *
362078 T-AGCTTTTCTAAGCTTTCAATCCTATTCA
1 TAAGCTTTGCTAAGCTTTCAATCCTACTCA
362107 TAAGCTTTGCTAAGCTT
1 TAAGCTTTGCTAAGCTT
362124 CACCCTCTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 15 0.38
31 15 0.38
32 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (30 bp):
TAAGCTTTGCTAAGCTTTCAATCCTACTCA
Found at i:363291 original size:30 final size:28
Alignment explanation
Indices: 363220--363301 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 28
363210 ACAACCTTAG
*
363220 TATT-CTAAGCTTTGCTAAGCTTTACTA
1 TATTCCTAAGCTTTGCTAAGCTTTAATA
*
363247 -ATTCTCTCATAGCTTTTCTAAGCTTTCAATCA
1 TATTC-CT-A-AGCTTTGCTAAGCTTT-AAT-A
363279 TATTCCTAAGCTTTGCTAAGCTT
1 TATTCCTAAGCTTTGCTAAGCTT
363302 CACCCTCTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
28 2 0.04
29 1 0.02
30 29 0.64
31 3 0.07
32 3 0.07
33 4 0.09
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (28 bp):
TATTCCTAAGCTTTGCTAAGCTTTAATA
Found at i:364484 original size:30 final size:29
Alignment explanation
Indices: 364406--364487 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
364396 ACAACCTCAG
*
364406 TATT-CTAAGCTTTGCTAAGC-TTTACTA
1 TATTCCTAAGCTTTGCTAAGCTTTTAATA
* *
364433 -ATTCTCTCATAGTTTTTCTAAGCTTTTAATCA
1 TATTC-CT-A-AGCTTTGCTAAGCTTTTAAT-A
364465 TATTCCTAAGCTTTGCTAAGCTT
1 TATTCCTAAGCTTTGCTAAGCTT
364488 CACCCTCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.07
28 2 0.05
29 1 0.02
30 24 0.56
31 6 0.14
32 3 0.07
33 4 0.09
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (29 bp):
TATTCCTAAGCTTTGCTAAGCTTTTAATA
Found at i:365666 original size:30 final size:29
Alignment explanation
Indices: 365588--365669 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
365578 ACAACCTCAG
*
365588 TATT-CTAAGCTTTGCTAAGC-TTTACTA
1 TATTCCTAAGCTTTGCTAAGCTTTTAATA
* *
365615 -ATTCTCTCATAGTTTTTCTAAGCTTTTAATCA
1 TATTC-CT-A-AGCTTTGCTAAGCTTTTAAT-A
365647 TATTCCTAAGCTTTGCTAAGCTT
1 TATTCCTAAGCTTTGCTAAGCTT
365670 CACCCTCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.07
28 2 0.05
29 1 0.02
30 24 0.56
31 6 0.14
32 3 0.07
33 4 0.09
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (29 bp):
TATTCCTAAGCTTTGCTAAGCTTTTAATA
Found at i:366843 original size:30 final size:28
Alignment explanation
Indices: 366772--366853 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 28
366762 ACAACCTCAG
*
366772 TATT-CTAAGCTTTGCTAAGCTTTACTA
1 TATTCCTAAGCTTTGCTAAGCTTTAATA
*
366799 -ATTCTCTCATAGCTTTTCTAAGCTTTCAATCA
1 TATTC-CT-A-AGCTTTGCTAAGCTTT-AAT-A
366831 TATTCCTAAGCTTTGCTAAGCTT
1 TATTCCTAAGCTTTGCTAAGCTT
366854 CACCCTCTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
28 2 0.04
29 1 0.02
30 29 0.64
31 3 0.07
32 3 0.07
33 4 0.09
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (28 bp):
TATTCCTAAGCTTTGCTAAGCTTTAATA
Found at i:368641 original size:29 final size:29
Alignment explanation
Indices: 368571--368692 Score: 85
Period size: 29 Copynumber: 4.3 Consensus size: 29
368561 TGGTGCAACT
*
368571 TTTTA-TAATT-TTTTAAAAA-AGTGACA
1 TTTTAGTAATTATTTTAAAAAGAGTGATA
* * *
368597 ATTTCGTAA-AATTTTTAAAAAGAGTGATA
1 TTTTAGTAATTA-TTTTAAAAAGAGTGATA
* *
368626 TTTTAGTAATTATTTTGAAAAGA-TGTTA
1 TTTTAGTAATTATTTTAAAAAGAGTGATA
* * * *
368654 TTTTGGTAATTAATTTCAAAATG-GTGTTA
1 TTTTAGTAATT-ATTTTAAAAAGAGTGATA
*
368683 TTTTCGTAAT
1 TTTTAGTAAT
368693 GTTAAAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
26 3 0.04
27 3 0.04
28 23 0.31
29 45 0.60
30 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (29 bp):
TTTTAGTAATTATTTTAAAAAGAGTGATA
Found at i:368663 original size:28 final size:28
Alignment explanation
Indices: 368609--368692 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
368599 TTCGTAAAAT
*
368609 TTTTAAAAAGAGTGATATTTTAGTAATTA
1 TTTTAAAAAGA-TGTTATTTTAGTAATTA
* *
368638 TTTTGAAAAGATGTTATTTTGGTAATTAA
1 TTTTAAAAAGATGTTATTTTAGTAATT-A
* * * *
368667 TTTCAAAATGGTGTTATTTTCGTAAT
1 TTTTAAAAAGATGTTATTTTAGTAAT
368693 GTTAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.30
29 32 0.70
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (28 bp):
TTTTAAAAAGATGTTATTTTAGTAATTA
Found at i:369669 original size:42 final size:41
Alignment explanation
Indices: 369610--369776 Score: 253
Period size: 42 Copynumber: 4.0 Consensus size: 41
369600 GGAAGTATTA
369610 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
* *
369652 CCAGGTCCCTTTGCTGTGTGCGAAAGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
369694 CCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
* *
369736 CCAAGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
369777 TCCTAGGCTC
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 4 0.03
42 111 0.97
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:370524 original size:29 final size:28
Alignment explanation
Indices: 370479--370552 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
370469 TACGTTCGTA
* *
370479 CAAAATAGCACCATTTTGAAATTAATTAC
1 CAAAATAGCATCTTTTTGAAA-TAATTAC
**
370508 CAAAATAGCATCTTTTTTTAATAATTAC
1 CAAAATAGCATCTTTTTGAAATAATTAC
* *
370536 TAAAATATCACTCTTTT
1 CAAAATAGCA-TCTTTT
370553 AAAAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (28 bp):
CAAAATAGCATCTTTTTGAAATAATTAC
Found at i:370561 original size:28 final size:28
Alignment explanation
Indices: 370530--370632 Score: 71
Period size: 28 Copynumber: 3.6 Consensus size: 28
370520 TTTTTTTAAT
* *
370530 AATTACTAAAATATCACTCTTTTAAAAA
1 AATTACAAAAATAACACTCTTTTAAAAA
* * ** * *
370558 AATTTACGAAATTGCCACCTTTTTTTAAAA
1 AA-TTACAAAAATAACA-CTCTTTTAAAAA
* * *
370588 AATTACAAAAATAACACCCTTTCAAAAT
1 AATTACAAAAATAACACTCTTTTAAAAA
* *
370616 AATTACCAGAATAACAC
1 AATTACAAAAATAACAC
370633 CATTTCCCAA
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
28 24 0.43
29 20 0.36
30 12 0.21
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (28 bp):
AATTACAAAAATAACACTCTTTTAAAAA
Found at i:370605 original size:29 final size:29
Alignment explanation
Indices: 370502--370605 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
370492 TTTTGAAATT
* * * *
370502 AATTACCAAAATAGCATCTTTTTTT-AAT
1 AATTACAAAAATAACACCTTTTTTTAAAA
* * * *
370530 AATTACTAAAATATCA-CTCTTTTAAAAA
1 AATTACAAAAATAACACCTTTTTTTAAAA
* * **
370558 AATTTACGAAATTGCCACCTTTTTTTAAAA
1 AA-TTACAAAAATAACACCTTTTTTTAAAA
370588 AATTACAAAAATAACACC
1 AATTACAAAAATAACACC
370606 CTTTCAAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
27 6 0.10
28 18 0.31
29 22 0.38
30 12 0.21
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTACAAAAATAACACCTTTTTTTAAAA
Found at i:370633 original size:28 final size:29
Alignment explanation
Indices: 370584--370655 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
370574 ACCTTTTTTT
* *
370584 AAAA-AATTACAAAAATAACACCCTTT-C
1 AAAATAATTACCAAAATAACACCATTTCC
*
370611 AAAATAATTACCAGAATAACACCATTTCC
1 AAAATAATTACCAAAATAACACCATTTCC
*
370640 CAAATAATTACCAAAA
1 AAAATAATTACCAAAA
370656 CTTCACTCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 4 0.11
28 19 0.50
29 15 0.39
ACGTcount: A:0.54, C:0.22, G:0.01, T:0.22
Consensus pattern (29 bp):
AAAATAATTACCAAAATAACACCATTTCC
Found at i:375599 original size:43 final size:42
Alignment explanation
Indices: 375536--375741 Score: 222
Period size: 42 Copynumber: 4.9 Consensus size: 42
375526 CTATACACCA
* * *
375536 GTAAGGCTTAACATGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTTATCAT-TGCACACAGCAAAGGGA-CCT-GGAAAACT
*
375580 GTAAGGTTTATCATTGCACACAGCAAAGGGACCT-GAGAAACT
1 GTAAGGCTTATCATTGCACACAGCAAAGGGACCTGGA-AAACT
* * *
375622 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTATCATTGCACACAGCAAAGGGACCTGGAAAACT
*
375664 GTAAGGCTTATC-TTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTATCATT-GCACACAGCAAAGGGACCTGGAAAACT
* * * *
375706 ATAAGGC-TAACCTTCGCACATAGCAAAGGGACCTGG
1 GTAAGGCTTATCATT-GCACACAGCAAAGGGACCTGG
375742 TAATACTTCC
Statistics
Matches: 144, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
41 7 0.05
42 107 0.74
43 15 0.10
44 15 0.10
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (42 bp):
GTAAGGCTTATCATTGCACACAGCAAAGGGACCTGGAAAACT
Found at i:375622 original size:42 final size:42
Alignment explanation
Indices: 375575--375741 Score: 225
Period size: 42 Copynumber: 4.0 Consensus size: 42
375565 GAGCCTAGGA
* *
375575 AAACTGTAAGGTTTATCATT-GCACACAGCAAAGGGACCTGAG
1 AAACTGTAAGGCTTATCCTTCGCACACAGCAAAGGGACCTG-G
*
375617 AAACTGTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTGG
1 AAACTGTAAGGCTTATCCTTCGCACACAGCAAAGGGACCTGG
375658 TAAACTGTAAGGCTTAT-CTTCGCACACAGCAAAGGGACCTGGG
1 -AAACTGTAAGGCTTATCCTTCGCACACAGCAAAGGGACCT-GG
* * *
375701 AAACTATAAGGC-TAACCTTCGCACATAGCAAAGGGACCTGG
1 AAACTGTAAGGCTTATCCTTCGCACACAGCAAAGGGACCTGG
375742 TAATACTTCC
Statistics
Matches: 114, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
41 8 0.07
42 104 0.91
43 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTATCCTTCGCACACAGCAAAGGGACCTGG
Found at i:375683 original size:84 final size:84
Alignment explanation
Indices: 375575--375744 Score: 263
Period size: 84 Copynumber: 2.0 Consensus size: 84
375565 GAGCCTAGGA
* * *
375575 AAACTGTAAGGTTTATCATTGCACACAGCAAAGGGACCTGAGAAACTGTAAGGCTTACCCTT-GC
1 AAACTGTAAGGCTTATCATTGCACACAGCAAAGGGACCTGAGAAACTATAAGGC-TAACCTTCGC
375639 ACACAGCAAAGGGACCTGGT
65 ACACAGCAAAGGGACCTGGT
*
375659 AAACTGTAAGGCTTATC-TTCGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTAACCTTCGC
1 AAACTGTAAGGCTTATCATT-GCACACAGCAAAGGGACCTGAGAAACTATAAGGCTAACCTTCGC
*
375723 ACATAGCAAAGGGACCTGGT
65 ACACAGCAAAGGGACCTGGT
375743 AA
1 AA
375745 TACTTCCTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
83 8 0.10
84 71 0.90
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (84 bp):
AAACTGTAAGGCTTATCATTGCACACAGCAAAGGGACCTGAGAAACTATAAGGCTAACCTTCGCA
CACAGCAAAGGGACCTGGT
Found at i:376690 original size:29 final size:28
Alignment explanation
Indices: 376658--376719 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
376648 AACATTACGT
* *
376658 AAATAGAACCATTTTGAAATTAATTACCA
1 AAATAGAACC-TTTTCAAAATAATTACCA
* * *
376687 AAATAGCATCTTTTCAAAATAATTACTA
1 AAATAGAACCTTTTCAAAATAATTACCA
376715 AAATA
1 AAATA
376720 TCACTCTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (28 bp):
AAATAGAACCTTTTCAAAATAATTACCA
Found at i:376710 original size:28 final size:29
Alignment explanation
Indices: 376658--376828 Score: 125
Period size: 29 Copynumber: 6.0 Consensus size: 29
376648 AACATTACGT
* * *
376658 AAATAGAACCATTTTGAAATTAATTACCA
1 AAATAGCACCATTTTCAAAATAATTACCA
* *
376687 AAATAGCATC-TTTTCAAAATAATTACTA
1 AAATAGCACCATTTTCAAAATAATTACCA
* * * * *
376715 AAATATCACTCTTTTTAAAAAT-TTTACGA
1 AAATAGCAC-CATTTTCAAAATAATTACCA
* * * * *
376744 AATTATCA-CATTTTAAAAAAAAATA-CA
1 AAATAGCACCATTTTCAAAATAATTACCA
*
376771 AAATAGCACCCATTTTCAAATTAATTACCA
1 AAATAGCA-CCATTTTCAAAATAATTACCA
* * *
376801 GAATAGCACCATTTCCCAAATAATTACC
1 AAATAGCACCATTTTCAAAATAATTACC
376829 CAACGGTCAA
Statistics
Matches: 110, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
27 17 0.15
28 24 0.22
29 51 0.46
30 18 0.16
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATAGCACCATTTTCAAAATAATTACCA
Found at i:376862 original size:13 final size:13
Alignment explanation
Indices: 376844--376885 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
376834 GTCAACAGGT
376844 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
376857 GGTCAACGAGTCG
1 GGTCAACGGGTCG
376870 GGT---CGGGTCG
1 GGTCAACGGGTCG
376880 GGTCAA
1 GGTCAA
376886 AACCGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 9 0.38
13 15 0.62
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:378746 original size:203 final size:203
Alignment explanation
Indices: 378378--378780 Score: 586
Period size: 203 Copynumber: 2.0 Consensus size: 203
378368 AACTCGACTT
*
378378 TTTACTCAAATATCACTAAAATAAAAATTAACTAAGAAAAATTCACTCGTTTTAGATTATTTTTA
1 TTTACTCAAATATCACTAAAATAAAAATTAACTAAGAAAAATACACTCGTTTTAGATTATTTTTA
* *
378443 ACATTGACACATTTTTTGCCACGTAAGATAAAGTTGTGTATCGTGGAAAGTGGTTTCTAGGAGGC
66 ACATTGACACATTTTTTGCCACGTAAGATAAAGTTGCGTATCGTGGAAAGTGGTTTCTAAGAGGC
* * *
378508 TTTTTTTTTAGCAACGAAGGAATTTTATCC-AAAAAATAAAGAGAAGGAATTTTGTCCAAAAAGA
131 TTTTTTTGTAGAAACGAAAGAATTTTATCCAAAAAAATAAAGAG--GGAATTTTGTCCAAAAAGA
378572 A-TAAATGTG
194 AGTAAATGTG
*
378581 TTTACTCATATATCACTAAAATAAAAATTAACTAAG-AAAATAACACTCGTTTT-GTATTATTTT
1 TTTACTCAAATATCACTAAAATAAAAATTAACTAAGAAAAAT-ACACTCGTTTTAG-ATTATTTT
* * *
378644 TCACATTGACACATTTTTTTGCCACGTAAGATAAAAG-TGCGTTTTGTGGAAAGTGGTTT-TAAG
64 TAACATTGACACA-TTTTTTGCCACGTAAGAT-AAAGTTGCGTATCGTGGAAAGTGGTTTCTAAG
*
378707 AGGCATTTTTTTGTAGAAACGAAAGAATTTTAT-CAAAAAAATAAAGAGGGAATTTTGTCCCAAA
127 AGGC-TTTTTTTGTAGAAACGAAAGAATTTTATCCAAAAAAATAAAGAGGGAATTTTGTCCAAAA
*
378771 ATAAGTAAAT
191 AGAAGTAAAT
378781 AAATGTGTGT
Statistics
Matches: 181, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
202 24 0.13
203 78 0.43
204 75 0.41
205 4 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (203 bp):
TTTACTCAAATATCACTAAAATAAAAATTAACTAAGAAAAATACACTCGTTTTAGATTATTTTTA
ACATTGACACATTTTTTGCCACGTAAGATAAAGTTGCGTATCGTGGAAAGTGGTTTCTAAGAGGC
TTTTTTTGTAGAAACGAAAGAATTTTATCCAAAAAAATAAAGAGGGAATTTTGTCCAAAAAGAAG
TAAATGTG
Found at i:381921 original size:20 final size:20
Alignment explanation
Indices: 381898--382005 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
381888 GTTTCTAGAT
* *
381898 TCGCAACGTGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* ** *
381918 TCGCAACGTGATAAT-ACAAAA
1 TCGCAACGCGATTCTGAC--TA
381939 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
381959 ACGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
381979 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
381999 TCGCAAC
1 TCGCAAC
382006 ACTGAATTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 2 0.03
20 59 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:382874 original size:24 final size:24
Alignment explanation
Indices: 382823--382876 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
382813 GTATTCGAAA
* *
382823 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATAACCAGAC
* *
382847 TTTGATCTTGGTCAATAATCAGAT
1 TTTGATCTTGGTCAATAACCAGAC
382871 TTTGAT
1 TTTGAT
382877 GATGCTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATAACCAGAC
Found at i:383084 original size:12 final size:13
Alignment explanation
Indices: 383069--383101 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
383059 AAAAGAATAA
383069 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
383081 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
383095 GAAGAAA
1 GAAGAAA
383102 ATGCCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:383095 original size:14 final size:14
Alignment explanation
Indices: 383076--383102 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
383066 TAAGAAGAAA
383076 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
383090 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
383103 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:385116 original size:18 final size:18
Alignment explanation
Indices: 385093--385127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
385083 ATAAAAAGGT
*
385093 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
385111 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
385128 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:385323 original size:20 final size:20
Alignment explanation
Indices: 385298--385517 Score: 214
Period size: 20 Copynumber: 11.7 Consensus size: 20
385288 TTACACATTC
*
385298 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
385318 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
385338 ATTTGACTATCATAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
385357 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
385372 ATTTGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
385392 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
385412 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
385432 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
385452 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
385472 A----A--ATCACAACGCGT
1 ATTTGACTATCGCAACGCGA
*
385486 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
385506 A-TTGACTTTCGC
1 ATTTGACTATCGC
385518 GTTGCGATTT
Statistics
Matches: 165, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
14 17 0.10
15 3 0.02
16 1 0.01
18 1 0.01
19 12 0.07
20 131 0.79
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:385372 original size:34 final size:34
Alignment explanation
Indices: 385326--385503 Score: 115
Period size: 34 Copynumber: 4.9 Consensus size: 34
385316 GAATTTGACT
*
385326 ATCGCAACGCGAATTTGACTATCATAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCACAACGCAAAA
* *
385360 ATCGCAATGCGAATTTGACTATCGCAACGCAAATTTGA
1 ATCGCAACGCGAATTTGACTATCACAACGCAAA----A
* * * *
385398 CTATCGCAACGGGAATTTGACTATCGCAACGTGAATTTGATT
1 --ATCGCAACGCGAATTTGACTATCACAACG-CAA----A-A
* *
385440 ATCGCAACGAGAATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCACAACGCA-AAA
* * * *
385474 ATCACAACGCGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCACAACGC
385504 GAATTGACTT
Statistics
Matches: 117, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
34 55 0.47
35 1 0.01
38 2 0.02
39 1 0.01
40 55 0.47
41 2 0.02
45 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCACAACGCAAAA
Found at i:385388 original size:54 final size:53
Alignment explanation
Indices: 385306--385517 Score: 228
Period size: 54 Copynumber: 3.8 Consensus size: 53
385296 TCATTTGAAT
**
385306 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCATAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-AAAA
* * *
385360 ATCGCAATGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGGGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC--GAA----A-A
* * *
385420 ATCGCAACGTGAATTTGATTATCGCAACGAGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGA-AAA
* * * *
385474 ATCACAACGCGTATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
385518 GTTGCGATTT
Statistics
Matches: 132, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
53 10 0.08
54 71 0.54
55 3 0.02
56 1 0.01
58 2 0.02
59 2 0.02
60 43 0.33
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (53 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAA
Found at i:385536 original size:20 final size:20
Alignment explanation
Indices: 385507--385570 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
385497 GCAACGCGAA
*
385507 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
385527 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
385547 TTGATTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
385567 TTGA
1 TTGA
385571 GTTTAGCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:385743 original size:63 final size:65
Alignment explanation
Indices: 385658--385811 Score: 188
Period size: 70 Copynumber: 2.3 Consensus size: 65
385648 TTTATATTTC
*
385658 AATCAATTAAACAAGCACAAATAAGAA-TTA-TTTACACATCAATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCAATTAAACAAATCAACTTTTA-A
385721 -
65 G
* * *
385721 AATCAATTAAACAAGCAAAAATAATAATAATTCTTATTTTCCTCATCAATTAAACAAATCAACTT
1 AATCAATTAAACAAGC--AAA-AATAAGAA-T-TTATTTTACACATCAATTAAACAAATCAACTT
385786 TTAAG
61 TTAAG
*
385791 AATCAATTAAACAATCAAAAA
1 AATCAATTAAACAAGCAAAAA
385812 AGTGTACCCC
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
63 16 0.21
65 2 0.03
66 7 0.09
67 2 0.03
68 3 0.04
69 4 0.05
70 44 0.56
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (65 bp):
AATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCAATTAAACAAATCAACTTTTAAG
Found at i:387150 original size:21 final size:21
Alignment explanation
Indices: 387126--387227 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
387116 GTGGGAGAAA
*
387126 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
*
387147 CCTCTTGAACGGTGGA-AGGGG
1 CCTCTTGAACGAT-GACAGGGG
* * *
387168 ACTCTTG-AGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
387188 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
387209 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
387228 TGAGTCGGGC
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
19 2 0.03
20 15 0.23
21 45 0.69
22 3 0.05
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.21
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:387192 original size:20 final size:20
Alignment explanation
Indices: 387136--387195 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
387126 CCTCTTCAAC
387136 GATGACAGGGGCCTCTTGAACG
1 GATGA-AGGGGCCTCTTG-ACG
*
387158 G-TGGAAGGGGACTCTTGA-G
1 GAT-GAAGGGGCCTCTTGACG
387177 GATGATAGGGGCCTCTTGA
1 GATGA-AGGGGCCTCTTGA
387196 ACGATAGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 12 0.36
22 3 0.09
ACGTcount: A:0.22, C:0.17, G:0.40, T:0.22
Consensus pattern (20 bp):
GATGAAGGGGCCTCTTGACG
Found at i:387214 original size:41 final size:41
Alignment explanation
Indices: 387136--387227 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
387126 CCTCTTCAAC
* *
387136 GATGACAGGGGCCTCTTGAACGGTGGAAGGGGACTCTTGAG
1 GATGACAGGGGCCTCTTGAACGATGGAAGAGGACTCTTGAG
* * *
387177 GATGATAGGGGCCTCTTGAACGATAGG-AGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGAAGAGGACTCTTG-AG
387219 GATGACAGG
1 GATGACAGG
387228 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
41 32 0.74
42 11 0.26
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (41 bp):
GATGACAGGGGCCTCTTGAACGATGGAAGAGGACTCTTGAG
Found at i:387728 original size:20 final size:20
Alignment explanation
Indices: 387703--387746 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
387693 AATAGTTTCT
387703 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
387723 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
387743 GAAA
1 GAAA
387747 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:387860 original size:19 final size:20
Alignment explanation
Indices: 387833--387871 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
387823 ACAACGCGAA
*
387833 TTTAGTTTCACGTTGCGATT
1 TTTAGTTTCACATTGCGATT
*
387853 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCACATTGCGATT
387872 ATCCCATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCACATTGCGATT
Found at i:387907 original size:20 final size:20
Alignment explanation
Indices: 387882--387924 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
387872 ATCCCATTGT
387882 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
**
387902 GATAGTCATTTTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
387922 GAT
1 GAT
387925 TTTAAGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GATAGTCAAATTCGCGTTGC
Found at i:387934 original size:20 final size:20
Alignment explanation
Indices: 387892--387935 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
387882 GATAGTCAAA
* *
387892 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
**
387912 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATAGTAAGT
387932 TTCG
1 TTCG
387936 TGTTACGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTAAGT
Found at i:389765 original size:20 final size:20
Alignment explanation
Indices: 389742--389808 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
389732 TTTGAAACTT
389742 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
389762 AAAATCACAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
389782 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
389801 AAAATCGC
1 AAAATCGC
389809 GTTGAGATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 6 0.15
20 33 0.85
ACGTcount: A:0.51, C:0.24, G:0.13, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:390510 original size:19 final size:19
Alignment explanation
Indices: 390486--390522 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
390476 TGCGATACTG
*
390486 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
*
390505 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCAATTT
390523 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:391991 original size:10 final size:10
Alignment explanation
Indices: 391976--392006 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
391966 AATGGGGTGG
391976 CAGTTTGACC
1 CAGTTTGACC
391986 CAGTTTGACC
1 CAGTTTGACC
391996 CAGTTTGACC
1 CAGTTTGACC
392006 C
1 C
392007 GACCTGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.29
Consensus pattern (10 bp):
CAGTTTGACC
Found at i:392041 original size:18 final size:18
Alignment explanation
Indices: 392001--392043 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
391991 TGACCCAGTT
** *
392001 TGACCCGACCTGTTGACC
1 TGACCCGACCCATTGACA
*
392019 CGACCCGACCCATTGACA
1 TGACCCGACCCATTGACA
392037 TGACCCG
1 TGACCCG
392044 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.16
Consensus pattern (18 bp):
TGACCCGACCCATTGACA
Found at i:392894 original size:42 final size:42
Alignment explanation
Indices: 392782--392986 Score: 198
Period size: 43 Copynumber: 4.7 Consensus size: 42
392772 AGTATTACAA
* * * *
392782 GTTCTTTTTCTGTGTGTAAGGGGTAAGCCTTACAGTTTTCTCAT
1 GTTC-TTTGCTGTGTGCAA-GGGTAAGCCTTACAGTTTCCTCAG
* *
392826 GTTCCTTTGCTGTGTGCAAGGATAAGCTTTACAGTTTCC-CTAG
1 GTT-CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTC-AG
** *
392869 GTTCTTTAATGTGTGCAAGGGTAAGCCTTACAGTTTTCTCAG
1 GTTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTCAG
*
392911 GTTCATTTGCTGTGTGCAATGGTAAGCCTTACAGTTTTCCT-AG
1 GTTC-TTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCTCAG
* * * *
392954 GCTCATCTGCTTTGTGCACAGGTTAAGCCTTAC
1 GTTC-TTTGCTGTGTGCA-AGGGTAAGCCTTAC
392987 CGATGTACAG
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
42 37 0.27
43 65 0.48
44 32 0.24
45 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (42 bp):
GTTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTCAG
Found at i:392897 original size:85 final size:86
Alignment explanation
Indices: 392792--392954 Score: 258
Period size: 85 Copynumber: 1.9 Consensus size: 86
392782 GTTCTTTTTC
* * * *
392792 TGTGTGTAAGGGGTAAGCCTTACAGTTTTCTCATGTTCCTTTGCTGTGTGCAA-GGATAAGCTTT
1 TGTGTGCAAGGGGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAATGG-TAAGCCTT
392856 ACAGTTTCCCTAGGTTCTTTAA
65 ACAGTTTCCCTAGGTTCTTTAA
392878 TGTGTGCAA-GGGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAATGGTAAGCCTTA
1 TGTGTGCAAGGGGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAATGGTAAGCCTTA
*
392942 CAGTTTTCCTAGG
66 CAGTTTCCCTAGG
392955 CTCATCTGCT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 61 0.86
86 10 0.14
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (86 bp):
TGTGTGCAAGGGGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAATGGTAAGCCTTA
CAGTTTCCCTAGGTTCTTTAA
Found at i:392970 original size:43 final size:42
Alignment explanation
Indices: 392803--392986 Score: 203
Period size: 43 Copynumber: 4.3 Consensus size: 42
392793 GTGTGTAAGG
* *
392803 GGTAAGCCTTACAGTTTTCTCATGTTCCTTTGCTGTGTGCAA
1 GGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAA
* * **
392845 GGATAAGCTTTACAG-TTTCCCTAGGTTC-TTTAATGTGTGCAA
1 GG-TAAGCCTTACAGTTTTCTC-AGGTTCATTTGCTGTGTGCAA
392887 GGGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAA
1 -GGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAA
* * *
392930 TGGTAAGCCTTACAGTTTTC-CTAGGCTCATCTGCTTTGTGCACA
1 -GGTAAGCCTTACAGTTTTCTC-AGGTTCATTTGCTGTGTGCA-A
392974 GGTTAAGCCTTAC
1 GG-TAAGCCTTAC
392987 CGATGTACAG
Statistics
Matches: 121, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
42 37 0.31
43 73 0.60
44 11 0.09
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (42 bp):
GGTAAGCCTTACAGTTTTCTCAGGTTCATTTGCTGTGTGCAA
Found at i:393973 original size:20 final size:21
Alignment explanation
Indices: 393924--393973 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
393914 AAAGAATTTA
*
393924 TAAAAGTTATGATTTTGATTT
1 TAAAAGTTATGATTTTGATAT
**
393945 TAAGTGTTA-GATTTTGATAT
1 TAAAAGTTATGATTTTGATAT
393965 TAAAAGTTA
1 TAAAAGTTA
393974 AAATATTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAAAGTTATGATTTTGATAT
Found at i:394415 original size:2 final size:2
Alignment explanation
Indices: 394408--394445 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
394398 TGAAGCAAAC
394408 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
394446 TAAATTTATT
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:396541 original size:13 final size:13
Alignment explanation
Indices: 396523--396547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
396513 ATGATTAAAA
396523 TTTTAAAAAATAT
1 TTTTAAAAAATAT
396536 TTTTAAAAAATA
1 TTTTAAAAAATA
396548 ATTAAAAATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:399483 original size:20 final size:20
Alignment explanation
Indices: 399422--399484 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
399412 AAATTTCAAA
*
399422 TTTATTTTAAAATACTAAA-
1 TTTATTTTAAAATATTAAAT
* * *
399441 TTTATATTTATACACATTGAAT
1 TTTAT-TTTA-AAATATTAAAT
399463 TTTATTTTAAAATATTAAAT
1 TTTATTTTAAAATATTAAAT
399483 TT
1 TT
399485 GTTATAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 10 0.29
22 5 0.15
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTATTTTAAAATATTAAAT
Found at i:399523 original size:24 final size:24
Alignment explanation
Indices: 399454--399523 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
399444 ATATTTATAC
*
399454 ACATTGAATTTTATTTTAAAATATT
1 ACATT-AATTATATTTTAAAATATT
* ** *
399479 AAATTTGTTATAATTTT-AAATCTT
1 ACATTAATTAT-ATTTTAAAATATT
399503 ACATTAATTATATTTTAAAAT
1 ACATTAATTATATTTTAAAAT
399524 GTGTATATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
23 5 0.14
24 21 0.60
25 9 0.26
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (24 bp):
ACATTAATTATATTTTAAAATATT
Found at i:400447 original size:2 final size:2
Alignment explanation
Indices: 400440--400470 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
400430 TATAATTTTC
400440 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400471 CATTTTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:410132 original size:41 final size:41
Alignment explanation
Indices: 410083--410167 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
410073 CTCAAATCAA
*
410083 CATCTCAACTACTTCCATATGCAGTAAATAAGATATGTCAC
1 CATCTCAACTACTTCCATACGCAGTAAATAAGATATGTCAC
410124 CATCTCAACTACTTCCATACGCAGTAAATAAGATATGTCAC
1 CATCTCAACTACTTCCATACGCAGTAAATAAGATATGTCAC
410165 CAT
1 CAT
410168 AAGTATGATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (41 bp):
CATCTCAACTACTTCCATACGCAGTAAATAAGATATGTCAC
Found at i:411763 original size:3 final size:3
Alignment explanation
Indices: 411748--411781 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
411738 GGTTAAAGAA
*
411748 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
411782 AGTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:413131 original size:14 final size:16
Alignment explanation
Indices: 413107--413139 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
413097 GTTTATTTTG
413107 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
413122 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
413137 TTT
1 TTT
413140 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:414820 original size:14 final size:14
Alignment explanation
Indices: 414782--414830 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
414772 TTATTTAAGG
* *
414782 TTTAAGATTTTGGAT
1 TTTAAGA-TTTAGAA
*
414797 TTTAATATTTAGAA
1 TTTAAGATTTAGAA
*
414811 TTTAAGATTTAAAA
1 TTTAAGATTTAGAA
414825 TTTAAG
1 TTTAAG
414831 GTTTTAGGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 23 0.79
15 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (14 bp):
TTTAAGATTTAGAA
Found at i:415351 original size:78 final size:78
Alignment explanation
Indices: 415158--415343 Score: 275
Period size: 78 Copynumber: 2.4 Consensus size: 78
415148 TTTCCTGTAG
* * *
415158 AAAAAAATAATGTTTTAGGTAGTGCTTTACCGGAAATGTTAGACATTTTAGGTAGCACTCAATAT
1 AAAAAAATAATGTTTTAGGTAGTGTTTTACCGGAAATGTCAAACATTTTAGGTAGCACTCAATAT
**
415223 TAACATTTTGGTA
66 TAACATTTCAGTA
*
415236 AAAAAAATAATGTTTTAGGTAGTGTTTTACCGGAAATGTCAAACATTTTAGGTAGCGC-CAATAT
1 AAAAAAATAATGTTTTAGGTAGTGTTTTACCGGAAATGTCAAACATTTTAGGTAGCACTCAATAT
*
415300 TAACACTTTCATTA
66 TAACA-TTTCAGTA
* *
415314 GAAAAAATAATGTTTTAGGTAGCGTTTTAC
1 AAAAAAATAATGTTTTAGGTAGTGTTTTAC
415344 TGAAAATGGT
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 11 0.11
78 87 0.89
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (78 bp):
AAAAAAATAATGTTTTAGGTAGTGTTTTACCGGAAATGTCAAACATTTTAGGTAGCACTCAATAT
TAACATTTCAGTA
Found at i:416491 original size:36 final size:35
Alignment explanation
Indices: 416451--416580 Score: 134
Period size: 36 Copynumber: 3.6 Consensus size: 35
416441 GTGTTGGTGT
* *
416451 AGGTGGAGGACATGGAGGTGGTATTGGAGGAGGAAA
1 AGGTGGAGGA-TTGGTGGTGGTATTGGAGGAGGAAA
* * *
416487 AGGTGGAGGTATTGGTGGTGGTGTAGGAGGAGGACA
1 AGGTGGAGG-ATTGGTGGTGGTATTGGAGGAGGAAA
* * * *
416523 TGGAGGTGGTGTTGGTGGTGGTATTGGAGGAGGAAA
1 AGGTGGAGG-ATTGGTGGTGGTATTGGAGGAGGAAA
*
416559 AGGTGGAGGTTTTGGTGGTGGT
1 AGGTGGAGG-ATTGGTGGTGGT
416581 GTAGGTGGAG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
36 76 0.99
37 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.52, T:0.25
Consensus pattern (35 bp):
AGGTGGAGGATTGGTGGTGGTATTGGAGGAGGAAA
Found at i:416497 original size:24 final size:24
Alignment explanation
Indices: 416470--416573 Score: 66
Period size: 24 Copynumber: 4.3 Consensus size: 24
416460 ACATGGAGGT
416470 GGTATTGGAGGAGGAAAAGGTGGA
1 GGTATTGGAGGAGGAAAAGGTGGA
* * *** *
416494 GGTATTGGTGGTGGTGTAGGAGGA
1 GGTATTGGAGGAGGAAAAGGTGGA
* * **** *
416518 GG-ACATGGAGGTGGTGTTGGTGGT
1 GGTA-TTGGAGGAGGAAAAGGTGGA
416542 GGTATTGGAGGAGGAAAAGGTGGA
1 GGTATTGGAGGAGGAAAAGGTGGA
*
416566 GGTTTTGG
1 GGTATTGG
416574 TGGTGGTGTA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.52, T:0.25
Consensus pattern (24 bp):
GGTATTGGAGGAGGAAAAGGTGGA
Found at i:416562 original size:72 final size:72
Alignment explanation
Indices: 416467--416616 Score: 264
Period size: 72 Copynumber: 2.1 Consensus size: 72
416457 AGGACATGGA
416467 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTATTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGG
1 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTATTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGG
*
416532 TGTTGGT
66 TGTAGGT
* *
416539 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTTTTGGTGGTGGTGTAGGTGGAGGACATGGAGGTGG
1 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTATTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGG
416604 TGTAGGT
66 TGTAGGT
*
416611 AGTGGT
1 GGTGGT
416617 GGTGGCTTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.20, C:0.01, G:0.53, T:0.26
Consensus pattern (72 bp):
GGTGGTATTGGAGGAGGAAAAGGTGGAGGTATTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGG
TGTAGGT
Found at i:416586 original size:24 final size:24
Alignment explanation
Indices: 416487--416610 Score: 108
Period size: 24 Copynumber: 5.2 Consensus size: 24
416477 GAGGAGGAAA
*
416487 AGGTGGAGGTATTGGTGGTGGTGT
1 AGGTGGAGGTATTGGAGGTGGTGT
* *
416511 AGGAGGAGG-ACATGGAGGTGGTGT
1 AGGTGGAGGTA-TTGGAGGTGGTGT
* * * ***
416535 TGGTGGTGGTATTGGAGGAGGAAA
1 AGGTGGAGGTATTGGAGGTGGTGT
* *
416559 AGGTGGAGGTTTTGGTGGTGGTGT
1 AGGTGGAGGTATTGGAGGTGGTGT
*
416583 AGGTGGAGG-ACATGGAGGTGGTGT
1 AGGTGGAGGTA-TTGGAGGTGGTGT
416607 AGGT
1 AGGT
416611 AGTGGTGGTG
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
23 1 0.01
24 73 0.97
25 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.53, T:0.27
Consensus pattern (24 bp):
AGGTGGAGGTATTGGAGGTGGTGT
Found at i:416591 original size:36 final size:36
Alignment explanation
Indices: 416467--416592 Score: 153
Period size: 36 Copynumber: 3.5 Consensus size: 36
416457 AGGACATGGA
* *
416467 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTATTGGT
1 GGTGGTGTAGGAGGAGGAAAAGGTGGAGGTATTGGT
* * * * *
416503 GGTGGTGTAGGAGGAGGACATGGAGGTGGTGTTGGT
1 GGTGGTGTAGGAGGAGGAAAAGGTGGAGGTATTGGT
* * *
416539 GGTGGTATTGGAGGAGGAAAAGGTGGAGGTTTTGGT
1 GGTGGTGTAGGAGGAGGAAAAGGTGGAGGTATTGGT
*
416575 GGTGGTGTAGGTGGAGGA
1 GGTGGTGTAGGAGGAGGA
416593 CATGGAGGTG
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.21, C:0.01, G:0.53, T:0.25
Consensus pattern (36 bp):
GGTGGTGTAGGAGGAGGAAAAGGTGGAGGTATTGGT
Found at i:416616 original size:36 final size:36
Alignment explanation
Indices: 416498--416617 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
416488 GGTGGAGGTA
416498 TTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGGTG
1 TTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGGTG
* * * * * * *
416534 TTGGTGGTGGTATTGGAGGAGGAAAAGGTGGAGGTT
1 TTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGGTG
*
416570 TTGGTGGTGGTGTAGGTGGAGGACATGGAGGTGGTG
1 TTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGGTG
* *
416606 TAGGTAGTGGTG
1 TTGGTGGTGGTG
416618 GTGGCTTTGG
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.17, C:0.02, G:0.53, T:0.28
Consensus pattern (36 bp):
TTGGTGGTGGTGTAGGAGGAGGACATGGAGGTGGTG
Found at i:416618 original size:30 final size:30
Alignment explanation
Indices: 416584--416640 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
416574 TGGTGGTGTA
*
416584 GGTGGAGGAC-ATGGAGGTGGTGTAGGTAGT
1 GGTGGAGG-CTATGGAGGCGGTGTAGGTAGT
* *
416614 GGTGGTGGCTTTGGAGGCGGTGTAGGT
1 GGTGGAGGCTATGGAGGCGGTGTAGGT
416641 GGAGGACACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.14, C:0.05, G:0.54, T:0.26
Consensus pattern (30 bp):
GGTGGAGGCTATGGAGGCGGTGTAGGTAGT
Found at i:416636 original size:54 final size:54
Alignment explanation
Indices: 416560--416735 Score: 154
Period size: 54 Copynumber: 3.0 Consensus size: 54
416550 AGGAGGAAAA
* * * * *
416560 GGTGGAGGTTTTGGTGGTGGTGTAGGTGGAGGACATGGAGGTGGTGTAGGTAGT
1 GGTGGTGGATTTGGAGGCGGTGTAGGTGGAGGACATGGAGGTGGTGTAGGTGGT
* *
416614 GGTGGTGGCTTTGGAGGCGGTGTAGGTGGAGGACACGAAGGAGGTATTGGTGGTGGTGTAGGTGG
1 GGTGGTGGATTTGGAGGCGGTGTAGGTGGAGG--AC---------A-TGGAGGTGGTGTAGGTGG
416679 T
54 T
* * *
416680 GGTGGTGGATTTAGAGGCGGCGTAGGTGGAGGACATGGAGGTGGTGCAGGTGGT
1 GGTGGTGGATTTGGAGGCGGTGTAGGTGGAGGACATGGAGGTGGTGTAGGTGGT
416734 GG
1 GG
416736 ACATGGAGGT
Statistics
Matches: 99, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
54 47 0.47
55 1 0.01
56 2 0.02
64 2 0.02
65 1 0.01
66 46 0.46
ACGTcount: A:0.15, C:0.05, G:0.54, T:0.26
Consensus pattern (54 bp):
GGTGGTGGATTTGGAGGCGGTGTAGGTGGAGGACATGGAGGTGGTGTAGGTGGT
Found at i:416732 original size:66 final size:66
Alignment explanation
Indices: 416599--416735 Score: 184
Period size: 66 Copynumber: 2.1 Consensus size: 66
416589 AGGACATGGA
* * * **
416599 GGTGGTGTAGGTAGTGGTGGTGGCTTTGGAGGCGGTGTAGGTGGAGGACACGAAGGAGGTATTGG
1 GGTGGTGTAGGTAGTGGTGGTGGATTTAGAGGCGGCGTAGGTGGAGGACACGAAGGAGGTACAGG
416664 T
66 T
* * * * *
416665 GGTGGTGTAGGTGGTGGTGGTGGATTTAGAGGCGGCGTAGGTGGAGGACATGGAGGTGGTGCAGG
1 GGTGGTGTAGGTAGTGGTGGTGGATTTAGAGGCGGCGTAGGTGGAGGACACGAAGGAGGTACAGG
416730 T
66 T
416731 GGTGG
1 GGTGG
416736 ACATGGAGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.15, C:0.06, G:0.54, T:0.25
Consensus pattern (66 bp):
GGTGGTGTAGGTAGTGGTGGTGGATTTAGAGGCGGCGTAGGTGGAGGACACGAAGGAGGTACAGG
T
Found at i:416758 original size:24 final size:24
Alignment explanation
Indices: 416701--416758 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
416691 TAGAGGCGGC
* *
416701 GTAGGTGGAGGACATGGAGGTGGT
1 GTAGGTGGTGGACATGGAGGTGGA
*
416725 GCAGGTGGTGGACATGGAGGTGGA
1 GTAGGTGGTGGACATGGAGGTGGA
*
416749 GTAGGAGGTG
1 GTAGGTGGTG
416759 ATTTTGGAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.05, G:0.55, T:0.19
Consensus pattern (24 bp):
GTAGGTGGTGGACATGGAGGTGGA
Found at i:418832 original size:24 final size:24
Alignment explanation
Indices: 418800--418989 Score: 116
Period size: 24 Copynumber: 7.9 Consensus size: 24
418790 GTTGGTGGTA
*
418800 GTGTAGGTGGAGGACATGGAGGTG
1 GTGTAGGTGGAGGATATGGAGGTG
* * * *
418824 GTGTAGGTGGTGGCTTTGGAGACT-
1 GTGTAGGTGGAGGATATGGAG-GTG
* * * ***
418848 ATGTAGGTGAAGGACACAAAGGTG
1 GTGTAGGTGGAGGATATGGAGGTG
* * * * * *
418872 GTGCAGGTGGGGGTTTTGCAGGAG
1 GTGTAGGTGGAGGATATGGAGGTG
***
418896 GAAAAGGTGGAGG-TATCGGAGGTG
1 GTGTAGGTGGAGGATAT-GGAGGTG
*
418920 GTATAGGTGGAGGATATGGAGGTG
1 GTGTAGGTGGAGGATATGGAGGTG
*
418944 GTGTAGGTGGAAGATATGGAGGAT-
1 GTGTAGGTGGAGGATATGGAGG-TG
* *
418968 ATGGAGGTGGAGGATATGGAGG
1 GTGTAGGTGGAGGATATGGAGG
418990 CGGAGGAGGA
Statistics
Matches: 121, Mismatches: 40, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
23 3 0.02
24 113 0.93
25 5 0.04
ACGTcount: A:0.24, C:0.04, G:0.49, T:0.23
Consensus pattern (24 bp):
GTGTAGGTGGAGGATATGGAGGTG
Found at i:418942 original size:15 final size:15
Alignment explanation
Indices: 418924--418996 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
418914 GAGGTGGTAT
418924 AGGTGGAGGATATGG
1 AGGTGGAGGATATGG
* * **
418939 AGGTGGTGTAGGTGG
1 AGGTGGAGGATATGG
*
418954 AAGATATGGAGGATATGG
1 -AGGT--GGAGGATATGG
418972 AGGTGGAGGATATGG
1 AGGTGGAGGATATGG
*
418987 AGGCGGAGGA
1 AGGTGGAGGA
418997 GGATTAGTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
15 31 0.70
16 3 0.07
17 3 0.07
18 7 0.16
ACGTcount: A:0.27, C:0.01, G:0.52, T:0.19
Consensus pattern (15 bp):
AGGTGGAGGATATGG
Found at i:418997 original size:24 final size:23
Alignment explanation
Indices: 418924--418998 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
418914 GAGGTGGTAT
* *
418924 AGGTGGAGGATATGGAGGTGGTGT
1 AGGTGGAGGATATGGAGG-GGAGG
* **
418948 AGGTGGAAGATATGGAGGATATGG
1 AGGTGGAGGATATGGAGGGGA-GG
418972 AGGTGGAGGATATGGAGGCGGAGG
1 AGGTGGAGGATATGGAGG-GGAGG
418996 AGG
1 AGG
418999 ATTAGTTGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.53, T:0.19
Consensus pattern (23 bp):
AGGTGGAGGATATGGAGGGGAGG
Found at i:420010 original size:43 final size:43
Alignment explanation
Indices: 419949--420090 Score: 178
Period size: 43 Copynumber: 3.5 Consensus size: 43
419939 GTTCACGGCG
* *
419949 TTTTTA-A-AAACGCCGCAATAGGTGTTGATATTTAGCGGTGT
1 TTTTTAGACAAACGACGCAATAGGTGTTGATATTTAGCGGGGT
*
419990 TTTTTAGACAAACGACGCAATAAGTGTTGATATTTAGCGGGGT
1 TTTTTAGACAAACGACGCAATAGGTGTTGATATTTAGCGGGGT
*
420033 TTTTTAGACAAACGACGCAATA-G-GTT--TATTTAGCGAGGT
1 TTTTTAGACAAACGACGCAATAGGTGTTGATATTTAGCGGGGT
420072 TTTTT---CAAACG-CGCAATAG
1 TTTTTAGACAAACGACGCAATAG
420091 ATATTTAGCG
Statistics
Matches: 94, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.07
36 6 0.06
39 17 0.18
41 9 0.10
42 2 0.02
43 53 0.56
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTTTAGACAAACGACGCAATAGGTGTTGATATTTAGCGGGGT
Found at i:420182 original size:43 final size:41
Alignment explanation
Indices: 420135--420297 Score: 152
Period size: 43 Copynumber: 3.9 Consensus size: 41
420125 TTTTTCTTAT
420135 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGTCATAA
1 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTT-T-ATAA
** *
420178 AAACGCCGTAATAGGTGTTGATATTTAGCAGCGGTTTT-TAGA
1 AAACGCCACAATAGGTGTTGATATTTAGCGGC-GTTTTATA-A
* * *
420220 CAAACG-CACAATAGGT-TATAATGTTTAGCGGCGTTTTATTA
1 -AAACGCCACAATAGGTGT-TGATATTTAGCGGCGTTTTATAA
* * * * *
420261 AAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTT
1 AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTT
420298 TCTCACAAAC
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
40 5 0.05
41 33 0.33
42 22 0.22
43 35 0.35
44 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
AAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTTATAA
Found at i:420306 original size:83 final size:86
Alignment explanation
Indices: 420110--420308 Score: 212
Period size: 83 Copynumber: 2.4 Consensus size: 86
420100 GAATGCGCAA
* * * *
420110 TTGATA-TTAGCGGTATTTTTCTTATAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGTC
1 TTGATATTTAGCGGCATTTTTCTCACAAACGCCACAATAGGTGTTAATATTTAGCGGCGTTTGTC
*
420174 ATAAAAACGCCGTAATAGGTG
66 ATAAAAACGCCGCAATAGGTG
* * ** *
420195 TTGATATTTAGCAGCGGTTTTT-AGACAAACG-CACAATAGGT-TATAATGTTTAGCGGCGTTT-
1 TTGATATTTAGCGGC-ATTTTTCTCACAAACGCCACAATAGGTGT-TAATATTTAGCGGCGTTTG
* *
420256 T-ATTAAAACGCCGCAGTAGGTG
64 TCATAAAAACGCCGCAATAGGTG
* *
420278 TTGATGTTTTGCGGCATTTTTCTCACAAACG
1 TTGATATTTAGCGGCATTTTTCTCACAAACG
420309 TCGTAGTAGG
Statistics
Matches: 93, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
82 5 0.05
83 37 0.40
84 2 0.02
85 32 0.34
86 12 0.13
87 5 0.05
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (86 bp):
TTGATATTTAGCGGCATTTTTCTCACAAACGCCACAATAGGTGTTAATATTTAGCGGCGTTTGTC
ATAAAAACGCCGCAATAGGTG
Found at i:420318 original size:43 final size:43
Alignment explanation
Indices: 420261--420357 Score: 131
Period size: 43 Copynumber: 2.3 Consensus size: 43
420251 CGTTTTATTA
*
420261 AAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTTTCTCAC
1 AAACGCCGTAGTAGGTGTTGATGTTTTGCGGCATTTTTCTCAC
* * ** * *
420304 AAACGTCGTAGTAGGTTTTGATGTTTTGTTGCGTTTTTCTCAT
1 AAACGCCGTAGTAGGTGTTGATGTTTTGCGGCATTTTTCTCAC
420347 AAACGCCGTAG
1 AAACGCCGTAG
420358 GCATTGATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (43 bp):
AAACGCCGTAGTAGGTGTTGATGTTTTGCGGCATTTTTCTCAC
Done.