Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008071.1 Hibiscus syriacus cultivar Beakdansim tig00110569_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: 1969971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 7 of 8
Found at i:1525734 original size:19 final size:20
Alignment explanation
Indices: 1525691--1525746 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1525681 ACGAAAATGA
1525691 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1525711 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1525730 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1525747 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1525773 original size:18 final size:18
Alignment explanation
Indices: 1525719--1525846 Score: 109
Period size: 14 Copynumber: 7.7 Consensus size: 18
1525709 GGAAATGGCT
1525719 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
1525738 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
*
1525752 ATCGCAATGTGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1525770 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
1525784 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
1525802 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
*
1525816 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
1525835 ATCGCAATGCGA
1 ATCGCAATGCGA
1525847 TTTGTGTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
14 27 0.31
16 18 0.21
17 4 0.05
18 18 0.21
19 20 0.23
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:1525777 original size:32 final size:33
Alignment explanation
Indices: 1525719--1525841 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
1525709 GGAAATGGCT
1525719 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1525752 ATCGCAATGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1525784 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1525816 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1525842 TGCGATTTGT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 62 0.72
33 24 0.28
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1525877 original size:14 final size:14
Alignment explanation
Indices: 1525858--1525914 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
1525848 TTGTGTTTCG
*
1525858 CGTTGCAATTTTGT
1 CGTTGCGATTTTGT
*
1525872 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1525888 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1525904 CGTTGCGATTT
1 CGTTGCGATTT
1525915 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.58
16 4 0.11
18 11 0.31
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1525928 original size:32 final size:32
Alignment explanation
Indices: 1525853--1525930 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
1525843 GCGATTTGTG
*
1525853 TTTCGCGTTGCAATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1525885 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
*
1525917 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1525931 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:1525949 original size:20 final size:19
Alignment explanation
Indices: 1525915--1525969 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1525905 GTTGCGATTT
*
1525915 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1525934 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1525954 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1525970 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1527079 original size:10 final size:9
Alignment explanation
Indices: 1527056--1527083 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1527046 GTTAGTGTTT
1527056 ATTTTTTAA
1 ATTTTTTAA
1527065 ATTTTTTAA
1 ATTTTTTAA
1527074 ATTTTTTAA
1 ATTTTTTAA
1527083 A
1 A
1527084 GGTGTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:1527889 original size:13 final size:13
Alignment explanation
Indices: 1527842--1527894 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1527832 TTGATTGTTT
1527842 AATTGATTTGTAA
1 AATTGATTTGTAA
*
1527855 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
1527869 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
1527883 AATTGATGTGTA
1 AATTGATTTGTA
1527895 CATAATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:1528006 original size:14 final size:14
Alignment explanation
Indices: 1527987--1528040 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1527977 CGAAATGGCT
1527987 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1528001 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1528020 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1528034 ATCGCAA
1 ATCGCAA
1528041 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1529154 original size:24 final size:24
Alignment explanation
Indices: 1529127--1529180 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1529117 GTATTCGAAA
* *
1529127 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1529151 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1529175 TTTGAT
1 TTTGAT
1529181 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1529372 original size:12 final size:12
Alignment explanation
Indices: 1529355--1529379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1529345 ATATAATACT
1529355 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1529367 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1529379 G
1 G
1529380 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:1531693 original size:19 final size:19
Alignment explanation
Indices: 1531671--1531762 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
1531661 GGAAATTACT
1531671 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1531690 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1531704 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
1531723 ATCGTAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1531737 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1531756 ATCGCAA
1 ATCGCAA
1531763 CGAGGGAATC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 17 0.32
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 24 0.45
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1531713 original size:33 final size:33
Alignment explanation
Indices: 1531671--1531782 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 33
1531661 GGAAATTACT
1531671 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
1531704 ATCGCAATGCGAAATGAAAATCGTAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1531736 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1531770 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1531783 TTTAATTTCG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.01
33 65 0.97
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1531800 original size:19 final size:20
Alignment explanation
Indices: 1531778--1531820 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1531768 GAATCGCAAC
1531778 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1531797 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1531817 GCGA
1 GCGA
1531821 TTCTCTCGTT
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:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1531805 original size:14 final size:14
Alignment explanation
Indices: 1531806--1531839 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1531796 TGCGATTTTC
1531806 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1531820 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1531834 ATTTTC
1 ATTTTC
1531840 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1531980 original size:14 final size:14
Alignment explanation
Indices: 1531961--1531997 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1531951 CATCAATTAA
1531961 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1531975 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1531989 ACAAATCAA
1 ACAAATCAA
1531998 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1533421 original size:21 final size:21
Alignment explanation
Indices: 1533355--1533421 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1533345 GTGAATCGGG
*
1533355 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1533375 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1533397 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1533418 CTCT
1 CTCT
1533422 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1535561 original size:33 final size:33
Alignment explanation
Indices: 1535504--1535602 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1535494 ACGAGATAAT
*
1535504 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1535538 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1535571 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1535603 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1535617 original size:39 final size:38
Alignment explanation
Indices: 1535574--1535656 Score: 148
Period size: 39 Copynumber: 2.2 Consensus size: 38
1535564 GCGACCAGAC
1535574 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1535613 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1535651 AATCGC
1 AATCGC
1535657 GTTGCGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 16 0.37
39 27 0.63
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1535663 original size:19 final size:19
Alignment explanation
Indices: 1535479--1535656 Score: 160
Period size: 19 Copynumber: 9.7 Consensus size: 19
1535469 TCTTTTGGTT
* *
1535479 GAAATGAAAATCGTAACGA
1 GAAATGAAAATCGCAACGC
*
1535498 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1535518 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1535536 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1535552 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1535570 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1535585 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1535605 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1535624 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1535643 GAAATGAAAATCGC
1 GAAATGAAAATCGC
1535657 GTTGCGATTA
Statistics
Matches: 131, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.15
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 56 0.43
20 44 0.34
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1536250 original size:20 final size:20
Alignment explanation
Indices: 1536225--1536277 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1536215 GCGCTATGTA
1536225 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1536245 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1536265 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1536278 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1536338 original size:41 final size:41
Alignment explanation
Indices: 1536246--1536340 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
1536236 GAAAGTCAGA
* * * * ** *
1536246 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
1536287 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
1536329 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1536341 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:1536451 original size:21 final size:21
Alignment explanation
Indices: 1536390--1536443 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1536380 ACTGTATACC
1536390 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
1536411 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
1536432 ATCGCAACGCGA
1 ATCGCAACGCGA
1536444 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:1553730 original size:141 final size:141
Alignment explanation
Indices: 1553039--1554064 Score: 998
Period size: 141 Copynumber: 7.2 Consensus size: 141
1553029 TTTCACAACA
* * * * * *
1553039 ACTAAGACCGAGAAGATCACCATCACCGATTCCATTGGTGATGAGAAAAACCGCATTGATGACGG
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGG-G--GAGAAAAACCGCGTTGGTGACGA
* * * * * **
1553104 TGGAA--AAGTACTCGGATATGGAGAATTCTGATCAGCAAGATAAAGAACATAATGATCCCGATA
63 T-GAAGCAA-CACTCCGAAATGGAGGATTCTG---AGCAAGATAAGGAACATAATGATCGAGATA
1553167 AAGAAAGCGAACAACCCAC
123 AAGAAAGCGAACAACCCAC
* * * * * *
1553186 ACTAGGACCAAGAAGATCAACGTCACCGATACCGATGGTGATGAGAAAGAA-TGCAG-TGGTTAC
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGG-G--GAGAAA-AACCGC-GTTGGTGAC
* ** * * * **
1553249 GGTGAAGCAGTACT-CGGACTTGA-GAGTTCTGAGCAAGATAAGGAACATAATGATCCTGATAAA
61 GATGAAGCAACACTCCGAAATGGAGGA-TTCTGAGCAAGATAAGGAACATAATGATCGAGATAAA
*
1553312 GAAAGCGAACAACTCAC
125 GAAAGCGAACAACCCAC
* * ** * ** * *
1553329 ACTAGGACCGAGAAGATCACCATCACCGATACCGATAGTGATGAGAAAGATGGCGGTGGTGACGG
1 ACTAAGACCAAGAAGATCACCATCACCGATACC-A-A-TGGGGAGAAAAACCGCGTTGGTGACGA
* * * * * * *
1553394 TGAAGCAGCATTCCGAAATGGAGGATTCTGAGCAAGATGAGAAACATAAAGATCGGGATAAAGAC
63 TGAAGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAA
1553459 AGCGAACAACCCAC
128 AGCGAACAACCCAC
* * * * * * **
1553473 ATTAACACCGAGAAGATCACCATCACCGATGCCAATGGTGATGAGAAAGACCGCATTGACGACGA
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGG-G--GAGAAAAACCGCGTTGGTGACGA
* * *
1553538 CGAAACAACACCCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAA
63 TGAAGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAA
1553603 AGCGAA-AACCCTAC
128 AGCGAACAACCC-AC
* * *
1553617 ACTAAGACCAAAAAGATCACCATCACCGATACCAATGGGGGGAAAAACCGCGTTGGTGACGACGA
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGGGGAGAAAAACCGCGTTGGTGACGATGA
* *
1553682 AGCAACACTCCGAAATAGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAAAGT
66 AGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAAAGC
*
1553747 GAACAACCCAT
131 GAACAACCCAC
* *
1553758 ACGAAGAACAAGAAGATCACCATCACCGATACCAATGGGG-GAACAAACCGCGTTGGTGACGATG
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGGGGAGAA-AAACCGCGTTGGTGACGATG
*
1553822 AAGCAACACTCCGAAATAGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAAAG
65 AAGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAAAG
* *
1553887 TGAACAACCCAT
130 CGAACAACCCAC
* * * ** * *
1553899 ACGAAGAACAAGAAGATCACCGTCACCGATACCGTTGGGAAGAAAGACCGCGTTGGTGACGATGA
1 ACTAAGACCAAGAAGATCACCATCACCGATACCAATGGGGAGAAAAACCGCGTTGGTGACGATGA
* * * * * * * * *
1553964 AG---CAGTCGGAAATGGAGAATTCCGAGCAAGTTAAGGGACATGACGATC-ATGTTAAAGAAAG
66 AGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGA-GATAAAGAAAG
1554025 CGAACAACCCAC
130 CGAACAACCCAC
*
1554037 ACTGAAG-CCAAGAAGATCACAATCACCG
1 ACT-AAGACCAAGAAGATCACCATCACCG
1554065 TTAACAGCAA
Statistics
Matches: 753, Mismatches: 105, Indels: 51
0.83 0.12 0.06
Matches are distributed among these distances:
137 1 0.00
138 77 0.10
139 3 0.00
140 3 0.00
141 279 0.37
142 11 0.01
143 109 0.14
144 194 0.26
145 4 0.01
146 14 0.02
147 55 0.07
148 3 0.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.15
Consensus pattern (141 bp):
ACTAAGACCAAGAAGATCACCATCACCGATACCAATGGGGAGAAAAACCGCGTTGGTGACGATGA
AGCAACACTCCGAAATGGAGGATTCTGAGCAAGATAAGGAACATAATGATCGAGATAAAGAAAGC
GAACAACCCAC
Found at i:1556421 original size:13 final size:13
Alignment explanation
Indices: 1556399--1556470 Score: 81
Period size: 13 Copynumber: 5.2 Consensus size: 13
1556389 CACAACCCGG
*
1556399 CCCGAACCGTTGA
1 CCCGACCCGTTGA
1556412 CCCGACCCGTTGACCCGA
1 CCCGACCCGTT-----GA
*
1556430 CCCGACCCGTTTA
1 CCCGACCCGTTGA
1556443 CCCGACCCGTTGA
1 CCCGACCCGTTGA
1556456 CCCGACCCGTTGA
1 CCCGACCCGTTGA
1556469 CC
1 CC
1556471 GTTGACCCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 38 0.75
18 13 0.25
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (13 bp):
CCCGACCCGTTGA
Found at i:1556434 original size:31 final size:31
Alignment explanation
Indices: 1556393--1556478 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
1556383 ACCGGTCACA
*
1556393 ACCCGGCCCGAACCGTTGACCCGACCCGTTG
1 ACCCGACCCGAACCGTTGACCCGACCCGTTG
* *
1556424 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGAACCGTTGACCCGACCCGTTG
*
1556455 ACCCGACCCGTTGACCGTTGACCC
1 ACCCGACCCG--AACCGTTGACCC
1556479 ATTGACCGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.81
33 9 0.19
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGAACCGTTGACCCGACCCGTTG
Found at i:1556445 original size:26 final size:27
Alignment explanation
Indices: 1556415--1556478 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
1556405 CCGTTGACCC
1556415 GACCCGTTGACCC-GACCCGACCCGTT
1 GACCCGTTGACCCTGACCCGACCCGTT
*
1556441 TACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGTTGACCC--TGACCCGACCCGTT
1556467 GA-CCGTTGACCC
1 GACCCGTTGACCC
1556479 ATTGACCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
23 5 0.17
25 2 0.07
26 18 0.60
28 5 0.17
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (27 bp):
GACCCGTTGACCCTGACCCGACCCGTT
Found at i:1556457 original size:8 final size:8
Alignment explanation
Indices: 1556446--1556502 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
1556436 CCGTTTACCC
1556446 GACCCGTT
1 GACCCGTT
1556454 GACCC---
1 GACCCGTT
1556459 GACCCGTT
1 GACCCGTT
1556467 GA-CCGTT
1 GACCCGTT
*
1556474 GACCCATT
1 GACCCGTT
1556482 GA-CCGTT
1 GACCCGTT
1556489 GACCACTGTT
1 GACC-C-GTT
1556499 GACC
1 GACC
1556503 AAAACTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 5 0.12
7 13 0.32
8 14 0.35
9 1 0.03
10 7 0.17
ACGTcount: A:0.18, C:0.37, G:0.23, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1556464 original size:18 final size:18
Alignment explanation
Indices: 1556410--1556451 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1556400 CCGAACCGTT
1556410 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
1556428 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
1556446 GACCCG
1 GACCCG
1556452 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1556483 original size:15 final size:15
Alignment explanation
Indices: 1556459--1556492 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1556449 CCGTTGACCC
*
1556459 GACCCGTTGACCGTT
1 GACCCATTGACCGTT
1556474 GACCCATTGACCGTT
1 GACCCATTGACCGTT
1556489 GACC
1 GACC
1556493 ACTGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (15 bp):
GACCCATTGACCGTT
Found at i:1557806 original size:18 final size:18
Alignment explanation
Indices: 1557780--1557815 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1557770 TCGAAAGGAC
*
1557780 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1557798 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1557816 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1558989 original size:23 final size:23
Alignment explanation
Indices: 1558963--1559036 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
1558953 AATTCTATTA
*
1558963 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
*
1558986 TGAT-ATTGACATGGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
1559009 TGATACATGACCTGGATTCTGATG
1 TGAT-CATGACCTGGATTCTGATC
1559033 TGAT
1 TGAT
1559037 ACTTGACTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 24 0.55
24 19 0.43
25 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:1559024 original size:24 final size:24
Alignment explanation
Indices: 1558969--1559043 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1558959 ATTATGATCC
1558969 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
1558992 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
1559016 TGACCTGGATTCTGATGTGATACT
1 TGACCTGGATTCTGATCTGATACT
1559040 TGAC
1 TGAC
1559044 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:1560599 original size:24 final size:24
Alignment explanation
Indices: 1560572--1560633 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1560562 GTTCGTGAAC
*
1560572 GTTCGATTATGTTCGCTCGATTAT
1 GTTCGTTTATGTTCGCTCGATTAT
* *
1560596 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGCTCGATTAT
1560620 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1560634 AGTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGCTCGATTAT
Found at i:1560626 original size:14 final size:14
Alignment explanation
Indices: 1560571--1560626 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1560561 CGTTCGTGAA
1560571 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1560585 CGCTCGATTATGTT
1 CGTTCGATTATGTT
1560599 CG-T---TTATGTT
1 CGTTCGATTATGTT
*
1560609 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
1560623 CGTT
1 CGTT
1560627 TATGTTCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1560643 original size:24 final size:24
Alignment explanation
Indices: 1560572--1560646 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
1560562 GTTCGTGAAC
* *
1560572 GTTCGATTATGTTCGCTC-GATTAT
1 GTTCGTTTATGTTCGTTCAG-TTAT
*
1560596 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
*
1560620 GTTCGTTTATGTTCAG-TCATTTAT
1 GTTCGTTTATGTTC-GTTCAGTTAT
1560644 GTT
1 GTT
1560647 TAACCCAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCAGTTAT
Found at i:1561327 original size:11 final size:11
Alignment explanation
Indices: 1561311--1561362 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1561301 TAGGGCAATG
*
1561311 TCGAGCTTGAA
1 TCGAGCTAGAA
1561322 TCGAGCTAGAA
1 TCGAGCTAGAA
1561333 TCGAGCTCAGAA
1 TCGAGCT-AGAA
* **
1561345 TCAAGCTTCAA
1 TCGAGCTAGAA
1561356 TCGAGCT
1 TCGAGCT
1561363 CGAGTCTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (11 bp):
TCGAGCTAGAA
Found at i:1561351 original size:23 final size:23
Alignment explanation
Indices: 1561311--1561363 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1561301 TAGGGCAATG
* * *
1561311 TCGAGCT-TGAATCGAGCTAGAA
1 TCGAGCTCAGAATCAAGCTACAA
*
1561333 TCGAGCTCAGAATCAAGCTTCAA
1 TCGAGCTCAGAATCAAGCTACAA
1561356 TCGAGCTC
1 TCGAGCTC
1561364 GAGTCTCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
TCGAGCTCAGAATCAAGCTACAA
Found at i:1561612 original size:16 final size:16
Alignment explanation
Indices: 1561589--1561649 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
1561579 GGGTCTCCAA
*
1561589 CGTTTATGTTCTTGTT
1 CGTTTATGTTCGTGTT
*
1561605 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1561621 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1561637 CGTTTATGTTCGT
1 CGTTTATGTTCGT
1561650 TTATTTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.57
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1565487 original size:16 final size:15
Alignment explanation
Indices: 1565455--1565508 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1565445 ACAGTCTCTC
1565455 AATCATTCAAC-ATTT
1 AATCATTCAACGA-TT
*
1565470 AAATCATTCAGCGATT
1 -AATCATTCAACGATT
* *
1565486 AATCATTCATCGCTT
1 AATCATTCAACGATT
1565501 AATCATTC
1 AATCATTC
1565509 TGAAGCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 21 0.62
16 12 0.35
17 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (15 bp):
AATCATTCAACGATT
Found at i:1565491 original size:15 final size:15
Alignment explanation
Indices: 1565471--1565508 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1565461 TCAACATTTA
1565471 AATCATTCAGCGATT
1 AATCATTCAGCGATT
* *
1565486 AATCATTCATCGCTT
1 AATCATTCAGCGATT
1565501 AATCATTC
1 AATCATTC
1565509 TGAAGCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (15 bp):
AATCATTCAGCGATT
Found at i:1598545 original size:20 final size:19
Alignment explanation
Indices: 1598522--1598568 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1598512 CGATATACCA
1598522 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1598542 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1598562 GGTAAAA
1 GGTAAAA
1598569 CGTTACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1598602 original size:182 final size:179
Alignment explanation
Indices: 1598310--1598781 Score: 701
Period size: 180 Copynumber: 2.6 Consensus size: 179
1598300 GATCCAAATT
* * * **
1598310 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
1598375 AAATCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
* *
1598440 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 GTGAATTTAAAAGAAAAGCAG-TTTAAAGCCTATAAAGTGTCGATAC-TTTA
*
1598492 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1598557 AAACCGGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
** *
1598622 TGAATTTAAAAGAAAAGCAGTTTAGCGCCTATAATGTGTCGATACTTTA
131 TGAATTTAAAAGAAAAGCAGTTTAAAGCCTATAAAGTGTCGATACTTTA
* * *
1598671 AAAATATATATCGATCCATAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGAT
1 AAAA-ATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1598736 AAAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT
1598782 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
179 8 0.03
180 122 0.46
181 38 0.14
182 97 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (179 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAAAAGCAGTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:1598725 original size:20 final size:19
Alignment explanation
Indices: 1598702--1598748 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1598692 CGATATAACA
*
1598702 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
1598722 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1598742 GGTAAAA
1 GGTAAAA
1598749 CGATACCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1600994 original size:21 final size:21
Alignment explanation
Indices: 1600968--1601031 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
1600958 AAGACAATCA
*
1600968 AGAGTCGAAGATAAACTTGAT
1 AGAGTCGAAGATAAACTTGAG
*
1600989 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGATAAACTTGAG
*
1601010 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATAAACTTGAG
1601031 A
1 A
1601032 TGCATAAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.19
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTTGAG
Found at i:1601108 original size:33 final size:33
Alignment explanation
Indices: 1601066--1601131 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1601056 AAATAGATGG
* *
1601066 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGAGTGA
* *
1601099 AGTGGTGAAAGAAGTTGGGGTGTTAAGGAGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGAGTGA
1601132 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGAGTGA
Found at i:1602944 original size:19 final size:19
Alignment explanation
Indices: 1602920--1602968 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1602910 AATGTAGGGT
1602920 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1602939 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1602958 TAATTTTGTAT
1 TAATTTTGTAT
1602969 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1603984 original size:200 final size:200
Alignment explanation
Indices: 1603202--1603965 Score: 1332
Period size: 200 Copynumber: 3.8 Consensus size: 200
1603192 AATTTACAAT
*
1603202 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1603267 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCAGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1603332 ATGAGAGAATAGGTCTAAATAATGTATTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1603397 AATGA
196 AATGA
*
1603402 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1603467 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1603532 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTTGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1603597 AATGA
196 AATGA
* *
1603602 ATGGTAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAGCAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1603667 CGAAACCCATAAGTATAATGCAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1603732 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAA
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
1603797 AATAA
196 AATGA
*
1603802 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1603867 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1603932 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
1603966 GTTTAATGTT
Statistics
Matches: 537, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
200 534 0.99
201 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1605478 original size:6 final size:6
Alignment explanation
Indices: 1605467--1605524 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
1605457 CAAGCGGTCA
* * * * *
1605467 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
1605515 ATGATG ATGA
1 ATGAAG ATGA
1605525 TCCTATAACA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:1605525 original size:12 final size:12
Alignment explanation
Indices: 1605467--1605524 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
1605457 CAAGCGGTCA
*
1605467 ATGAAGATGAAG
1 ATGACGATGAAG
*
1605479 CTGACGATGAAG
1 ATGACGATGAAG
1605491 ATGACGATGAAG
1 ATGACGATGAAG
*
1605503 ATGACGATGATG
1 ATGACGATGAAG
*
1605515 ATGATGATGA
1 ATGACGATGA
1605525 TCCTATAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1606248 original size:21 final size:21
Alignment explanation
Indices: 1606222--1606266 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1606212 GATTTCTGGG
* *
1606222 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1606243 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1606264 CAA
1 CAA
1606267 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1607627 original size:100 final size:101
Alignment explanation
Indices: 1607441--1607756 Score: 562
Period size: 100 Copynumber: 3.1 Consensus size: 101
1607431 GTCGAGGGTC
1607441 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATA--TATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1607506 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1607544 TATGTGGTCCTTCGGGACATATATATTCTTTGGAATATGTGTGAAGTCTGGTGA-ACACATACTT
1 TATGTGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1607608 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1607644 TATGTGGTCCTTCGGGACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TATGTGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
1607709 GATCCATAGTATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1607745 TATGTGGTCCTT
1 TATGTGGTCCTT
1607757 ATGGACATTA
Statistics
Matches: 206, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
100 98 0.48
101 85 0.41
103 23 0.11
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1607824 original size:23 final size:23
Alignment explanation
Indices: 1607771--1607832 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1607761 ACATTATTAT
1607771 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* * *
1607794 ACGACACTACGGTGCAATTCTAT
1 ATGGCACTACGGTGCAATTCTAC
* *
1607817 GTGGCACTTCGGTGCA
1 ATGGCACTACGGTGCA
1607833 TTTATATGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:1610076 original size:183 final size:183
Alignment explanation
Indices: 1609763--1610350 Score: 950
Period size: 183 Copynumber: 3.2 Consensus size: 183
1609753 CAAAGTTTTC
*
1609763 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * * *
1609828 C-AAAAGTGTCG--ATTGAAAAAATATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
1609890 TATAATCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAAACGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * *
1609946 ATACTTTTTAATATTGTGTCGGTACTTTATGTTCAGAATGGAAGAAAAATGTGTTGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
1610011 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTTTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1610076 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AAACGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * * *
1610129 ACACTTTTTAATAATGTGTCAGTACTTTATGTCCGGAATGGAAGAAAAATGTGTCGATTCCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
1610194 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGACAATTTTGTAATA-
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1610258 AAACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AAAC-GGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1610312 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
1610351 TATAATGTAC
Statistics
Matches: 376, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
182 3 0.01
183 360 0.96
184 10 0.03
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AAACGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1610437 original size:120 final size:120
Alignment explanation
Indices: 1610224--1610590 Score: 637
Period size: 120 Copynumber: 3.1 Consensus size: 120
1610214 ACATCGGAAC
* * * *
1610224 CCAGAATTATAATGTAATAGACAATTTTGTAATA-AAACTGGTATAAATATACCGGTTTTATGAG
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAAC-GGTATAAGTATACCGGTTTTATTAG
* *
1610288 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
65 CGAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
*
1610344 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAGCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAACGGTATAAGTATACCGGTTTTATTAGC
*
1610409 GAATAGGTCTACAATCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
*
1610464 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAACGGTATAAGTATACCGGTTTTATTAGC
1610529 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
1610584 CCAGAAT
1 CCAGAAT
1610591 GGAAGAAAAA
Statistics
Matches: 236, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 233 0.99
121 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTACTAGATAATTTTGTAATATAAACGGTATAAGTATACCGGTTTTATTAGC
GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:1619372 original size:23 final size:21
Alignment explanation
Indices: 1619319--1619380 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1619309 TTTTGGTGCA
*
1619319 GAGGGAATCGATTCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
1619340 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCCTT
1619361 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1619381 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1619406 original size:19 final size:20
Alignment explanation
Indices: 1619363--1619400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1619353 CCTCCTTTGA
*
1619363 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1619383 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1619401 CTGGGGTTCT
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:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1623761 original size:87 final size:87
Alignment explanation
Indices: 1623657--1623910 Score: 456
Period size: 87 Copynumber: 2.9 Consensus size: 87
1623647 AAATAGGTCA
* *
1623657 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1623722 CCCGTTAAATACATATTTTATT
66 CCCGTTAAATACATATTTTATT
1623744 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
1623809 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACATATTTTATT
*
1623831 ATATAAGCGCTATCTATTATATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
1623896 CCGGTTAAATA-ATAT
66 CCCGTTAAATACATAT
1623911 AACATAACCG
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
86 3 0.02
87 158 0.98
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACATATTTTATT
Found at i:1623791 original size:23 final size:23
Alignment explanation
Indices: 1623741--1623785 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1623731 TACATATTTT
* *
1623741 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1623764 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1623786 TGTTATTGTA
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:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1623878 original size:23 final size:23
Alignment explanation
Indices: 1623818--1623878 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
1623808 TCCCGTTAAA
* *
1623818 TACCTATTTTATTATATAAGCGC
1 TACCTAATATATTATATAAGCGC
* * *
1623841 TATCTATTATATTATATAAGCGT
1 TACCTAATATATTATATAAGCGC
*
1623864 TACCTAATATGTTAT
1 TACCTAATATATTAT
1623879 TGTACTTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (23 bp):
TACCTAATATATTATATAAGCGC
Found at i:1645384 original size:3 final size:3
Alignment explanation
Indices: 1645376--1645401 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1645366 CAACAGGAAC
1645376 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1645402 ATCCATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1655341 original size:24 final size:24
Alignment explanation
Indices: 1655314--1655446 Score: 160
Period size: 24 Copynumber: 5.4 Consensus size: 24
1655304 AATTTGAACA
*
1655314 GCAGCGGCAGTTGGAACATCAGCG
1 GCAGCAGCAGTTGGAACATCAGCG
1655338 GCAGCAGCAGTTGGAACATCAGCG
1 GCAGCAGCAGTTGGAACATCAGCG
1655362 GCAGCAGCAGTTGGAACATCAGCGG
1 GCAGCAGCAGTTGGAACATCAGC-G
* *
1655387 CAGCAGCAGCAGTTGGAACTTCAACG
1 --GCAGCAGCAGTTGGAACATCAGCG
* *
1655413 ACAGCAGCAGCTT-GAACTTCAGCG
1 GCAGCAGCAG-TTGGAACATCAGCG
* *
1655437 ACAGCGGCAG
1 GCAGCAGCAG
1655447 CAGCAGCTTG
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
24 74 0.75
25 3 0.03
26 1 0.01
27 21 0.21
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.13
Consensus pattern (24 bp):
GCAGCAGCAGTTGGAACATCAGCG
Found at i:1655346 original size:30 final size:29
Alignment explanation
Indices: 1655333--1655597 Score: 256
Period size: 30 Copynumber: 9.4 Consensus size: 29
1655323 GTTGGAACAT
* *
1655333 CAGCGGCAGCAGCAGTTGGAACATCAGCG-
1 CAGCAGCAGCAGCAGTT-GAACTTCAGCGA
* *
1655362 --GCAGCA---GCAGTTGGAACATCAGCGG
1 CAGCAGCAGCAGCAGTT-GAACTTCAGCGA
*
1655387 CAGCA---GCAGCAGTTGGAACTTCAACG-
1 CAGCAGCAGCAGCAGTT-GAACTTCAGCGA
1655413 -A-CAGCAGCAGC--TTGAACTTCAGCGA
1 CAGCAGCAGCAGCAGTTGAACTTCAGCGA
*
1655438 CAGCGGCAGCAGCAGCTTGAACTTCAGCGA
1 CAGCAGCAGCAGCAG-TTGAACTTCAGCGA
*
1655468 CAGCGGCAGCAGCAGCTTGAACTTCAGCGA
1 CAGCAGCAGCAGCAG-TTGAACTTCAGCGA
1655498 CAGCAGCAGCAGCAGCTTGAACTTCAGCGA
1 CAGCAGCAGCAGCAG-TTGAACTTCAGCGA
1655528 CAGCAGCAGCAGCAGCTTGAACTTCAGCGA
1 CAGCAGCAGCAGCAG-TTGAACTTCAGCGA
* * *
1655558 CGGCAGCATCAGC--TTGAACTTCAGCGG
1 CAGCAGCAGCAGCAGTTGAACTTCAGCGA
*
1655585 CGGCAGCAGCAGC
1 CAGCAGCAGCAGC
1655598 TTCGTAACCA
Statistics
Matches: 211, Mismatches: 10, Indels: 32
0.83 0.04 0.13
Matches are distributed among these distances:
24 30 0.14
25 3 0.01
26 1 0.00
27 63 0.30
30 114 0.54
ACGTcount: A:0.28, C:0.29, G:0.30, T:0.13
Consensus pattern (29 bp):
CAGCAGCAGCAGCAGTTGAACTTCAGCGA
Found at i:1655396 original size:51 final size:51
Alignment explanation
Indices: 1655314--1655449 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
1655304 AATTTGAACA
* *
1655314 GCAGCGGCAGTTGGAACATCAGC-G--GCAGCAGCAGTTGGAACATCAGCG
1 GCAGCAGCAGTTGGAACATCAGCGGCAGCAGCAGCAGTTGGAACATCAACG
*
1655362 GCAGCAGCAGTTGGAACATCAGCGGCAGCAGCAGCAGTTGGAACTTCAACG
1 GCAGCAGCAGTTGGAACATCAGCGGCAGCAGCAGCAGTTGGAACATCAACG
* * * *
1655413 ACAGCAGCAGCTT-GAACTTCAGCGACAGCGGCAGCAG
1 GCAGCAGCAG-TTGGAACATCAGCGGCAGCAGCAGCAG
1655450 CAGCTTGAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
48 22 0.29
49 1 0.01
51 52 0.68
52 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.12
Consensus pattern (51 bp):
GCAGCAGCAGTTGGAACATCAGCGGCAGCAGCAGCAGTTGGAACATCAACG
Found at i:1655484 original size:60 final size:60
Alignment explanation
Indices: 1655414--1655599 Score: 303
Period size: 60 Copynumber: 3.2 Consensus size: 60
1655404 ACTTCAACGA
1655414 CAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGG
1 CAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGG
* *
1655474 CAGCAGCAGCTTGAACTTCAGCGACAGCAGCAGCAGCAGCTTGAACTTCAGCGACAGCAG
1 CAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGG
*
1655534 CAGCAGCAGCTTGAACTTCAGCG--A-CGGCAGCATCAGCTTGAACTTCAGCG---GCGG
1 CAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGG
1655588 CAGCAGCAGCTT
1 CAGCAGCAGCTT
1655600 CGTAACCATC
Statistics
Matches: 121, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
54 15 0.12
57 24 0.20
58 1 0.01
60 81 0.67
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (60 bp):
CAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGG
Found at i:1655539 original size:90 final size:87
Alignment explanation
Indices: 1655357--1655597 Score: 309
Period size: 90 Copynumber: 2.8 Consensus size: 87
1655347 GTTGGAACAT
* * * *
1655357 CAGCGGCAGCAGCAG-TTGGAACATCAGCGGCAGCAGCAGCAG-TTGGAACTTCA---AC-G-A-
1 CAGCAGCAGCAGCAGCTT-GAACTTCAGCGACGGCAGCAGCAGCTT-GAACTTCAGCGACAGCAG
1655414 CAGCAGCAGCTTGAACTTCAGCGA
64 CAGCAGCAGCTTGAACTTCAGCGA
*
1655438 CAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCGGCAGCAGCAGCTTGAACTTCAGCGACAGCA
1 CAGCAGCAGCAGCAGCTTGAACTTCAGCG--A-CGGCAGCAGCAGCTTGAACTTCAGCGACAGCA
1655503 GCAGCAGCAGCTTGAACTTCAGCGA
63 GCAGCAGCAGCTTGAACTTCAGCGA
* * *
1655528 CAGCAGCAGCAGCAGCTTGAACTTCAGCGACGGCAGCATCAGCTTGAACTTCAGCGGCGGCAGCA
1 CAGCAGCAGCAGCAGCTTGAACTTCAGCGACGGCAGCAGCAGCTTGAACTTCAGCGACAGCAGCA
1655593 GCAGC
66 GCAGC
1655598 TTCGTAACCA
Statistics
Matches: 142, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
81 25 0.18
82 2 0.01
84 19 0.13
85 2 0.01
87 39 0.27
88 2 0.01
89 1 0.01
90 52 0.37
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.13
Consensus pattern (87 bp):
CAGCAGCAGCAGCAGCTTGAACTTCAGCGACGGCAGCAGCAGCTTGAACTTCAGCGACAGCAGCA
GCAGCAGCTTGAACTTCAGCGA
Found at i:1659122 original size:21 final size:22
Alignment explanation
Indices: 1659098--1659139 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1659088 ATATTTTTAG
1659098 TTAAAATATA-TAAATTGATTA
1 TTAAAATATATTAAATTGATTA
* *
1659119 TTAAATTATATTTAATTGATT
1 TTAAAATATATTAAATTGATT
1659140 TTTTGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TTAAAATATATTAAATTGATTA
Found at i:1659229 original size:31 final size:29
Alignment explanation
Indices: 1659145--1659245 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
1659135 TGATTTTTTG
1659145 TTATTAAAATTTTAA-AAATTATAAAATAA
1 TTATT-AAATTTTAAGAAATTATAAAATAA
* *
1659174 TCATTAAATTTTAAGAAATTATAAAGTAA
1 TTATTAAATTTTAAGAAATTATAAAATAA
*
1659203 TTATTAAA-TTTATTGAACTATTATAAAATAA
1 TTATTAAATTTTA-AGAA--ATTATAAAATAA
1659234 -TATTTAAATTTT
1 TTA-TTAAATTTT
1659246 TCAAAATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 13 0.21
29 27 0.44
30 2 0.03
31 16 0.26
32 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
TTATTAAATTTTAAGAAATTATAAAATAA
Found at i:1663026 original size:3 final size:3
Alignment explanation
Indices: 1663018--1663055 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1663008 ATGCAGTCTT
1663018 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1663056 GTGAACAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1663848 original size:2 final size:2
Alignment explanation
Indices: 1663841--1663892 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
1663831 GTTGGGTCTT
* * *
1663841 TC TC TC TC TC CC TC TC TC TC CC TC CC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1663882 TC TC TC TC TC T
1 TC TC TC TC TC T
1663893 ATATATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:1663897 original size:2 final size:2
Alignment explanation
Indices: 1663892--1663919 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1663882 TCTCTCTCTC
1663892 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
1663920 ATAATTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1666109 original size:186 final size:185
Alignment explanation
Indices: 1665784--1666173 Score: 644
Period size: 186 Copynumber: 2.1 Consensus size: 185
1665774 TTTTCTAATT
*
1665784 TATATAA-A-ATTAAATATTTTATAATTCAAAAAAAACAGTTTATAATTAATTTAAATAATATAT
1 TATATAATATATTAAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
1665847 AATTATAAAATAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 AATTATAAAATAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* * **
1665912 TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGTTCATATGTTA
131 TGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCCGAGCCCATATGTTA
* * *
1665967 TATATAATATATTTAATATTTTTTAATTC-AAAAAAATAGTTTACAATTAATTTAAATAATATAT
1 TATATAATATATTAAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
1666031 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
66 AATTATAAAAT-AAAA-TTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
1666096 ATTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCCGAGCCCATATGTTA
129 ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCCGAGCCCATATGTTA
1666153 TATATAATATA-TAATATATTT
1 TATATAATATATTAA-ATATTT
1666174 AAAATTTAAA
Statistics
Matches: 192, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
183 7 0.04
184 45 0.23
185 23 0.12
186 117 0.61
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (185 bp):
TATATAATATATTAAATATTTTATAATTCAAAAAAAACAGTTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCCGAGCCCATATGTTA
Found at i:1673948 original size:21 final size:21
Alignment explanation
Indices: 1673922--1673973 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1673912 ATCTGATTGG
1673922 AACTGCAGGGAATTACACTTA
1 AACTGCAGGGAATTACACTTA
1673943 AACTGCAGGGAATTACACTTA
1 AACTGCAGGGAATTACACTTA
*
1673964 AACTGAAGGG
1 AACTGCAGGG
1673974 TGGCTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
AACTGCAGGGAATTACACTTA
Found at i:1674559 original size:17 final size:18
Alignment explanation
Indices: 1674527--1674561 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1674517 AATACATATC
*
1674527 AATATTTTTGTGATAATT
1 AATATTTTTGTAATAATT
1674545 AATATTTTT-TAATAATT
1 AATATTTTTGTAATAATT
1674562 TTAGTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATATTTTTGTAATAATT
Found at i:1683610 original size:17 final size:17
Alignment explanation
Indices: 1683576--1683627 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1683566 AACGGACAAA
* *
1683576 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
1683593 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
1683610 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
1683625 TTT
1 TTT
1683628 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:1684917 original size:2 final size:2
Alignment explanation
Indices: 1684910--1684936 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1684900 TTCGGATTCA
1684910 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 A
1684937 GCTGGTTAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1690365 original size:63 final size:63
Alignment explanation
Indices: 1690261--1690386 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
1690251 AAGGGAATTA
* *
1690261 AACCGATTTGGGGACCAAATTAAATGTTTTTTAAAATAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
*
1690324 AACCGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1690387 CTTTTAGCAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:1691396 original size:41 final size:41
Alignment explanation
Indices: 1691346--1691424 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1691336 TAAATAAAAT
*
1691346 TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
1 TAATACTAATATATATATGTAAATACTATAAAAGTGTGGAG
*
1691387 TAATACTAATATATATATGTAAGTACTATAAAAGTGTG
1 TAATACTAATATATATATGTAAATACTATAAAAGTGTG
1691425 AAGACGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.37
Consensus pattern (41 bp):
TAATACTAATATATATATGTAAATACTATAAAAGTGTGGAG
Found at i:1692049 original size:105 final size:105
Alignment explanation
Indices: 1691802--1692504 Score: 1093
Period size: 105 Copynumber: 6.7 Consensus size: 105
1691792 GTATATAGCT
* **** *
1691802 CCTTCGTCGTGACGTTGAACTTATACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
1691867 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTC
* * *
1691908 CCTTCGTCGTGAAGTTGAACATGCGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
1691973 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTC
* *
1692013 ACTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATTCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1692078 GGCTCTGAAA-TGAGGAAATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGA-GAAATGTTTATTGACAACCAGCGGTC
* *
1692118 CCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAACTT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
1692183 GACTCTGGAATTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTC
1692223 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * * *
1692288 GACTCTGGAATTGAGAAACGTTTGTTGACAACCAGTGGTC
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTC
*
1692328 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * * *
1692393 GGCTCTGAAATTGAGAGATTTTTGTGGACAACCAGTGGTC
66 GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTC
1692433 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1692498 GGCTCTG
66 GGCTCTG
1692505 GGTAAAACCT
Statistics
Matches: 559, Mismatches: 36, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
104 2 0.00
105 481 0.86
106 76 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTC
Found at i:1693318 original size:14 final size:14
Alignment explanation
Indices: 1693299--1693332 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1693289 CACCCTAAAC
1693299 GTTTTTCTCTTTTT
1 GTTTTTCTCTTTTT
* *
1693313 GTTTTTTTGTTTTT
1 GTTTTTCTCTTTTT
1693327 GTTTTT
1 GTTTTT
1693333 TTTCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (14 bp):
GTTTTTCTCTTTTT
Found at i:1693333 original size:14 final size:14
Alignment explanation
Indices: 1693308--1693334 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1693298 CGTTTTTCTC
1693308 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
1693322 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
1693335 TCATTTTTTT
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:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:1704219 original size:63 final size:63
Alignment explanation
Indices: 1704120--1704245 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
1704110 AAGGGAATTA
*
1704120 AACCGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
*
1704183 AACCGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1704246 CTTTTAGCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:1704232 original size:31 final size:30
Alignment explanation
Indices: 1704145--1704241 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 30
1704135 CAAATTAAAT
*
1704145 GTTTTTTAAAACAGAGGGAGCCAAAATGAA
1 GTTTTTCAAAACAGAGGGAGCCAAAATGAA
* ** * *
1704175 G-TTTACCCAACCGATTTGGG-GACCAAATTGAA
1 GTTTTTCAAAACAGA---GGGAG-CCAAAATGAA
1704207 TGTTTTTCAAAACAGAGGGAGCCAAAATGAA
1 -GTTTTTCAAAACAGAGGGAGCCAAAATGAA
1704238 GTTT
1 GTTT
1704242 ACCCCTTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
29 8 0.16
30 5 0.10
31 13 0.27
32 13 0.27
33 1 0.02
34 9 0.18
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (30 bp):
GTTTTTCAAAACAGAGGGAGCCAAAATGAA
Found at i:1705261 original size:41 final size:41
Alignment explanation
Indices: 1705211--1705289 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1705201 TAAATAAAAT
*
1705211 TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
1 TAATACTAATATATATATGTAAATACTATAAAAGTGTGGAG
*
1705252 TAATACTAATATATATATGTAAGTACTATAAAAGTGTG
1 TAATACTAATATATATATGTAAATACTATAAAAGTGTG
1705290 AAGACGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.37
Consensus pattern (41 bp):
TAATACTAATATATATATGTAAATACTATAAAAGTGTGGAG
Found at i:1706987 original size:54 final size:54
Alignment explanation
Indices: 1706929--1707033 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
1706919 GGGAAACCGC
* * * *
1706929 TCGTCAAAGC-GCTCAGTATGCGGCGGAGAAGGGTGGACAAGCGACGGACACTGT
1 TCGTC-AAGCTGCTCAGAAGGCGGCGGAGAAGGGTGGACAAACGAAGGACACTGT
* *
1706983 TCGTCGAGCTGCTCAGAAGGCGGCGGAGATGGGTGGACAAACGAAGGACAC
1 TCGTCAAGCTGCTCAGAAGGCGGCGGAGAAGGGTGGACAAACGAAGGACAC
1707034 GATCGTCGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 3 0.07
54 41 0.93
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (54 bp):
TCGTCAAGCTGCTCAGAAGGCGGCGGAGAAGGGTGGACAAACGAAGGACACTGT
Found at i:1718591 original size:36 final size:36
Alignment explanation
Indices: 1718558--1718664 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
1718548 TATTATCAGT
*
1718558 TTTGATACATTCGTGTATTAATATTATCATATCAAC
1 TTTGGTACATTCGTGTATTAATATTATCATATCAAC
* *
1718594 TTTGGTACATTCGTGTATCAATGTTATCATATCAAC
1 TTTGGTACATTCGTGTATTAATATTATCATATCAAC
*
1718630 TTTGGTACATTCGTGTATTGATATTATCATATCAA
1 TTTGGTACATTCGTGTATTAATATTATCATATCAA
1718665 TGTCCAGCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (36 bp):
TTTGGTACATTCGTGTATTAATATTATCATATCAAC
Found at i:1720468 original size:2 final size:2
Alignment explanation
Indices: 1720461--1720495 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1720451 CGACTTAATC
1720461 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 A
1720496 AAGGATGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1724657 original size:24 final size:24
Alignment explanation
Indices: 1724625--1724672 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1724615 AAACAACATC
*
1724625 CGCAACATAAAACATTATTACTTT
1 CGCAACATAAAACATAATTACTTT
1724649 CGCAACATAAAACATAATTACTTT
1 CGCAACATAAAACATAATTACTTT
1724673 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (24 bp):
CGCAACATAAAACATAATTACTTT
Found at i:1726462 original size:29 final size:29
Alignment explanation
Indices: 1726417--1726474 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1726407 GTGTTAGTCG
*
1726417 TAGGTCGCCATGCCTTCCAGACAATCTAC
1 TAGGTCGCCATGCCTTCCAGACAAGCTAC
* *
1726446 TAGGTCGCCATGTCTTCCCGACAAGCTAC
1 TAGGTCGCCATGCCTTCCAGACAAGCTAC
1726475 GAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCAGACAAGCTAC
Found at i:1735108 original size:2 final size:2
Alignment explanation
Indices: 1735095--1735146 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
1735085 ATTAAAATAG
* * *
1735095 AT AT AA AT AT AT AT A- AT A- AC AA 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
1735135 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1735147 TAAATTCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1735624 original size:2 final size:2
Alignment explanation
Indices: 1735619--1735647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1735609 ACACGAAGTG
1735619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1735648 TGCATATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1741286 original size:2 final size:2
Alignment explanation
Indices: 1741275--1741330 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1741265 GCATAATTAG
1741275 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1741316 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1741331 TTCGATTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1744047 original size:38 final size:39
Alignment explanation
Indices: 1744003--1744076 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
1743993 AGTTACTCAT
*
1744003 CAATTCA-GTATGAATGATACCTGTGATAAGAGGAGATA
1 CAATTCATGTATGAAAGATACCTGTGATAAGAGGAGATA
1744041 CAATTCATGTATGAAAGATACCTGTGATAAGAGGAG
1 CAATTCATGTATGAAAGATACCTGTGATAAGAGGAG
1744077 TATCTGGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (39 bp):
CAATTCATGTATGAAAGATACCTGTGATAAGAGGAGATA
Found at i:1748140 original size:36 final size:31
Alignment explanation
Indices: 1748073--1748146 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 31
1748063 GGAAAACAGA
* *
1748073 GAAAAATGGGGGAAGCACGGCGTGAACTGAT
1 GAAAAATGGGGGAAGCACGGCGGGAAATGAT
1748104 GAAAAATGGGGGAAGATCAAGCGCGCGGGAAATGAT
1 GAAAAATGGGGGAAG--C-A-CG-GCGGGAAATGAT
1748140 GAAAAAT
1 GAAAAAT
1748147 AAAGGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 15 0.42
33 1 0.03
34 1 0.03
35 2 0.06
36 17 0.47
ACGTcount: A:0.41, C:0.11, G:0.36, T:0.12
Consensus pattern (31 bp):
GAAAAATGGGGGAAGCACGGCGGGAAATGAT
Found at i:1750465 original size:17 final size:17
Alignment explanation
Indices: 1750443--1750477 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1750433 AGAACGGCTA
1750443 AACCGTCTGCTTATTCG
1 AACCGTCTGCTTATTCG
1750460 AACCGTCTGCTTATTCG
1 AACCGTCTGCTTATTCG
1750477 A
1 A
1750478 CCATTGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (17 bp):
AACCGTCTGCTTATTCG
Found at i:1753779 original size:18 final size:18
Alignment explanation
Indices: 1753758--1753796 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1753748 AAATCTCTAC
1753758 TTTTAAATAAAAATAATA
1 TTTTAAATAAAAATAATA
* * *
1753776 TTTTTAATAAATATATTA
1 TTTTAAATAAAAATAATA
1753794 TTT
1 TTT
1753797 CGGGTTGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAATAAAAATAATA
Found at i:1759654 original size:35 final size:36
Alignment explanation
Indices: 1759615--1759689 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
1759605 AAACGGGAAC
*
1759615 GGGAAAAATCGTTTATGTTAAACGGGGA-CGGGATG
1 GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
*
1759650 GGGAAAAACCGTTTATGTTAAACGGGGATGGGGATG
1 GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
1759686 GGGA
1 GGGA
1759690 TGAGTTTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 27 0.73
36 10 0.27
ACGTcount: A:0.31, C:0.08, G:0.40, T:0.21
Consensus pattern (36 bp):
GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
Found at i:1760530 original size:15 final size:15
Alignment explanation
Indices: 1760510--1760539 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1760500 TGTGAACCAA
1760510 ACGCACCCTGAGGGG
1 ACGCACCCTGAGGGG
1760525 ACGCACCCTGAGGGG
1 ACGCACCCTGAGGGG
1760540 GTGTTTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.40, T:0.07
Consensus pattern (15 bp):
ACGCACCCTGAGGGG
Found at i:1770987 original size:44 final size:42
Alignment explanation
Indices: 1770935--1771018 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 42
1770925 ATTTTACTTA
1770935 AAATATATTAAATTATTCATATC-TTGATTCAACTTTTAACACT
1 AAATATATTAAATTATT--TATCGTTGATTCAACTTTTAACACT
1770978 AAATGATATTAAATTATTTATCGTTTGATTCAACTTTTAAC
1 AAAT-ATATTAAATTATTTATCG-TTGATTCAACTTTTAAC
1771019 GTTACTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
42 4 0.11
43 4 0.11
44 30 0.79
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (42 bp):
AAATATATTAAATTATTTATCGTTGATTCAACTTTTAACACT
Found at i:1777728 original size:38 final size:38
Alignment explanation
Indices: 1777677--1777752 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
1777667 CATTGGAAAG
*
1777677 AAAGAAGCATAGAATGACATCCTA-TATCAGGTTCGAAT
1 AAAGAAGCATAGAATGACAT-CGAGTATCAGGTTCGAAT
1777715 AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
1 AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
1777753 GATCTAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (38 bp):
AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
Found at i:1783128 original size:562 final size:561
Alignment explanation
Indices: 1782495--1783535 Score: 1597
Period size: 562 Copynumber: 1.9 Consensus size: 561
1782485 GTTGTATTTT
* * * * *
1782495 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACCGTGTTTGGTTAAAGGAATAAAATATTATTT
1 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTACCATGTTTGGTTAAAAGAATAAAAGATTATTA
* *
1782560 GAATGTATATTTAACCAAATTGTCTTTATTATATATTTGTATAATATT-ACAAATTGTAAAATAT
66 GAATGTATATTTAACCAAATTGTCCTTATTATATATTTGT-T-ATATTAACAAATTGAAAAATAT
* *
1782624 TTATATATTTTCTTTAAAAAA-TTAAATTCATAATATTTATATAA-TTTTTTTACAAAATTAAAA
129 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAATGTATATAATTTTTTTTACAAAATTAAAA
1782687 ATATAAAAAAGGTTTTAATGAAAGGGTAAAAAAAATTGAACCCCTGAACTTCATATAAAATTTTA
194 ATAT-AAAAAGG-TTTAATGAAAGGGTAAAAAAAATTGAACCCCTGAACTTCATATAAAATTTTA
*
1782752 ATTATAG-ATTTTTTTTGTAAATCTAAAATAATTTAAGGATAAATTTATAATTTAACATTCGTAG
257 ATTATAGTATTTTTTTTGTAAATCTAAAATAATTTAAGAATAAATTTATAATTTAACATTCGTAG
* *
1782816 AATTTTTATTATTCAATGACAGAAGAATGATATTTTTGAAAAAAAAATAAAAATTTAAGGGCATT
322 AAATTTTATTATTCAATGACAGAAGAATGATATTTTTGAAAAAAAAA-AAAAA-TTAAGGACATT
*** ** *
1782881 TTAGTCCAAAACGCCGGTAATGTTACAATAACTAAGGGAAGGGAGGTAATGACATTACTGGTAAT
385 TTAGTCCAAAACGCCGGTAATCCAACAATAACTAAGAAAAGGGAGGTAATGACATTACCGGTAAT
* *
1782946 ATACCCCAAAAAATCTACTA-TTGGTAATAAAATATTACCGGGAATAAGATTCCCGGCCAACCAA
450 ATACCCCAAAAAATCCACCATTTGGTAATAAAATATTACCGGGAATAAGATTCCCGGCCAACCAA
1783010 ACATGGGAATGTGGGATTCTACAATCCTTGAACCAAACACCCCCTTA
515 ACATGGGAATGTGGGATTCTACAATCCTTGAACCAAACACCCCCTTA
*
1783057 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTATCATGTTTGGTTAAAAGAATAAAAGATTATTA
1 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTACCATGTTTGGTTAAAAGAATAAAAGATTATTA
* * * *
1783122 GAATGTATATTTGACCAAATTGTCCTTATTATATATTTGTTTTTTTAACAAGTTGAAAAATATTT
66 GAATGTATATTTAACCAAATTGTCCTTATTATATATTTGTTATATTAACAAATTGAAAAATATTT
*
1783187 ATATATTTTCTTTAAAAAATTTAAATTCATAAAATGTATATAATTTTTTTTTACAAAATTGAAAA
131 ATATATTTTCTTTAAAAAATTTAAATTCATAAAATGTATATAA-TTTTTTTTACAAAATTAAAAA
***** *
1783252 TATAAAAAGGTTTAATGAAAGGGTAAATTTTTTTTAACCCCTGAACTTCATATAAAATTTTAATT
195 TATAAAAAGGTTTAATGAAAGGGTAAAAAAAATTGAACCCCTGAACTTCATATAAAATTTTAATT
* *
1783317 ATAGTATTTTTTTTGTAAATCTAAAATAGTTTAAGAATAAATTTATAATTTAACCTTCGTAGAAA
260 ATAGTATTTTTTTTGTAAATCTAAAATAATTTAAGAATAAATTTATAATTTAACATTCGTAGAAA
* * *
1783382 TTTTATTATTCAATGACAGAAGAATTATATTTTTGAAAGAAACAAAAAATTAAGGACATTTTAGT
325 TTTTATTATTCAATGACAGAAGAATGATATTTTTGAAAAAAAAAAAAAATTAAGGACATTTTAGT
* * * * *
1783447 CCAAAACGCCGGTAATCCAATAATACCTACGAAAAGGGAGGTAATGACATTTCCGGTAATATAGC
390 CCAAAACGCCGGTAATCCAACAATAACTAAGAAAAGGGAGGTAATGACATTACCGGTAATATACC
*
1783512 CTAAAAAATCCACCATTTGGTAAT
455 CCAAAAAATCCACCATTTGGTAAT
1783536 CTTGCATTAC
Statistics
Matches: 430, Mismatches: 43, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
560 3 0.01
561 117 0.27
562 184 0.43
563 104 0.24
564 22 0.05
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (561 bp):
GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTACCATGTTTGGTTAAAAGAATAAAAGATTATTA
GAATGTATATTTAACCAAATTGTCCTTATTATATATTTGTTATATTAACAAATTGAAAAATATTT
ATATATTTTCTTTAAAAAATTTAAATTCATAAAATGTATATAATTTTTTTTACAAAATTAAAAAT
ATAAAAAGGTTTAATGAAAGGGTAAAAAAAATTGAACCCCTGAACTTCATATAAAATTTTAATTA
TAGTATTTTTTTTGTAAATCTAAAATAATTTAAGAATAAATTTATAATTTAACATTCGTAGAAAT
TTTATTATTCAATGACAGAAGAATGATATTTTTGAAAAAAAAAAAAAATTAAGGACATTTTAGTC
CAAAACGCCGGTAATCCAACAATAACTAAGAAAAGGGAGGTAATGACATTACCGGTAATATACCC
CAAAAAATCCACCATTTGGTAATAAAATATTACCGGGAATAAGATTCCCGGCCAACCAAACATGG
GAATGTGGGATTCTACAATCCTTGAACCAAACACCCCCTTA
Found at i:1783740 original size:21 final size:19
Alignment explanation
Indices: 1783702--1783740 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1783692 ATTCTTTTCA
1783702 TCTTTATTTTTACTTTAAG
1 TCTTTATTTTTACTTTAAG
*
1783721 TCTTTACTTATTTTCTTTAA
1 TCTTTA-TT-TTTACTTTAA
1783741 AAAATGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.64
Consensus pattern (19 bp):
TCTTTATTTTTACTTTAAG
Found at i:1785605 original size:17 final size:18
Alignment explanation
Indices: 1785573--1785607 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1785563 GTGAAAAAGA
*
1785573 TTATTACTATGTAATAAT
1 TTATTACTAAGTAATAAT
1785591 TTATTAC-AAGTAATAAT
1 TTATTACTAAGTAATAAT
1785608 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATTACTAAGTAATAAT
Found at i:1785769 original size:3 final size:3
Alignment explanation
Indices: 1785761--1785799 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1785751 ATTCTAAATT
1785761 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1785800 GAGTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1785855 original size:25 final size:24
Alignment explanation
Indices: 1785827--1785881 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1785817 ATGTTACTAA
*
1785827 ATTTTAGTAGTTAAAATTATTTAAT-
1 ATTTTAATA-TTAAAATTA-TTAATC
*
1785852 ATTTTAATATTTAAATTATTAATC
1 ATTTTAATATTAAAATTATTAATC
1785876 ATTTTA
1 ATTTTA
1785882 TAATTTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 14 0.52
25 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTTTAATATTAAAATTATTAATC
Found at i:1786108 original size:20 final size:21
Alignment explanation
Indices: 1786072--1786120 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1786062 AATCATTTAA
*
1786072 AAATATA-AAATTGATATATT
1 AAATATATTAATTGATATATT
*
1786092 AATTATATTAATT-ATATATT
1 AAATATATTAATTGATATATT
1786112 AAATATATT
1 AAATATATT
1786121 TTTTCTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATATTAATTGATATATT
Found at i:1788254 original size:84 final size:84
Alignment explanation
Indices: 1788113--1788277 Score: 285
Period size: 84 Copynumber: 2.0 Consensus size: 84
1788103 GGCAAGCAAA
*
1788113 TTCAATCGGTGGCCCTCAATCTGTTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
1 TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
*
1788178 CTCAGGGTGGTTCAATACC
66 CTCAAGGTGGTTCAATACC
* * *
1788197 TTCAATTGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCGAGTTCTGCTATTTTGGGAT
1 TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
1788262 CTCAAGGTGGTTCAAT
66 CTCAAGGTGGTTCAAT
1788278 GCCTCCACAG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (84 bp):
TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
CTCAAGGTGGTTCAATACC
Found at i:1789844 original size:33 final size:33
Alignment explanation
Indices: 1789807--1789872 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1789797 CTATATAATC
* * *
1789807 TCAAGTGGACGGTTTTGTATAGTTGGTTTTGGG
1 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
1789840 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
1 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
1789873 ATATGATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.36, T:0.39
Consensus pattern (33 bp):
TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
Found at i:1796850 original size:38 final size:38
Alignment explanation
Indices: 1796808--1796922 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
1796798 AGTGACTCTA
* *
1796808 ATGGTTAAAATGAATGTTATTTTCTCTTGAGGTTTCGG
1 ATGGTTAAAAGGAGTGTTATTTTCTCTTGAGGTTTCGG
**
1796846 ATGGTTAAAAGGAGTGTTATCCTCTCTTGAGGTTTCGG
1 ATGGTTAAAAGGAGTGTTATTTTCTCTTGAGGTTTCGG
** *
1796884 ATGGTTAAAAGGAGTACTATTTTTCTCTTGAAGTTTCGG
1 ATGGTTAAAAGGAGTGTTA-TTTTCTCTTGAGGTTTCGG
1796923 GTGAGAACAG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
38 51 0.76
39 16 0.24
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.41
Consensus pattern (38 bp):
ATGGTTAAAAGGAGTGTTATTTTCTCTTGAGGTTTCGG
Found at i:1797960 original size:61 final size:62
Alignment explanation
Indices: 1797853--1798010 Score: 214
Period size: 61 Copynumber: 2.6 Consensus size: 62
1797843 CTAATATTTC
* * *
1797853 CTATGATCAA-TTTTTTGTCCATCTCTATTTATTAT-GAAAGTCGTTAAATTTTTAGTGAAT
1 CTATGATCAACTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTAAAT
* * *
1797913 CTATGTTCTACTCTTTTGTCGATCTCTATTTATTATAG-AAGTTGTTAAATTTTTAGTAAAT
1 CTATGATCAACTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTAAAT
* * *
1797974 CTATGATGAATTCTTTTGTCGATTTCTATTTATTATA
1 CTATGATCAACTCTTTTGTCGATCTCTATTTATTATA
1798011 AAATGGTTGA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 8 0.09
61 76 0.89
62 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (62 bp):
CTATGATCAACTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTAAAT
Found at i:1798075 original size:56 final size:59
Alignment explanation
Indices: 1797971--1798121 Score: 164
Period size: 56 Copynumber: 2.6 Consensus size: 59
1797961 ATTTTTAGTA
* * * *
1797971 AATCTATGATGAATTCTTTTGTCGATTTCTATTTATTATAAAATGGTTG-A-ATT-ATTG
1 AATCTATGAT-AATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGCATATTCAGTG
* * * *
1798028 AATCTATGATAATTATTTTGTCGTTTTCGATTTATTATTATACGGTTGCATTTTCAGTG
1 AATCTATGATAATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGCATATTCAGTG
* * *
1798087 AATATATGATTATTTCTTTTGTCGTTTTTGATTTA
1 AATCTATGA-TAATTCTTTTGTCGTTTTCGATTTA
1798122 ATATCTATCA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
56 32 0.41
57 11 0.14
58 2 0.03
59 11 0.14
60 22 0.28
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (59 bp):
AATCTATGATAATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGCATATTCAGTG
Found at i:1800098 original size:2 final size:2
Alignment explanation
Indices: 1800091--1800116 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1800081 AATTCTAATT
1800091 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
1800117 GGGGTGAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1814649 original size:20 final size:21
Alignment explanation
Indices: 1814616--1814655 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1814606 AAAAATTAGG
1814616 TAAATTATACG-TTTAGTATT
1 TAAATTATACGTTTTAGTATT
1814636 TAAATTATTA-GTTTTAGTAT
1 TAAATTA-TACGTTTTAGTAT
1814656 GTTTCAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TAAATTATACGTTTTAGTATT
Found at i:1816033 original size:2 final size:2
Alignment explanation
Indices: 1816026--1816065 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1816016 TTTTTAATGG
1816026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1816066 GCATTAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1816466 original size:16 final size:16
Alignment explanation
Indices: 1816445--1816477 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1816435 TAATAAATAA
1816445 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1816461 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1816477 A
1 A
1816478 AAATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1816558 original size:10 final size:10
Alignment explanation
Indices: 1816543--1816610 Score: 64
Period size: 10 Copynumber: 6.1 Consensus size: 10
1816533 TATTTAATAA
1816543 ATAAACGAAC
1 ATAAACGAAC
1816553 ATAAACGAAC
1 ATAAACGAAC
*
1816563 ACGAACGAACGAAC
1 A--TA--AACGAAC
1816577 ATAAACGAACAC
1 ATAAACG-A-AC
1816589 AATAAACGAAC
1 -ATAAACGAAC
1816600 ATAAACGAAC
1 ATAAACGAAC
1816610 A
1 A
1816611 ACATAAACAC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 26 0.53
11 3 0.06
12 5 0.10
13 7 0.14
14 8 0.16
ACGTcount: A:0.59, C:0.22, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1816600 original size:23 final size:23
Alignment explanation
Indices: 1816542--1816618 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
1816532 TTATTTAATA
1816542 AATAAACGAACATAAACGAACAC
1 AATAAACGAACATAAACGAACAC
**
1816565 GAACGAACGAACATAAACGAACAC
1 -AATAAACGAACATAAACGAACAC
1816589 AATAAACGAACATAAACGAACA-
1 AATAAACGAACATAAACGAACAC
1816611 ACATAAAC
1 A-ATAAAC
1816619 ACACAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
22 1 0.02
23 26 0.54
24 21 0.44
ACGTcount: A:0.60, C:0.22, G:0.10, T:0.08
Consensus pattern (23 bp):
AATAAACGAACATAAACGAACAC
Found at i:1816624 original size:13 final size:13
Alignment explanation
Indices: 1816550--1816618 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
1816540 TAAATAAACG
1816550 AACATAAACGAAC
1 AACATAAACGAAC
*
1816563 -AC--GAACGAAC
1 AACATAAACGAAC
1816573 GAACATAAACGAAC
1 -AACATAAACGAAC
1816587 -ACAATAAACG---
1 AAC-ATAAACGAAC
1816597 AACATAAACGAAC
1 AACATAAACGAAC
1816610 AACATAAAC
1 AACATAAAC
1816619 ACACAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
10 14 0.31
11 2 0.04
12 6 0.13
13 16 0.36
14 7 0.16
ACGTcount: A:0.59, C:0.23, G:0.10, T:0.07
Consensus pattern (13 bp):
AACATAAACGAAC
Found at i:1816903 original size:24 final size:26
Alignment explanation
Indices: 1816872--1816927 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
1816862 TGTCCTATGT
1816872 TCGAACATAAATGAACGAACATA-AA
1 TCGAACATAAATGAACGAACATATAA
1816897 T-GAACATAAATGAACGAACATATAA
1 TCGAACATAAATGAACGAACATATAA
1816922 TCGAAC
1 TCGAAC
1816928 GTTCACGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (26 bp):
TCGAACATAAATGAACGAACATATAA
Found at i:1816927 original size:16 final size:14
Alignment explanation
Indices: 1816873--1816928 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
1816863 GTCCTATGTT
1816873 CGAACATAAATGAA
1 CGAACATAAATGAA
1816887 CGAACATAAAT---
1 CGAACATAAATGAA
1816898 -GAACATAAATGAA
1 CGAACATAAATGAA
1816911 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
1816927 CG
1 CG
1816929 TTCACGAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.28
14 18 0.50
15 3 0.08
16 5 0.14
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Done.