Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 64
Found at i:1222322 original size:18 final size:19
Alignment explanation
Indices: 1222301--1222344 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1222291 TCCACTTCGG
*
1222301 GAGCCATCACCTC-GCCCA
1 GAGCCATCACCTCACCCCA
*
1222319 GAGCTATCACCTCACCCCA
1 GAGCCATCACCTCACCCCA
1222338 GAGCCAT
1 GAGCCAT
1222345 ATCTGATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.25, C:0.45, G:0.16, T:0.14
Consensus pattern (19 bp):
GAGCCATCACCTCACCCCA
Found at i:1222851 original size:20 final size:19
Alignment explanation
Indices: 1222828--1222872 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1222818 CGCAACACGA
*
1222828 AAATGATTATCGCAATGCGG
1 AAATGACTATCGCAATGC-G
*
1222848 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
1222867 AAATGA
1 AAATGA
1222873 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:1222878 original size:19 final size:19
Alignment explanation
Indices: 1222836--1222951 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
1222826 GAAAATGATT
***
1222836 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
1222856 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1222875 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1222889 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1222907 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1222921 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1222940 ATCGCAATGCGA
1 ATCGCAATGCGA
1222952 TTTGTGTTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.35
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1222891 original size:14 final size:14
Alignment explanation
Indices: 1222872--1222929 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1222862 ATGCGAAATG
1222872 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1222886 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1222902 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1222918 AAAATCGCAACG
1 AAAATCGCAACG
1222930 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1222914 original size:32 final size:33
Alignment explanation
Indices: 1222856--1222946 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1222846 GGAAATGGCT
1222856 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1222889 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1222921 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1222947 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1223038 original size:39 final size:39
Alignment explanation
Indices: 1222988--1223062 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1222978 GTTGCGATTT
**
1222988 CATTTCGCGTTGCGATTTTCA-TTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGC
*
1223026 CATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTTCGCATTGCGAT
1223063 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 5 0.16
39 14 0.44
40 13 0.41
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGC
Found at i:1223072 original size:20 final size:19
Alignment explanation
Indices: 1222977--1223081 Score: 104
Period size: 20 Copynumber: 5.4 Consensus size: 19
1222967 GCGATTTTGT
1222977 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1222995 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1223014 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1223034 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1223054 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1223074 TGTTGCGA
1 CGTTGCGA
1223082 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
18 8 0.11
19 23 0.32
20 39 0.53
21 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1224943 original size:14 final size:14
Alignment explanation
Indices: 1224924--1224959 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1224914 ATTGTTTAAT
1224924 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1224938 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1224952 TGATTTGT
1 TGATTTGT
1224960 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1225098 original size:19 final size:19
Alignment explanation
Indices: 1225076--1225114 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1225066 ATCGCAACGA
1225076 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1225095 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1225114 G
1 G
1225115 GCAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1225162 original size:20 final size:20
Alignment explanation
Indices: 1225137--1225194 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1225127 TCGCATTGCG
*
1225137 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1225157 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1225177 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1225195 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1226277 original size:24 final size:24
Alignment explanation
Indices: 1226243--1226296 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1226233 GTATTCGAAA
* *
1226243 TTTGATCTTGGTAAATACCCGGAC
1 TTTGATATTGGTAAATACACGGAC
* *
1226267 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTAAATACACGGAC
1226291 TTTGAT
1 TTTGAT
1226297 GATGTTTCAG
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:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTAAATACACGGAC
Found at i:1228854 original size:19 final size:19
Alignment explanation
Indices: 1228763--1228893 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
1228753 GGAAATTACT
*
1228763 ATCGCAATGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
*
1228782 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1228796 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1228815 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1228829 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1228848 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1228862 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1228881 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1228894 TTTAATTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 25 0.31
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.47
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1228896 original size:33 final size:33
Alignment explanation
Indices: 1228764--1228896 Score: 205
Period size: 33 Copynumber: 4.0 Consensus size: 33
1228754 GAAATTACTA
* * *
1228764 TCGCAATGCGAAATGGAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
1228797 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
1228830 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1228863 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1228896 T
1 T
1228897 AATTTCGCGT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 1 0.01
33 93 0.99
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:1228942 original size:19 final size:19
Alignment explanation
Indices: 1228918--1228964 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1228908 GTGATTCTCT
1228918 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1228937 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1228956 CATTGCGAT
1 CGTTGCGAT
1228965 AGTACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1229090 original size:14 final size:14
Alignment explanation
Indices: 1229071--1229107 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1229061 CATCAATTAA
1229071 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1229085 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1229099 ACAAATCAA
1 ACAAATCAA
1229108 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:1230547 original size:42 final size:42
Alignment explanation
Indices: 1230501--1230580 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1230491 CGATGACAGT
* * *
1230501 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1230543 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1230581 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1232458 original size:20 final size:19
Alignment explanation
Indices: 1232413--1232550 Score: 64
Period size: 20 Copynumber: 7.7 Consensus size: 19
1232403 TCTTTTGGTT
1232413 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1232432 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
1232453 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
1232472 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
1232486 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
1232505 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
* * *
1232519 GAAA-AAAAATCGTAACGC
1 GAAATGAAAATCGCAACGA
1232537 GAAATGAAAATCGC
1 GAAATGAAAATCGC
1232551 TGGCGATCTA
Statistics
Matches: 88, Mismatches: 19, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
14 18 0.20
16 4 0.05
17 3 0.03
18 14 0.16
19 19 0.22
20 28 0.32
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1232495 original size:33 final size:33
Alignment explanation
Indices: 1232438--1232522 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
1232428 ACGAGATAAT
*
1232438 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1232472 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1232505 GAGAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAA
1232523 AAAAATCGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1232548 original size:19 final size:18
Alignment explanation
Indices: 1232508--1232550 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1232498 GCGACGAGAG
1232508 AATCGCAACGCGAAAAAA
1 AATCGCAACGCGAAAAAA
* *
1232526 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAA-AAA
1232545 AATCGC
1 AATCGC
1232551 TGGCGATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (18 bp):
AATCGCAACGCGAAAAAA
Found at i:1235841 original size:14 final size:14
Alignment explanation
Indices: 1235822--1235857 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1235812 ATTGTTTAAT
1235822 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1235836 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1235850 TGATTTGT
1 TGATTTGT
1235858 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1236039 original size:19 final size:19
Alignment explanation
Indices: 1235964--1236030 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1235954 AAAAAGTACT
*
1235964 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1235983 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1235997 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1236016 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1236031 TAAATTCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1236057 original size:19 final size:19
Alignment explanation
Indices: 1236035--1236185 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1236025 CGAAATTAAA
1236035 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1236054 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1236069 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1236087 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1236101 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
1236120 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1236135 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1236153 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1236172 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1236186 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1236081 original size:33 final size:32
Alignment explanation
Indices: 1236039--1236165 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1236029 ATTAAATTCG
1236039 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1236072 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1236105 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1236138 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1236166 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1236117 original size:66 final size:66
Alignment explanation
Indices: 1236032--1236164 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1236022 ACGCGAAATT
*
1236032 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1236097 G
66 G
* *
1236098 AAATTAGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1236163 G
66 G
1236164 A
1 A
1236165 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1238473 original size:12 final size:12
Alignment explanation
Indices: 1238456--1238480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1238446 TCTTCGGGGA
1238456 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1238468 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1238480 C
1 C
1238481 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1239789 original size:20 final size:20
Alignment explanation
Indices: 1239764--1239841 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
1239754 ATTCATTTGA
1239764 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1239784 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1239804 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1239824 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1239842 CGCAATGCGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1239884 original size:14 final size:14
Alignment explanation
Indices: 1239865--1239918 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1239855 GAAAATCGCA
1239865 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1239879 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1239896 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1239912 TTGCGAT
1 TTGCGAT
1239919 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1239884 original size:33 final size:33
Alignment explanation
Indices: 1239847--1239917 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1239837 AAAATCGCAA
1239847 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1239880 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1239913 TGCGA
1 TGCGA
1239918 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1239926 original size:33 final size:33
Alignment explanation
Indices: 1239860--1239929 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1239850 GAAATGAAAA
***
1239860 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1239893 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1239926 TCGC
1 TCGC
1239930 GTTGTGATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1240044 original size:14 final size:14
Alignment explanation
Indices: 1240025--1240061 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1240015 CATCAATTAA
1240025 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1240039 ACAAATCATCTTTT
1 ACAAATCAACATTT
1240053 ACAAATCAA
1 ACAAATCAA
1240062 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1241952 original size:20 final size:20
Alignment explanation
Indices: 1241929--1241982 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1241919 GAAACTTAAA
1241929 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1241949 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* *
1241969 ATCGTAATGCGAAA
1 ATCGCAACGCGAAA
1241983 TGAAAATCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1242004 original size:14 final size:14
Alignment explanation
Indices: 1241985--1242042 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1241975 ATGCGAAATG
*
1241985 AAAATCACAACGAC
1 AAAATCGCAACGAC
* *
1241999 AAAATCTCAACGCGAA
1 AAAATCGCAA--CGAC
1242015 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1242031 AAAATCGCAACG
1 AAAATCGCAACG
1242043 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.50, C:0.26, G:0.14, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1242028 original size:32 final size:33
Alignment explanation
Indices: 1241977--1242047 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
1241967 CTATCGTAAT
*
1241977 GCGAAATGAAAATCACAACGACAAAATCTCAAC
1 GCGAAATGAAAATCACAACGACAAAATCGCAAC
*
1242010 GCGAAATG-AAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCACAACGACAAAATCGCAAC
1242042 GCGAAA
1 GCGAAA
1242048 CACAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 28 0.78
33 8 0.22
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (33 bp):
GCGAAATGAAAATCACAACGACAAAATCGCAAC
Found at i:1242084 original size:20 final size:20
Alignment explanation
Indices: 1242059--1242104 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1242049 ACAAATCGCA
1242059 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1242079 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1242099 TTGCGA
1 TTGCGA
1242105 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1242612 original size:18 final size:18
Alignment explanation
Indices: 1242586--1242630 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1242576 GTCGATCAGA
*
1242586 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1242604 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1242622 TGATGGCTC
1 TGATGGCTC
1242631 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1243998 original size:20 final size:20
Alignment explanation
Indices: 1243950--1244008 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1243940 AATAGTTTCT
** *
1243950 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1243970 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1243990 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1244009 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1244528 original size:20 final size:20
Alignment explanation
Indices: 1244502--1244574 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
1244492 GATTATGTAT
1244502 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1244522 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1244542 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1244562 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1244575 TTTTGTATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1244609 original size:21 final size:20
Alignment explanation
Indices: 1244585--1244636 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
1244575 TTTTGTATTG
*
1244585 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* * **
1244606 TCGCGTTGTGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1244626 TCGCATTGCGA
1 TCGCATTGCGA
1244637 ATTGGGAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1245599 original size:18 final size:18
Alignment explanation
Indices: 1245576--1245618 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1245566 AGACCCGGAT
*
1245576 CCGACCCGATTAACTGAC
1 CCGACCCAATTAACTGAC
*
1245594 CCGACCCAATTAACTTAC
1 CCGACCCAATTAACTGAC
1245612 CCGACCC
1 CCGACCC
1245619 TATTGGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.44, G:0.12, T:0.16
Consensus pattern (18 bp):
CCGACCCAATTAACTGAC
Found at i:1248293 original size:15 final size:16
Alignment explanation
Indices: 1248255--1248295 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1248245 ATAGAGCTTC
*
1248255 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
1248271 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
1248287 T-AATCATTC
1 TGAATCATTC
1248296 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:1249456 original size:19 final size:19
Alignment explanation
Indices: 1249421--1249457 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1249411 ATGACCAACA
*
1249421 AAATCGCAATGCAATCTCT
1 AAATCGCAACGCAATCTCT
*
1249440 AAATCGCAACGCGATCTC
1 AAATCGCAACGCAATCTC
1249458 CATTATCGCA
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:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCT
Found at i:1249568 original size:20 final size:20
Alignment explanation
Indices: 1249543--1249586 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1249533 GATTTTAGAT
1249543 AATCGCAATGCGAATATCTA
1 AATCGCAATGCGAATATCTA
1249563 AATCGCAATGCGAATATCTA
1 AATCGCAATGCGAATATCTA
1249583 AATC
1 AATC
1249587 ACAACGCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (20 bp):
AATCGCAATGCGAATATCTA
Found at i:1249595 original size:20 final size:20
Alignment explanation
Indices: 1249552--1249595 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1249542 TAATCGCAAT
* *
1249552 GCGAATATCTAAATCGCAAT
1 GCGAATATCTAAATCACAAC
1249572 GCGAATATCTAAATCACAAC
1 GCGAATATCTAAATCACAAC
1249592 GCGA
1 GCGA
1249596 TAACACGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
GCGAATATCTAAATCACAAC
Found at i:1249630 original size:20 final size:20
Alignment explanation
Indices: 1249605--1249649 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1249595 ATAACACGTG
* *
1249605 ATCGCAACGCGATTCGGACT
1 ATCGCAACGAGATTCAGACT
1249625 ATCGCAACGAGATTCAGACT
1 ATCGCAACGAGATTCAGACT
1249645 ATCGC
1 ATCGC
1249650 GTTGCGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGATTCAGACT
Found at i:1249847 original size:22 final size:22
Alignment explanation
Indices: 1249819--1249888 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
1249809 CTACGGTGAC
1249819 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * * *
1249841 ATTCGTCCCCATTTTCGACAAA
1 ATCCGTCCCCATCTCCGACGAA
*
1249863 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1249885 ATCC
1 ATCC
1249889 ATCTATCTCC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.41, G:0.13, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1250275 original size:33 final size:34
Alignment explanation
Indices: 1250232--1250312 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 34
1250222 CAACGACAAA
*
1250232 ATTCGCGTTGCGATTATCTCGTTGCGATA-TCCA-
1 ATTCGCGTTGCGATTATCTCGTTACGATAGT-CAG
*
1250265 TTTCGCGTTGCGATTATCTCGTTACGATAGTCAG
1 ATTCGCGTTGCGATTATCTCGTTACGATAGTCAG
1250299 ATTCGCGTTGCGAT
1 ATTCGCGTTGCGAT
1250313 AATCATTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.67
34 14 0.33
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (34 bp):
ATTCGCGTTGCGATTATCTCGTTACGATAGTCAG
Found at i:1250312 original size:20 final size:20
Alignment explanation
Indices: 1250284--1250332 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1250274 GCGATTATCT
* *
1250284 CGTTACGATAGTCAGATTCG
1 CGTTGCGATAATCAGATTCG
**
1250304 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAGATTCG
*
1250324 TGTTGCGAT
1 CGTTGCGAT
1250333 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCAGATTCG
Found at i:1250338 original size:20 final size:20
Alignment explanation
Indices: 1250300--1250355 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1250290 GATAGTCAGA
* **
1250300 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
1250320 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1250340 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1250356 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1250362 original size:20 final size:20
Alignment explanation
Indices: 1250319--1250362 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1250309 CGATAATCAT
* *
1250319 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1250339 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1250359 TTTC
1 TTTC
1250363 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1252233 original size:31 final size:31
Alignment explanation
Indices: 1252177--1252238 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1252167 TTGTCTTTGT
*
1252177 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTT-AACTTAGTAAATTCATA
1252209 TTTGTCTTTTGGATT-ACTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTAACTTAGTAAATTCAT
1252239 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.50
32 12 0.43
33 2 0.07
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTAACTTAGTAAATTCATA
Found at i:1252382 original size:20 final size:20
Alignment explanation
Indices: 1252357--1252443 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
1252347 AGAAGAATAG
*
1252357 TCGCAACACGAAAATGATTA
1 TCGCAACACGAAAATGACTA
* **
1252377 TCGCAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
** **
1252397 TCGCAACGTGAATTTGACTA
1 TCGCAACACGAAAATGACTA
** **
1252417 TCGCAACGTGAATTTGACTA
1 TCGCAACACGAAAATGACTA
1252437 TCGCAAC
1 TCGCAAC
1252444 GGGATAATCG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1252444 original size:20 final size:20
Alignment explanation
Indices: 1252375--1252444 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1252365 CGAAAATGAT
*
1252375 TATCGCAACGCGAATTTGAC
1 TATCGCAACGTGAATTTGAC
1252395 TATCGCAACGTGAATTTGAC
1 TATCGCAACGTGAATTTGAC
1252415 TATCGCAACGTGAATTTGAC
1 TATCGCAACGTGAATTTGAC
1252435 TATCGCAACG
1 TATCGCAACG
1252445 GGATAATCGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
TATCGCAACGTGAATTTGAC
Found at i:1252509 original size:19 final size:19
Alignment explanation
Indices: 1252487--1252523 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1252477 CGCGAATTTA
*
1252487 GTTTTGCGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTT
1252506 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1252524 CTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.14, G:0.27, T:0.54
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTT
Found at i:1252524 original size:14 final size:14
Alignment explanation
Indices: 1252507--1252567 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
1252497 GCGATTTTTG
1252507 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
1252521 TTTCTCGTTGCGATAGT
1 TTTCGCGTTGCG--A-T
1252538 CATTTCGCGTTGCGAT
1 --TTTCGCGTTGCGAT
* *
1252554 TATCTCGTTGCGAT
1 TTTCGCGTTGCGAT
1252568 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 23 0.61
16 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:1252544 original size:33 final size:34
Alignment explanation
Indices: 1252507--1252584 Score: 131
Period size: 33 Copynumber: 2.3 Consensus size: 34
1252497 GCGATTTTTG
*
1252507 TTTCGCGTTGCGATTTTCTCGTTGCGATAGTC-A
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1252540 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
*
1252574 ATTCGCGTTGC
1 TTTCGCGTTGC
1252585 AATCATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
33 31 0.74
34 11 0.26
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
Found at i:1252621 original size:20 final size:20
Alignment explanation
Indices: 1252596--1252635 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1252586 ATCATTTTTT
1252596 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
1252616 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
1252636 AGAAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:1253148 original size:21 final size:21
Alignment explanation
Indices: 1253116--1253220 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
1253106 GACTCACCTG
* *
1253116 TCATCATTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1253137 TTATCGTTCAAGAGTCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1253158 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1253179 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1253200 TCATCGTTAAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1253221 CCAACATTCT
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1253213 original size:42 final size:42
Alignment explanation
Indices: 1253112--1253218 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1253102 GCCCGACTCA
* * * * *
1253112 CCTGTCATCATTCAAGAGGCCTCTCTTATCGTTCAAGAGTCC
1 CCTGTCATCATTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
* **
1253154 CCTATCATCCCTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
* *
1253196 CCTGTCATCGTTAAAGAGGTCCC
1 CCTGTCATCATTCAAGA-GTCCC
1253219 TCCCAACATT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 47 0.90
43 5 0.10
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
Found at i:1254672 original size:36 final size:30
Alignment explanation
Indices: 1254592--1254657 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
1254582 ATAAGAGTTG
*
1254592 ATTTGTTTAACTGATATGTAAATAATTCTT
1 ATTTGTTTAATTGATATGTAAATAATTCTT
*
1254622 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATATGTAAATAATTCTT
1254652 ATTTGT
1 ATTTGT
1254658 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (30 bp):
ATTTGTTTAATTGATATGTAAATAATTCTT
Found at i:1254828 original size:20 final size:20
Alignment explanation
Indices: 1254807--1255104 Score: 211
Period size: 20 Copynumber: 15.8 Consensus size: 20
1254797 GCGATTTTCT
*
1254807 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
*
1254827 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1254847 CGTTGTGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1254866 CATTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
1254880 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
1254900 CGTTTTGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1254920 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
** *
1254940 CGTTGCGATAGTCATTTTCT
1 CGTTGCGATAGTCAAATTCG
* *
1254960 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
1254974 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1254994 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1255014 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
1255028 CGTTGCGATATTCGAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
1255048 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCG
* * *
1255068 TGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1255088 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1255105 GAATGTGTAA
Statistics
Matches: 219, Mismatches: 41, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
14 30 0.14
16 3 0.01
17 1 0.00
18 2 0.01
19 15 0.07
20 168 0.77
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1254833 original size:34 final size:34
Alignment explanation
Indices: 1254773--1254903 Score: 111
Period size: 34 Copynumber: 3.7 Consensus size: 34
1254763 ATCATATTCG
* * * *
1254773 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
1254807 CGTTGCGATAGTCAAATTCTCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* * * *
1254847 CGTTGTGATAGTC-ATTTCGCATTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1254880 CGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAGTCAAATTCGCGTT
1254904 TTGATAGTTA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
33 14 0.18
34 33 0.43
36 1 0.01
37 1 0.01
39 12 0.16
40 15 0.20
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:1254991 original size:74 final size:72
Alignment explanation
Indices: 1254821--1255101 Score: 255
Period size: 74 Copynumber: 3.8 Consensus size: 72
1254811 GCGATAGTCA
* * * * *
1254821 AATTCTCGTTGCGATAATCAAATTCGCGTTGTGATAGTCA-TTTCGCATTGCGATTA-TCTCGTT
1 AATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGA-TAGTC-AGTT
* *
1254884 GCGATAGTCA
64 GC-ATATTCG
* ** * * *
1254894 AATTCGCGTTTTGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTC
1 AATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAGTTGC
1254959 -TCATTGCG
66 AT-ATT-CG
* * * *
1254967 ATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA-TCCCGT
1 AAT-TCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGA-TAGT-CAGT
1255031 TGCGATATTCG
63 TGC-ATATTCG
* ** * *
1255042 AATTCACGTTGCGATAGTCATATTCATGTTGTGATAGTCATATTCGCGTTGCGATAGTCA
1 AATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCA
1255102 AATGAATGTG
Statistics
Matches: 168, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
71 1 0.01
72 2 0.01
73 45 0.27
74 106 0.63
75 10 0.06
76 3 0.02
77 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (72 bp):
AATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAGTTGC
ATATTCG
Found at i:1255002 original size:54 final size:54
Alignment explanation
Indices: 1254920--1255062 Score: 232
Period size: 54 Copynumber: 2.6 Consensus size: 54
1254910 GTTAAATTCG
** *
1254920 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCTCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1254974 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * *
1255028 CGTTGCGATATTCGAATTCACGTTGCGATAGTCAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAT
1255063 ATTCATGTTG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:1255302 original size:18 final size:18
Alignment explanation
Indices: 1255279--1255313 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1255269 AAGCCGGTTG
*
1255279 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1255297 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1255314 GCCTTTTGCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1257370 original size:14 final size:14
Alignment explanation
Indices: 1257351--1257377 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1257341 TCCCGTGGCA
1257351 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1257365 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
1257378 TTTCTTCTTG
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:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1257383 original size:12 final size:13
Alignment explanation
Indices: 1257352--1257384 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1257342 CCCGTGGCAT
1257352 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
1257365 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
1257378 TTTCTTC
1 TTTCTTC
1257385 TTGATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:1257611 original size:24 final size:24
Alignment explanation
Indices: 1257577--1257630 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1257567 CTGAAACATC
1257577 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1257601 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1257625 ATCAAA
1 ATCAAA
1257631 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1258479 original size:20 final size:20
Alignment explanation
Indices: 1258451--1258598 Score: 165
Period size: 20 Copynumber: 7.3 Consensus size: 20
1258441 AATTCAGTGA
*
1258451 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1258471 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
1258491 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
1258512 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
** *
1258532 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCGT
* *
1258553 TGCGATAGTCCGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
*
1258573 TGCGATAGTCAGAATCGCAT
1 TGCGATAGTCAGAATCGCGT
1258593 TGCGAT
1 TGCGAT
1258599 TTACATATTC
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.04
20 69 0.65
21 29 0.27
22 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1258509 original size:41 final size:41
Alignment explanation
Indices: 1258464--1258578 Score: 203
Period size: 41 Copynumber: 2.8 Consensus size: 41
1258454 GTTAGTCAGA
1258464 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1258505 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
* * *
1258546 ATCGCATTGCGATAGTCCGAATCTCGTTGCGAT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGAT
1258579 AGTCAGAATC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATT
Found at i:1258510 original size:21 final size:21
Alignment explanation
Indices: 1258484--1258558 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
1258474 GATAGTCAGA
1258484 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
**
1258505 ATCGCGTTGCGAT-A-GTCAGA
1 ATCGCGTTGCGATCACGT-ATT
1258525 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
*
1258546 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1258559 AGTCCGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 27 0.59
22 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (21 bp):
ATCGCGTTGCGATCACGTATT
Found at i:1258521 original size:61 final size:61
Alignment explanation
Indices: 1258451--1258598 Score: 167
Period size: 61 Copynumber: 2.4 Consensus size: 61
1258441 AATTCAGTGA
* * **
1258451 TGCGTTAGTCAGAATCGCGTTGCGAT-A-GTCAGAATCGCGTTGCGATCACGT-ATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGT-AGAATCGCATTGCGAT-A-GTCAGAATCGCGT
** * *
1258512 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCATTGCGATAGTCCGAATCTCGT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGTAGAATCGCATTGCGATAGTCAGAATCGCGT
*
1258573 TGCGATAGTCAGAATCGCATTGCGAT
1 TGCGATAGTCAGAATCGCGTTGCGAT
1258599 TTACATATTC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
60 2 0.03
61 57 0.76
62 14 0.19
63 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATCACGTAGAATCGCATTGCGATAGTCAGAATCGCGT
Found at i:1258637 original size:21 final size:20
Alignment explanation
Indices: 1258585--1258660 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 20
1258575 CGATAGTCAG
* *
1258585 AATCGCATTGCGATTTAC-AT
1 AATCGCAATGCGATTT-CGAA
* * *
1258605 ATTCGCATTGCGATTATCTAA
1 AATCGCAATGCGATT-TCGAA
1258626 AATCGCAATGCGGATTTCGAA
1 AATCGCAATGC-GATTTCGAA
1258647 AATCGCAATGCGAT
1 AATCGCAATGCGAT
1258661 GGTCAAAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 18 0.38
21 26 0.54
22 4 0.08
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
AATCGCAATGCGATTTCGAA
Found at i:1258652 original size:102 final size:102
Alignment explanation
Indices: 1258450--1258679 Score: 243
Period size: 102 Copynumber: 2.3 Consensus size: 102
1258440 AAATTCAGTG
* * * *
1258450 ATGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTTGC
1 ATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATCACATATTATCGCATTGC
* ** **
1258515 GATAGTCAGAATCGCGTTGCGATCACGTATTATCGCA
66 GATAGTCAAAATCGCAATGCGATCACGTAAAATCGCA
* * * *
1258552 TTGCGATAGTCCGAATCTCGTTGCGATAGTCAGAATCGCATTGCGATTTACATA-T-TCGCATTG
1 ATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGA-TCACATATTATCGCATTG
**
1258615 CGATTA-TCTAAAATCGCAATGCGGATTTCG-AAAATCGCA
65 CGA-TAGTC-AAAATCGCAATGC-GATCACGTAAAATCGCA
* *
1258654 ATGCGATGGTCAAAATCGCGTTGCGA
1 ATGCGATAGTCAGAATCGCGTTGCGA
1258680 ATCTGGAAAC
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
101 12 0.12
102 82 0.79
103 10 0.10
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (102 bp):
ATGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCATTGCGATCACATATTATCGCATTGC
GATAGTCAAAATCGCAATGCGATCACGTAAAATCGCA
Found at i:1258670 original size:20 final size:21
Alignment explanation
Indices: 1258624--1258672 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1258614 GCGATTATCT
*
1258624 AAAATCGCAATGCGGATTTCG
1 AAAATCGCAATGCGGATGTCG
1258645 AAAATCGCAATGC-GATGGTC-
1 AAAATCGCAATGCGGAT-GTCG
1258665 AAAATCGC
1 AAAATCGC
1258673 GTTGCGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAATCGCAATGCGGATGTCG
Found at i:1258717 original size:20 final size:19
Alignment explanation
Indices: 1258693--1258739 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1258683 TGGAAACTGA
*
1258693 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
1258713 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
1258732 ATTGCGAT
1 ATTGCGAT
1258740 TTTGTTAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:1258729 original size:19 final size:19
Alignment explanation
Indices: 1258705--1258741 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1258695 TGCGATAATG
*
1258705 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1258724 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1258742 TGTTAGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1260568 original size:2 final size:2
Alignment explanation
Indices: 1260563--1260600 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1260553 TTAAAAAATA
1260563 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
1260601 TAATCTGGAG
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:1262225 original size:16 final size:16
Alignment explanation
Indices: 1262204--1262236 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1262194 TTACCAAGAC
1262204 TTCAATAATGTTAGGA
1 TTCAATAATGTTAGGA
1262220 TTCAATAATGTTAGGA
1 TTCAATAATGTTAGGA
1262236 T
1 T
1262237 GTGGAGAGAC
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:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTCAATAATGTTAGGA
Found at i:1267485 original size:16 final size:16
Alignment explanation
Indices: 1267464--1267496 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1267454 TTACCAAGAC
1267464 TTCAATAATGTTAGGA
1 TTCAATAATGTTAGGA
1267480 TTCAATAATGTTAGGA
1 TTCAATAATGTTAGGA
1267496 T
1 T
1267497 GTGGAGAGAC
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:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTCAATAATGTTAGGA
Found at i:1271501 original size:30 final size:29
Alignment explanation
Indices: 1271465--1271548 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 29
1271455 AGGCTCAAAA
1271465 TTATTATTATGGTTCTAATTTTTTTAATAT
1 TTATTATTATGGTTCT-ATTTTTTTAATAT
* * *
1271495 TTATTATTAT-ATGCT-TATTTTTAATAT
1 TTATTATTATGGTTCTATTTTTTTAATAT
* *
1271522 TTATTATTATGGGTCTATTTTTATAAT
1 TTATTATTATGGTTCTATTTTTTTAAT
1271549 TTTTTTAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
27 21 0.48
28 2 0.05
29 11 0.25
30 10 0.23
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (29 bp):
TTATTATTATGGTTCTATTTTTTTAATAT
Found at i:1272324 original size:19 final size:20
Alignment explanation
Indices: 1272300--1272349 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1272290 TTTTTAAGAG
1272300 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1272319 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1272339 AAAATCGCAAC
1 AAAATCGCAAC
1272350 ATTAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1272344 original size:20 final size:20
Alignment explanation
Indices: 1272298--1272557 Score: 112
Period size: 20 Copynumber: 12.7 Consensus size: 20
1272288 TTTTTTTAAG
*
1272298 AGAAAATCGCAACGCGATAT
1 AGAAAATCGCAACGCGATTT
*
1272318 -CAAAATCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
*** ***
1272337 AGAAAATCGCAACATTAAAA
1 AGAAAATCGCAACGCGATTT
**
1272357 AGAAAATCGCAACG-G-TCAAA
1 AGAAAATCGCAACGCGAT--TT
*
1272377 AGAAAATCGCAACGCGAGCTT
1 AGAAAATCGCAACGCGA-TTT
** **
1272398 CCAAGTTCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
* *
1272418 AGAAGAAAATCGCAATGCGATTG
1 ---AGAAAATCGCAACGCGATTT
* * *
1272441 ATAGAATCGCAATGCGATTT
1 AGAAAATCGCAACGCGATTT
* * * *
1272461 ATATAATCGCAATGCGATTG
1 AGAAAATCGCAACGCGATTT
* *
1272481 AGAGAGTCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTT
* * *
1272501 AGAAGAAAATCGCAATGCGACTG
1 ---AGAAAATCGCAACGCGATTT
* * * *
1272524 AGAGAATCGCAATGCGACTG
1 AGAAAATCGCAACGCGATTT
*
1272544 AGAGAATCGCAACG
1 AGAAAATCGCAACG
1272558 TTGAAAAATC
Statistics
Matches: 185, Mismatches: 43, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
19 17 0.09
20 125 0.68
21 14 0.08
23 29 0.16
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AGAAAATCGCAACGCGATTT
Found at i:1272460 original size:43 final size:43
Alignment explanation
Indices: 1272404--1272540 Score: 190
Period size: 43 Copynumber: 3.3 Consensus size: 43
1272394 GCTTCCAAGT
*
1272404 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
* * * *
1272447 TCGCAATGCGATTT---ATATAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
*
1272487 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
*
1272530 TCGCAATGCGA
1 TCGCAACGCGA
1272541 CTGAGAGAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 35 0.44
43 45 0.56
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (43 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAA
Found at i:1272672 original size:6 final size:6
Alignment explanation
Indices: 1272661--1272761 Score: 181
Period size: 6 Copynumber: 17.3 Consensus size: 6
1272651 GACACGTATT
1272661 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1272709 ACCACG ACCACG ACCACG ACCACG ACCACG A-C-C- ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1272754 ACCACG AC
1 ACCACG AC
1272762 GAGACGAGAC
Statistics
Matches: 92, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 2 0.02
6 87 0.95
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1273454 original size:6 final size:6
Alignment explanation
Indices: 1273445--1273519 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
1273435 CCGTCTCGTC
1273445 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1273493 TCGTGG TCGTGG TCGTGG TCGTGG TCG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCG
1273520 GTAATACGTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:1273624 original size:20 final size:20
Alignment explanation
Indices: 1273599--1273638 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1273589 TTTTTAACTA
1273599 TTCTTTTGAC-CGTTGCGATT
1 TTCTTTT-ACGCGTTGCGATT
*
1273619 TTCTTTTTCGCGTTGCGATT
1 TTCTTTTACGCGTTGCGATT
1273639 CTATAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.07, C:0.20, G:0.20, T:0.53
Consensus pattern (20 bp):
TTCTTTTACGCGTTGCGATT
Found at i:1273649 original size:20 final size:20
Alignment explanation
Indices: 1273626--1273801 Score: 226
Period size: 20 Copynumber: 8.7 Consensus size: 20
1273616 ATTTTCTTTT
* * *
1273626 TCGCGTTGCGATTCTATAAA
1 TCGCATTGCGATTCTCTCAA
*
1273646 TCGCATTGCGATTCTCTCAG
1 TCGCATTGCGATTCTCTCAA
1273666 TCGCATTGCGATTTTCTTCTCAA
1 TCGCATTGCGA--TTC-TCTCAA
* *
1273689 TCGCGTTGCGACTCTCTCAA
1 TCGCATTGCGATTCTCTCAA
*
1273709 TCGCATTGCGACTCTCTCAA
1 TCGCATTGCGATTCTCTCAA
*
1273729 TCGCATTGCGACTCTCTCAA
1 TCGCATTGCGATTCTCTCAA
* *
1273749 TCGCATTGCGACTCTATCAA
1 TCGCATTGCGATTCTCTCAA
*
1273769 TCGCATTGCGATTCTATCAA
1 TCGCATTGCGATTCTCTCAA
1273789 TCGCATTGCGATT
1 TCGCATTGCGATT
1273802 TTCTTCTAAA
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
20 123 0.86
21 2 0.01
22 3 0.02
23 15 0.10
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTCTCTCAA
Found at i:1273682 original size:60 final size:60
Alignment explanation
Indices: 1273611--1273822 Score: 262
Period size: 60 Copynumber: 3.4 Consensus size: 60
1273601 CTTTTGACCG
* * * *
1273611 TTGCGATTTTCTTTTTCGCGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTTATCGCGTTGCGACTCTATCAATCGCATTGCGATTCTCTCAATCGCA
* *
1273671 TTGCGATTTTCTTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCA
1 TTGCGATTTTCTT-T--ATCGCGTTGCGACTCTATCAATCGCATTGCGATTCTCTCAATCGCA
* * ** * *
1273734 TTGCGACTCTCTCAATCGCATTGCGACTCTATCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTTTATCGCGTTGCGACTCTATCAATCGCATTGCGATTCTCTCAATCGCA
1273794 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTTTCTT-T--ATCGCGTTGCGA
1273823 ACTTGGAAGC
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
60 65 0.51
61 1 0.01
63 61 0.48
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (60 bp):
TTGCGATTTTCTTTATCGCGTTGCGACTCTATCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:1273861 original size:20 final size:20
Alignment explanation
Indices: 1273836--1273889 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1273826 TGGAAGCTCG
*
1273836 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
1273856 CGTTGC-ACTTTTCTTTTTAA
1 CGTTGCGA-TTTTCTTTTGAA
1273876 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1273890 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:1273916 original size:19 final size:19
Alignment explanation
Indices: 1273876--1273946 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
1273866 TTCTTTTTAA
1273876 CGTTGCGATTTTCTAA-ATCG
1 CGTTGCGA-TTT-TAATATCG
1273896 CGTTGCGATTTTAATATCG
1 CGTTGCGATTTTAATATCG
*
1273915 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTAATATCG
1273934 CGTTGCGATTTTA
1 CGTTGCGATTTTA
1273947 TTGGTCATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
18 3 0.06
19 37 0.77
20 8 0.17
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTAATATCG
Found at i:1274846 original size:24 final size:24
Alignment explanation
Indices: 1274819--1274864 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1274809 GAACGGGATG
1274819 CTAAAATGATATAAAAACTAAATA
1 CTAAAATGATATAAAAACTAAATA
1274843 CTAAAATGATATAAAAACTAAA
1 CTAAAATGATATAAAAACTAAA
1274865 GTTTTTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (24 bp):
CTAAAATGATATAAAAACTAAATA
Found at i:1282702 original size:24 final size:25
Alignment explanation
Indices: 1282657--1282708 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
1282647 TTAATAAGCT
1282657 AATGCAAAATAAGAATGCGAATGCA
1 AATGCAAAATAAGAATGCGAATGCA
*
1282682 AATGCAAAATAA-AATGCGAATGGA
1 AATGCAAAATAAGAATGCGAATGCA
1282706 AAT
1 AAT
1282709 ACATACAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.54, C:0.10, G:0.19, T:0.17
Consensus pattern (25 bp):
AATGCAAAATAAGAATGCGAATGCA
Found at i:1292401 original size:7 final size:7
Alignment explanation
Indices: 1292384--1292547 Score: 99
Period size: 7 Copynumber: 22.7 Consensus size: 7
1292374 TATACACTGC
*
1292384 TATATAA
1 TATATTA
*
1292391 TATATTT
1 TATATTA
1292398 TATA-TA
1 TATATTA
1292404 T-TATTA
1 TATATTA
*
1292410 AATATTA
1 TATATTA
*
1292417 TATTATAAA
1 TA-TAT-TA
1292426 GTATATTA
1 -TATATTA
*
1292434 TATATAA
1 TATATTA
*
1292441 TAGTAGTA
1 TA-TATTA
1292449 TATATTA
1 TATATTA
*
1292456 CATA-TA
1 TATATTA
1292462 TCATATTA
1 T-ATATTA
1292470 TGATATTA
1 T-ATATTA
1292478 TATATTA
1 TATATTA
*
1292485 T-GATTA
1 TATATTA
1292491 T-TATTA
1 TATATTA
1292497 T-TATTA
1 TATATTA
1292503 TTATATTA
1 -TATATTA
1292511 TAATATTA
1 T-ATATTA
1292519 T-TATTA
1 TATATTA
1292525 TTATTCATTA
1 -TA-T-ATTA
1292535 TATATATA
1 TATAT-TA
1292543 TATAT
1 TATAT
1292548 ACTTATTTTA
Statistics
Matches: 125, Mismatches: 16, Indels: 31
0.73 0.09 0.18
Matches are distributed among these distances:
5 2 0.02
6 26 0.21
7 45 0.36
8 39 0.31
9 7 0.06
10 6 0.05
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATTA
Found at i:1292420 original size:15 final size:15
Alignment explanation
Indices: 1292400--1292527 Score: 53
Period size: 15 Copynumber: 8.7 Consensus size: 15
1292390 ATATATTTTA
1292400 TATATTATTAAATAT
1 TATATTATTAAATAT
*
1292415 TATATTA-T-AA-AG
1 TATATTATTAAATAT
*
1292427 TATATTATATATAATAG
1 TATATTAT-TA-AATAT
*
1292444 TAGTATATATTACATA-
1 TA-TAT-TATTAAATAT
*
1292460 TATCA-TATTATGATAT
1 TAT-ATTATTA-AATAT
1292476 TATA-TATT--ATGAT
1 TATATTATTAAAT-AT
*
1292489 TATTATTATT-ATTAT
1 TA-TATTATTAAATAT
1292504 TATATTA-T-AATAT
1 TATATTATTAAATAT
1292517 TATTATTATTA
1 TA-TATTATTA
1292528 TTCATTATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 33
0.71 0.04 0.26
Matches are distributed among these distances:
12 10 0.11
13 13 0.14
14 19 0.21
15 25 0.27
16 9 0.10
17 7 0.08
18 5 0.05
19 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATTATTAAATAT
Found at i:1292452 original size:22 final size:21
Alignment explanation
Indices: 1292427--1292482 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1292417 TATTATAAAG
1292427 TATATTATATATAAT-AGTAGTA
1 TATATTATATAT-ATCA-TAGTA
* *
1292449 TATATTACATATATCATATTA
1 TATATTATATATATCATAGTA
1292470 TGATATTATATAT
1 T-ATATTATATAT
1292483 TATGATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATTATATATATCATAGTA
Found at i:1292495 original size:3 final size:3
Alignment explanation
Indices: 1292473--1292535 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1292463 CATATTATGA
* *
1292473 TAT TAT ATAT TAT GAT TAT TAT TAT TAT TAT TA- TAT TA- TAA TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1292517 TAT TAT TAT TAT TCAT TAT
1 TAT TAT TAT TAT T-AT TAT
1292536 ATATATATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1292499 original size:44 final size:41
Alignment explanation
Indices: 1292428--1292539 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 41
1292418 ATTATAAAGT
* * * *
1292428 ATATTATATATAATAGTAGTATATATTACATATATCATATTATG
1 ATATTATATATTATATTATTATATATT--AT-TATCATATTATA
*
1292472 ATATTATATATTATGATTATTAT-TATTATTATTATATTATA
1 ATATTATATATTAT-ATTATTATATATTATTATCATATTATA
1292513 ATATTAT-TATTATTATTCATTATATAT
1 ATATTATATATTA-TATT-ATTATATAT
1292540 ATATATATAC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
40 8 0.14
41 23 0.39
42 5 0.08
44 17 0.29
45 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (41 bp):
ATATTATATATTATATTATTATATATTATTATCATATTATA
Found at i:1292563 original size:31 final size:30
Alignment explanation
Indices: 1292474--1292564 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 30
1292464 ATATTATGAT
1292474 ATTATATAT-TATGAT-TATTATTATTATT-
1 ATTATATATATAT-ATATATTATTATTATTC
1292502 ATTATAT-TATA-ATATTATTATTATTATTC
1 ATTATATATATATATA-TATTATTATTATTC
1292531 ATTATATATATATATATACTTATT-TTATTTC
1 ATTATATATATATATATA-TTATTATTA-TTC
1292562 ATT
1 ATT
1292565 TTTATTTAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 22 0.40
29 7 0.13
30 9 0.16
31 14 0.25
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (30 bp):
ATTATATATATATATATATTATTATTATTC
Found at i:1293093 original size:22 final size:22
Alignment explanation
Indices: 1293068--1293110 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1293058 AAAAAAAAGG
1293068 AAAAA-CC-CAAAACAACAACAAC
1 AAAAAGCCACAAAA-AA-AACAAC
1293090 AAAAAGCCACAAAAAAAACAA
1 AAAAAGCCACAAAAAAAACAA
1293111 ACGAAGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.72, C:0.26, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAGCCACAAAAAAAACAAC
Found at i:1295750 original size:2 final size:2
Alignment explanation
Indices: 1295745--1295876 Score: 65
Period size: 2 Copynumber: 69.5 Consensus size: 2
1295735 TATATGCTAC
* * *
1295745 TA TA TA -A TA TA T- TT TA TA TG T- TA TA TA T- TA TA TG TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* *
1295784 AA T- TA TA TA TA T- TA TA TA GTG TA TA TA TA TA TA TA T- TA CT-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
1295824 TA T- TA TA TA GTA TA T- TA TA TA TA -A TA GTA GTA TA TA T- TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA
*
1295863 CA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA T
1295877 TTATTTATTT
Statistics
Matches: 102, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
1 13 0.13
2 79 0.77
3 10 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1295762 original size:7 final size:7
Alignment explanation
Indices: 1295745--1295889 Score: 84
Period size: 7 Copynumber: 20.1 Consensus size: 7
1295735 TATATGCTAC
*
1295745 TATATAA
1 TATATAT
*
1295752 TATATTT
1 TATATAT
*
1295759 TATATGT
1 TATATAT
1295766 TATATAT
1 TATATAT
*
1295773 TATATGT
1 TATATAT
* *
1295780 CATAAATT
1 TATATA-T
1295788 ATATATAT
1 -TATATAT
1295796 TATATAGT
1 TATATA-T
1295804 GTATATAT
1 -TATATAT
1295812 ATATATAT
1 -TATATAT
1295820 TACT-TAT
1 TA-TATAT
1295827 TATATA-
1 TATATAT
*
1295833 -GTATAT
1 TATATAT
1295839 TATATAT
1 TATATAT
* *
1295846 AATAGTAG
1 TATA-TAT
1295854 TATATAT
1 TATATAT
1295861 TACATATAT
1 T--ATATAT
1295870 TATATAT
1 TATATAT
1295877 T-TAT-T
1 TATATAT
*
1295882 TATTTAT
1 TATATAT
1295889 T
1 T
1295890 TACTTATTTT
Statistics
Matches: 107, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
5 6 0.06
6 6 0.06
7 61 0.57
8 17 0.16
9 17 0.16
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:1297255 original size:24 final size:24
Alignment explanation
Indices: 1297223--1297277 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1297213 TGTTAAAGAA
1297223 GATGGTGGTATTGAGAGTGATAGG
1 GATGGTGGTATTGAGAGTGATAGG
1297247 GATGGTGGTATTGAGAGTGATAGG
1 GATGGTGGTATTGAGAGTGATAGG
1297271 GATGGTG
1 GATGGTG
1297278 ATGAGGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.47, T:0.29
Consensus pattern (24 bp):
GATGGTGGTATTGAGAGTGATAGG
Found at i:1299482 original size:21 final size:21
Alignment explanation
Indices: 1299456--1299500 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1299446 GATTTCTGGG
* *
1299456 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1299477 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1299498 CAA
1 CAA
1299501 ACGACAGAAT
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:1300212 original size:31 final size:31
Alignment explanation
Indices: 1300174--1300298 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
1300164 AGGGTCGAGG
1300174 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1300205 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1300236 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1300267 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1300298 G
1 G
1300299 GTCCTTCGGG
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 90 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1301332 original size:22 final size:21
Alignment explanation
Indices: 1301270--1301333 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1301260 AGTCGAGGGT
1301270 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* * *
1301291 CTCATAGGTCATTCGAGACATA
1 TTCATAGGTCCTTCGGGACA-A
* *
1301313 TTCACAGGTCCTTAGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1301334 ATCTCATATG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:1306756 original size:6 final size:6
Alignment explanation
Indices: 1306741--1306772 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1306731 GTTCGTCTCG
1306741 GGTC-T GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1306773 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:1307068 original size:38 final size:38
Alignment explanation
Indices: 1307026--1307101 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1307016 GAGTTATAAC
*
1307026 AGCTGAACAATGATGCAATGAACCTGGACTATTTTTTA
1 AGCTGAACAATGATGCAATGAAACTGGACTATTTTTTA
1307064 AGCTGAACAATGATGCAATGAAACTGGACTATTTTTTA
1 AGCTGAACAATGATGCAATGAAACTGGACTATTTTTTA
1307102 GCCAGGTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (38 bp):
AGCTGAACAATGATGCAATGAAACTGGACTATTTTTTA
Found at i:1309348 original size:14 final size:13
Alignment explanation
Indices: 1309315--1309358 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
1309305 ATACTTATTA
1309315 TTCTTA-TTCTTC
1 TTCTTATTTCTTC
1309327 TTCTTTATTTCTATC
1 TTC-TTATTTCT-TC
1309342 TTCTTATTATCTTC
1 TTCTTATT-TCTTC
1309356 TTC
1 TTC
1309359 AAGTTTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 3 0.11
14 14 0.50
15 8 0.29
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTATTTCTTC
Found at i:1309356 original size:18 final size:17
Alignment explanation
Indices: 1309308--1309358 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1309298 AGTCTTCATA
*
1309308 CTTATTATTCTTATTCTT
1 CTTATTA-TCTTCTTCTT
*
1309326 CTTCTTTAT-TTCTATCTT
1 CTT-ATTATCTTCT-TCTT
1309344 CTTATTATCTTCTTC
1 CTTATTATCTTCTTC
1309359 AAGTTTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 9 0.33
18 15 0.56
19 3 0.11
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTATTATCTTCTTCTT
Found at i:1309929 original size:18 final size:18
Alignment explanation
Indices: 1309902--1309948 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1309892 AACCTATCTT
*
1309902 CATCAACATCAGC-ATCAA
1 CATCACCATCAGCAAT-AA
*
1309920 CATCACCATCATCAATAA
1 CATCACCATCAGCAATAA
1309938 CATCACCATCA
1 CATCACCATCA
1309949 CTGTCCGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19
Consensus pattern (18 bp):
CATCACCATCAGCAATAA
Found at i:1311795 original size:4 final size:4
Alignment explanation
Indices: 1311786--1311872 Score: 52
Period size: 4 Copynumber: 20.8 Consensus size: 4
1311776 ATATCATTTC
* * *
1311786 AAAT AAAT -AAT CGAAT AAAT AAAAT AGAT AACAG A-AT AAATT AAAT
1 AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AA-AT AAAT AAA-T AAAT
* * *
1311832 AAAT AAAAT ACAT AATT GAAT AAAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAA
1311873 ATACATACGA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
3 5 0.08
4 39 0.61
5 20 0.31
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1311816 original size:9 final size:9
Alignment explanation
Indices: 1311799--1311875 Score: 68
Period size: 9 Copynumber: 8.4 Consensus size: 9
1311789 TAAATAATCG
1311799 AATAAATAA
1 AATAAATAA
*
1311808 AATAGATAACA
1 AATAAAT-A-A
*
1311819 GAATAAATTA
1 -AATAAATAA
1311829 AATAAATAA
1 AATAAATAA
*
1311838 AATACAT-A
1 AATAAATAA
* *
1311846 ATTGAATAA
1 AATAAATAA
1311855 AATAAAT-A
1 AATAAATAA
1311863 AATAAATAA
1 AATAAATAA
1311872 AATA
1 AATA
1311876 CATACGAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
8 13 0.25
9 31 0.58
10 2 0.04
11 1 0.02
12 6 0.11
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.25
Consensus pattern (9 bp):
AATAAATAA
Found at i:1311816 original size:21 final size:21
Alignment explanation
Indices: 1311786--1311837 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1311776 ATATCATTTC
1311786 AAATAAATAATC-GAATAAATA
1 AAATAAATAA-CAGAATAAATA
* *
1311807 AAATAGATAACAGAATAAATT
1 AAATAAATAACAGAATAAATA
1311828 AAATAAATAA
1 AAATAAATAA
1311838 AATACATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAAATAACAGAATAAATA
Found at i:1311835 original size:30 final size:30
Alignment explanation
Indices: 1311799--1311868 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1311789 TAAATAATCG
* *
1311799 AATAAATAAAATAGATAACAGAATAAATTA
1 AATAAATAAAATACATAACAGAATAAAATA
**
1311829 AATAAATAAAATACATAATTGAATAAAATA
1 AATAAATAAAATACATAACAGAATAAAATA
1311859 AATAAATAAA
1 AATAAATAAA
1311869 TAAAATACAT
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:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (30 bp):
AATAAATAAAATACATAACAGAATAAAATA
Found at i:1311855 original size:17 final size:17
Alignment explanation
Indices: 1311827--1311879 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
1311817 CAGAATAAAT
1311827 TAAATAAATAAAATACA
1 TAAATAAATAAAATACA
* * *
1311844 TAATTGAATAAAATAAA
1 TAAATAAATAAAATACA
1311861 TAAATAAATAAAATACA
1 TAAATAAATAAAATACA
1311878 TA
1 TA
1311880 CGAATTTGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAATAAATAAAATACA
Found at i:1311861 original size:21 final size:21
Alignment explanation
Indices: 1311824--1311872 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1311814 TAACAGAATA
*
1311824 AATTAAATAAATAAAATACAT
1 AATTAAATAAATAAAATAAAT
*
1311845 AATTGAATAAA-ATAAATAAAT
1 AATTAAATAAATA-AAATAAAT
*
1311866 AAATAAA
1 AATTAAA
1311873 ATACATACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AATTAAATAAATAAAATAAAT
Found at i:1317095 original size:20 final size:20
Alignment explanation
Indices: 1317070--1317222 Score: 182
Period size: 20 Copynumber: 7.7 Consensus size: 20
1317060 GATTTTCAAG
** *
1317070 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
1317090 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
*
1317110 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1317130 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1317150 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
** *
1317170 AATCGCAACGATAATCAGTA
1 AATCGCAACGCGAATCCGTA
*
1317190 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
1317210 AATCGCAACGCGA
1 AATCGCAACGCGA
1317223 TTTTTAAAGC
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
20 113 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1317640 original size:33 final size:33
Alignment explanation
Indices: 1317601--1317671 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1317591 TTCACTTAGA
1317601 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1317634 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1317667 TTTCA
1 TTTCA
1317672 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1317777 original size:21 final size:20
Alignment explanation
Indices: 1317751--1317824 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
1317741 TGCAGAAGAG
1317751 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1317772 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1317792 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1317814 TCGCAACGAGA
1 TCGCAACGAGA
1317825 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1317831 original size:14 final size:14
Alignment explanation
Indices: 1317812--1317868 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1317802 GAAAAATGAA
1317812 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1317826 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1317845 AATCGTAACGAGAG
1 AATCGCAACGAGAG
1317859 AATCGCAACG
1 AATCGCAACG
1317869 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Done.