Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008726.1 Hibiscus syriacus cultivar Beakdansim tig00111792_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: 1298898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:692924 original size:26 final size:25
Alignment explanation
Indices: 692894--692943 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
692884 AATCCTGAAT
692894 ATTTAATTTAAATT-AAATAAATAAAG
1 ATTTAA-TTAAATTGAAAT-AATAAAG
*
692920 ATTTAATTAATTTGAAATAATAAA
1 ATTTAATTAAATTGAAATAATAAA
692944 ATCCCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTAATTAAATTGAAATAATAAAG
Found at i:711966 original size:15 final size:16
Alignment explanation
Indices: 711939--711968 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
711929 TTTTTTCACA
711939 CCTCTTGTCTTTTTTC
1 CCTCTTGTCTTTTTTC
711955 CCTCTT-TCTTTTTT
1 CCTCTTGTCTTTTTT
711969 ATCTTCTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (16 bp):
CCTCTTGTCTTTTTTC
Found at i:717324 original size:53 final size:53
Alignment explanation
Indices: 717205--717324 Score: 222
Period size: 53 Copynumber: 2.3 Consensus size: 53
717195 CCATAAGCAA
*
717205 GGTATCGATACCAGGAAATATCGAATGCAATTTGGGTATCGATACCCATACTT
1 GGTATCGATACCATGAAATATCGAATGCAATTTGGGTATCGATACCCATACTT
*
717258 GGTATCGATACCATGAAATATCGAATGTAATTTGGGTATCGATACCCATACTT
1 GGTATCGATACCATGAAATATCGAATGCAATTTGGGTATCGATACCCATACTT
717311 GGTATCGATACCAT
1 GGTATCGATACCAT
717325 AGCTAGGGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (53 bp):
GGTATCGATACCATGAAATATCGAATGCAATTTGGGTATCGATACCCATACTT
Found at i:718044 original size:18 final size:18
Alignment explanation
Indices: 718021--718061 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
718011 GGGCATATGG
*
718021 ATAGTGGTCCTTCGGGAT
1 ATAGTGGCCCTTCGGGAT
718039 ATAGTGGCCCTTCGGGAT
1 ATAGTGGCCCTTCGGGAT
718057 A-AGTG
1 ATAGTG
718062 AAGTGCCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
ATAGTGGCCCTTCGGGAT
Found at i:719597 original size:18 final size:18
Alignment explanation
Indices: 719574--719609 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
719564 ACCACTTAAA
719574 TCAATCAAGTTGATGTTT
1 TCAATCAAGTTGATGTTT
*
719592 TCAATCCAGTTGATGTTT
1 TCAATCAAGTTGATGTTT
719610 AACTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (18 bp):
TCAATCAAGTTGATGTTT
Found at i:720376 original size:21 final size:21
Alignment explanation
Indices: 720352--720391 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
720342 TAAACCAAAA
*
720352 AATATTTAATATTTAATATAT
1 AATATATAATATTTAATATAT
* *
720373 AATATATATTATTTTATAT
1 AATATATAATATTTAATAT
720392 TATTTATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATATAATATTTAATATAT
Found at i:721124 original size:19 final size:19
Alignment explanation
Indices: 721100--721145 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
721090 AAATTTGGTT
*
721100 TTTATATTAATTCCAATTC
1 TTTATATTAATTACAATTC
* *
721119 TTTATATTATTTATAATTC
1 TTTATATTAATTACAATTC
721138 -TTATATTA
1 TTTATATTA
721146 TAAATGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:721749 original size:23 final size:23
Alignment explanation
Indices: 721719--721818 Score: 166
Period size: 23 Copynumber: 4.4 Consensus size: 23
721709 CAGCAACCGA
* * *
721719 CAAGCATCACTGTACCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
721742 CAAGCATCATTGCATCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
721765 CAAGCATCATTGCATCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
721788 CAAGCATCATTGCATCAATTCAG
1 CAAGCATCATTGCATCAATTCAG
721811 C-AGCATCA
1 CAAGCATCA
721819 AGCATACATA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
22 7 0.09
23 67 0.91
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (23 bp):
CAAGCATCATTGCATCAATTCAG
Found at i:721935 original size:20 final size:20
Alignment explanation
Indices: 721902--721955 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
721892 AACCCTTACA
** *
721902 AATATCAAGTAGAAGCAACC
1 AATATCAAACAGAAGCAAAC
*
721922 AATATCAAACAGAATCAAAC
1 AATATCAAACAGAAGCAAAC
*
721942 AATATAAAACAGAA
1 AATATCAAACAGAA
721956 TCAAGCACCA
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:0.59, C:0.17, G:0.09, T:0.15
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:721956 original size:20 final size:20
Alignment explanation
Indices: 721921--721959 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
721911 TAGAAGCAAC
*
721921 CAATATCAAACAGAATCAAA
1 CAATATAAAACAGAATCAAA
721941 CAATATAAAACAGAATCAA
1 CAATATAAAACAGAATCAA
721960 GCACCAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.18, G:0.05, T:0.15
Consensus pattern (20 bp):
CAATATAAAACAGAATCAAA
Found at i:724019 original size:71 final size:70
Alignment explanation
Indices: 723869--724028 Score: 162
Period size: 71 Copynumber: 2.3 Consensus size: 70
723859 AAAAATATTT
* * * * *
723869 TTTTTAAAATCATATATTATATGTTTTCCAAAATGAGTTTTCAAAAATTATATTATATATTTTCA
1 TTTTAAAAATTATATATTATACGTTTTCCAAAAT-AGTTTTAAAAAATTATATTATACATTTTCA
*
723934 AAAATG
65 AAAACG
* *
723940 TTTAAAAAATTATATATTATACGTTTT-CAAAACT-GTTTTAAAAAATCATATATTATACGTTTT
1 TTTTAAAAATTATATATTATACGTTTTCCAAAA-TAGTTTTAAAAAAT--TATATTATACATTTT
* *
724003 TAAAACCG
63 CAAAAACG
* *
724011 TTTTAAAAAATGTATATT
1 TTTTAAAAATTATATATT
724029 TAAAATTATT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
69 11 0.15
70 5 0.07
71 57 0.78
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (70 bp):
TTTTAAAAATTATATATTATACGTTTTCCAAAATAGTTTTAAAAAATTATATTATACATTTTCAA
AAACG
Found at i:724027 original size:35 final size:35
Alignment explanation
Indices: 723841--724028 Score: 166
Period size: 36 Copynumber: 5.2 Consensus size: 35
723831 TCAAAGAAAC
* * * **
723841 TATATATTATATGTTTTCAAAAATATTTTTTTTAAAA
1 TATATATTATACGTTTTC-AAAA-CTGTTTTAAAAAA
* *
723878 TCATATATTATATGTTTTCCAAAA-TGAGTTTTCAAAAA
1 T-ATATATTATACGTTTT-CAAAACT--GTTTTAAAAAA
** *
723916 T-TATATTATATATTTTCAAAAATG-TTTAAAAAA
1 TATATATTATACGTTTTCAAAACTGTTTTAAAAAA
723949 TTATATATTATACGTTTTCAAAACTGTTTTAAAAAA
1 -TATATATTATACGTTTTCAAAACTGTTTTAAAAAA
* *
723985 TCATATATTATACGTTTTTAAAACCGTTTTAAAAAA
1 T-ATATATTATACGTTTTCAAAACTGTTTTAAAAAA
*
724021 TGTATATT
1 TATATATT
724029 TAAAATTATT
Statistics
Matches: 131, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
33 8 0.06
34 2 0.02
35 32 0.24
36 58 0.44
37 1 0.01
38 29 0.22
39 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (35 bp):
TATATATTATACGTTTTCAAAACTGTTTTAAAAAA
Found at i:728441 original size:18 final size:17
Alignment explanation
Indices: 728391--728441 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
728381 TGTTATTTTA
*
728391 ATTATTTTAATTAAGTTT
1 ATTATTTTAATT-TGTTT
728409 ATTATTATTTAATTTGTTT
1 ATTA-T-TTTAATTTGTTT
728428 CATTATTTTAATTT
1 -ATTATTTTAATTT
728442 TCTAGATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 12 0.41
19 6 0.21
20 11 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTATTTTAATTTGTTT
Found at i:729625 original size:64 final size:62
Alignment explanation
Indices: 729448--729656 Score: 196
Period size: 64 Copynumber: 3.3 Consensus size: 62
729438 GGCACTAAGA
* *
729448 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCCAGAGTGCATCGATGCATGGCTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAT--TCAG-GTGCATCGATGCATGG-TA
729512 -
62 T
* * *
729512 GTGCATCAATGCATCATATGCATTCGATGTTTTCAAAAATCCTCA-GTGCATC-AGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATAAT--TCAGGTGCATCGA-TGCATGGTA
729575 T
62 T
*
729576 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGG-AT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA--TAATTCA-GGTGCATCGATGCATGGTA-
729639 T
62 T
*
729640 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
729657 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
62 8 0.07
63 4 0.03
64 84 0.69
65 21 0.17
66 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATTCAGGTGCATCGATGCATGGTAT
Found at i:730017 original size:21 final size:20
Alignment explanation
Indices: 729993--730044 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 20
729983 CCCCCTTACT
729993 ATAACACTTCTCCCTTAAAAC
1 ATAACA-TTCTCCCTTAAAAC
730014 ATAACATT-T--CTTAAAAC
1 ATAACATTCTCCCTTAAAAC
730031 ATAACATTTCTCCC
1 ATAACA-TTCTCCC
730045 CTTTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 2 0.07
21 7 0.26
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACATTCTCCCTTAAAAC
Found at i:730028 original size:17 final size:17
Alignment explanation
Indices: 730006--730041 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
729996 ACACTTCTCC
730006 CTTAAAACATAACATTT
1 CTTAAAACATAACATTT
730023 CTTAAAACATAACATTT
1 CTTAAAACATAACATTT
730040 CT
1 CT
730042 CCCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (17 bp):
CTTAAAACATAACATTT
Found at i:730120 original size:2 final size:2
Alignment explanation
Indices: 730115--730141 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
730105 TAGCCAATTG
730115 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
730142 GCTTAAGCTG
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:735056 original size:22 final size:21
Alignment explanation
Indices: 735014--735053 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
735004 GAGTTTATTT
*
735014 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
735035 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
735054 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:737137 original size:65 final size:65
Alignment explanation
Indices: 736997--737157 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
736987 GTGCACTAAG
* * *
736997 AGTGCATCGACGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGAATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGAATCGATGCATGGCT
* * * *
737061 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGAATCGATGCATGGC
737124 T
65 T
* *
737125 ATGTGCAACGATGCATGAAATGCATTCGATGTT
1 A-GTGCATCGATGCATCAAATGCATTCGATGTT
737158 CAATTTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 30 0.35
65 52 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGAATCGATGCATGGCT
Found at i:737217 original size:20 final size:20
Alignment explanation
Indices: 737170--737219 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
737160 ATTTAATTCA
* *
737170 TGGTGCAACGATGCATGGAT
1 TGGTGCATCGATACATGGAT
737190 TGGTGCATCGATACATGGAT
1 TGGTGCATCGATACATGGAT
737210 TGGTGCATCG
1 TGGTGCATCG
737220 GTGCATCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (20 bp):
TGGTGCATCGATACATGGAT
Found at i:742069 original size:21 final size:21
Alignment explanation
Indices: 742045--742093 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
742035 ATATATTACT
*
742045 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
*
742066 TCTCTCTGTGCTGCCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
742087 TCTCTCT
1 TCTCTCT
742094 CTCTCTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.00, C:0.41, G:0.18, T:0.41
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:742102 original size:25 final size:24
Alignment explanation
Indices: 742045--742115 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
742035 ATATATTACT
* *
742045 TCTCTCTGTTCTGCCGCTG--C-C
1 TCTCTCTCTGCTGCCGCTGCTCTC
*
742066 TCTCTCTGTGCTGCCGCTGCTTCTC
1 TCTCTCTCTGCTGCCGCTGC-TCTC
*
742091 TCTCTCTCTGCTTCCGCTGCTCTC
1 TCTCTCTCTGCTGCCGCTGCTCTC
742115 T
1 T
742116 AGCTGCTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 18 0.42
24 6 0.14
25 19 0.44
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.41
Consensus pattern (24 bp):
TCTCTCTCTGCTGCCGCTGCTCTC
Found at i:742115 original size:20 final size:20
Alignment explanation
Indices: 742090--742146 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
742080 CGCTGCTTCT
742090 CTCTCTCTCTGCTTCCGCTG
1 CTCTCTCTCTGCTTCCGCTG
**
742110 CTCTCTAGCTGCTTCCGCTG
1 CTCTCTCTCTGCTTCCGCTG
*
742130 CTGCTCTCTCTGTTTCC
1 CT-CTCTCTCTGCTTCC
742147 CTTGCTTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.02, C:0.42, G:0.16, T:0.40
Consensus pattern (20 bp):
CTCTCTCTCTGCTTCCGCTG
Found at i:742152 original size:21 final size:22
Alignment explanation
Indices: 742092--742146 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
742082 CTGCTTCTCT
742092 CTCTCT-CTGCTT-C-C-GCTG
1 CTCTCTACTGCTTCCGCTGCTG
742110 CTCTCTAGCTGCTTCCGCTGCTG
1 CTCTCTA-CTGCTTCCGCTGCTG
*
742133 CTCTCT-CTGTTTCC
1 CTCTCTACTGCTTCC
742147 CTTGCTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.19
20 6 0.19
21 8 0.26
22 1 0.03
23 10 0.32
ACGTcount: A:0.02, C:0.42, G:0.16, T:0.40
Consensus pattern (22 bp):
CTCTCTACTGCTTCCGCTGCTG
Found at i:742694 original size:41 final size:43
Alignment explanation
Indices: 742637--742721 Score: 156
Period size: 41 Copynumber: 2.0 Consensus size: 43
742627 GAAATAAATG
742637 AAGATGAGTTTTGATACCC-AGGGAATCC-AGTTGGGTCCCAA
1 AAGATGAGTTTTGATACCCAAGGGAATCCAAGTTGGGTCCCAA
742678 AAGATGAGTTTTGATACCCAAGGGAATCCAAGTTGGGTCCCAA
1 AAGATGAGTTTTGATACCCAAGGGAATCCAAGTTGGGTCCCAA
742721 A
1 A
742722 GGTAACCTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 19 0.45
42 9 0.21
43 14 0.33
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (43 bp):
AAGATGAGTTTTGATACCCAAGGGAATCCAAGTTGGGTCCCAA
Found at i:744919 original size:39 final size:39
Alignment explanation
Indices: 744871--744981 Score: 138
Period size: 39 Copynumber: 2.8 Consensus size: 39
744861 TTATTTATAA
*
744871 TTCTCAAATTATTTCACTCTAACATTCTAAATTCCTAAT
1 TTCTTAAATTATTTCACTCTAACATTCTAAATTCCTAAT
* *
744910 TTCTTAAATT-TTGCCAC-CATAACATTCTAAATTCTTAAT
1 TTCTTAAATTATT-TCACTC-TAACATTCTAAATTCCTAAT
*
744949 TTCTTAAATTATTTCACAT-TAATATTCTAAATT
1 TTCTTAAATTATTTCAC-TCTAACATTCTAAATT
744982 ATTTTTTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
38 3 0.05
39 57 0.92
40 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (39 bp):
TTCTTAAATTATTTCACTCTAACATTCTAAATTCCTAAT
Found at i:746591 original size:65 final size:64
Alignment explanation
Indices: 746458--746610 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 64
746448 ACTAAGAATG
* * *
746458 CATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGTCTGGTA
1 CATCGATGCATGAAATGCATTCGACGTTTCAAAATAGCCAGAGTGCATCGATGCATGTATGGTA
* *
746522 CATCGATGCATCAAATGCATTCGACGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGTAT-
1 CATCGATGCATGAAATGCATTCGACG-TTTCA-AAATAGC-CAGAGTGCATCGATGCAT-GTATG
*
746584 GTT
62 GTA
746587 CATCGATGCATGAAATGCATTCGA
1 CATCGATGCATGAAATGCATTCGA
746611 TGTTCAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
64 25 0.32
65 47 0.60
66 6 0.08
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (64 bp):
CATCGATGCATGAAATGCATTCGACGTTTCAAAATAGCCAGAGTGCATCGATGCATGTATGGTA
Found at i:746656 original size:65 final size:62
Alignment explanation
Indices: 746456--746662 Score: 168
Period size: 65 Copynumber: 3.2 Consensus size: 62
746446 GCACTAAGAA
* * * * *
746456 TGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGTCTGG
1 TGCATCGATGCATGAAATGCATTCGATG-TTC-AATTAACCATAGTGCATCGATGCATGTATGG
* * * *
746520 TACATCGATGCATCAAATGCATTCGACGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGTA
1 TGCATCGATGCATGAAATGCATTCGA--TGTTCAAT-TAAC-CAT-AGTGCATCGATGCAT-GTA
746583 T-G
60 TGG
* * * *
746585 TTCATCGATGCATGAAATGCATTCGATGTTCAATTTATTCCATTGTGCATCGATGCATGGATTGG
1 TGCATCGATGCATGAAATGCATTCGATGTTCAA-TTA-ACCATAGTGCATCGATGCATGTA-TGG
*
746650 TGCATCGGTGCAT
1 TGCATCGATGCAT
746663 CACTTTGAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
63 7 0.06
64 44 0.39
65 58 0.51
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTCAATTAACCATAGTGCATCGATGCATGTATGG
Found at i:750237 original size:2 final size:2
Alignment explanation
Indices: 750230--750264 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
750220 ACTTTTTAGG
750230 TA TA TA 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 TA TA TA T
750265 GTTGAGTTGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:753181 original size:27 final size:27
Alignment explanation
Indices: 753143--753195 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
753133 GTATGATGTT
753143 CAAAGATCTGGTGCAGAAATTTTCAGA
1 CAAAGATCTGGTGCAGAAATTTTCAGA
753170 CAAAGATCTGGTGCAGAAATTTTCAG
1 CAAAGATCTGGTGCAGAAATTTTCAG
753196 TTTTGATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (27 bp):
CAAAGATCTGGTGCAGAAATTTTCAGA
Found at i:755331 original size:22 final size:22
Alignment explanation
Indices: 755290--755331 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
755280 TAATTTCAAA
* **
755290 TATAGTTTTTGAAAGTATATAG
1 TATAGGTTTTGAAAACATATAG
755312 TATAGGTTTTGAAAACATAT
1 TATAGGTTTTGAAAACATAT
755332 TTTTTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
TATAGGTTTTGAAAACATATAG
Found at i:755474 original size:38 final size:37
Alignment explanation
Indices: 755333--755478 Score: 116
Period size: 36 Copynumber: 3.9 Consensus size: 37
755323 AAAACATATT
* * ** *
755333 TTTTGAAAATATAAAATATATAG-TTTTTTAAAGCGG
1 TTTTGAAAACATATAATATATAGTTTTTTTAAAATGA
* *** *
755369 TTTTGAAAACATATAATGTATAGTTTTAAAAAAAATGT
1 TTTTGAAAACATATAATATATAGTTTT-TTTAAAATGA
* * * *
755407 TTTCTGAAAACGTGTAATATACA-ATTTTTTAAAATGA
1 TTT-TGAAAACATATAATATATAGTTTTTTTAAAATGA
*
755444 TTTTGAAAACGTATAATATATAGTTGTTTTTAAAA
1 TTTTGAAAACATATAATATATAGTT-TTTTTAAAA
755479 AAATGGGTTT
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
36 37 0.44
37 13 0.15
38 19 0.23
39 15 0.18
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACATATAATATATAGTTTTTTTAAAATGA
Found at i:755524 original size:20 final size:19
Alignment explanation
Indices: 755499--755548 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 19
755489 TTGAAAAGAT
755499 ATATAATATAGTTTTTGAAA
1 ATATAATATAGTTTTT-AAA
755519 ATATAATATATAGTTTTTAAA
1 ATAT-A-ATATAGTTTTTAAA
755540 ATA-AATATA
1 ATATAATATA
755549 ATGTACGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.18
19 1 0.04
20 4 0.14
21 7 0.25
22 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATAATATAGTTTTTAAA
Found at i:755527 original size:25 final size:24
Alignment explanation
Indices: 755485--755550 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
755475 AAAAAAATGG
*
755485 GTTTTTGAAAAGATATATAATATA
1 GTTTTTGAAAATATATATAATATA
755509 GTTTTTGAAAATATA-AT-ATATA
1 GTTTTTGAAAATATATATAATATA
*
755531 GTTTTT-AAAATAAATATAAT
1 GTTTTTGAAAATATATATAAT
755551 GTACGTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 4 0.11
24 14 0.37
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (24 bp):
GTTTTTGAAAATATATATAATATA
Found at i:755594 original size:12 final size:11
Alignment explanation
Indices: 755559--755636 Score: 56
Period size: 12 Copynumber: 6.9 Consensus size: 11
755549 ATGTACGTAT
755559 TATATTATATATA
1 TATATTAT-T-TA
*
755572 TATATTCTTTA
1 TATATTATTTA
755583 TAGTATTATTTA
1 TA-TATTATTTA
755595 T-TATT-TTATA
1 TATATTATT-TA
*
755605 TTTATTATATTA
1 TATATTAT-TTA
755617 TAATATTA-TTA
1 T-ATATTATTTA
755628 -ATATTATTT
1 TATATTATTT
755637 TTTGATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
9 8 0.15
10 9 0.16
11 11 0.20
12 14 0.25
13 13 0.24
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
TATATTATTTA
Found at i:755608 original size:14 final size:14
Alignment explanation
Indices: 755556--755634 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 14
755546 ATAATGTACG
755556 TATTATA-TTA-TA
1 TATTATATTTATTA
755568 TATATATATTCT-TTA
1 TAT-TATATT-TATTA
*
755583 TAGTATTATTTATTA
1 TATTA-TATTTATTA
*
755598 TTTTATATTTATTA
1 TATTATATTTATTA
755612 TATTATAATATTATTAA
1 TATTAT-AT-TTATT-A
755629 TATTAT
1 TATTAT
755635 TTTTTGATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
12 3 0.06
13 4 0.07
14 18 0.33
15 17 0.31
16 5 0.09
17 7 0.13
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (14 bp):
TATTATATTTATTA
Found at i:756958 original size:14 final size:14
Alignment explanation
Indices: 756922--756964 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
756912 TAATTTAAAG
756922 TTTTCTTTTACTTTA
1 TTTT-TTTTACTTTA
* * *
756937 TATATTTTAATTTA
1 TTTTTTTTACTTTA
756951 TTTTTTTTACTTTA
1 TTTTTTTTACTTTA
756965 ATGATTAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTACTTTA
Found at i:757437 original size:13 final size:14
Alignment explanation
Indices: 757410--757447 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
757400 AAAATTTAAT
757410 TTATCTATTTAATCC
1 TTAT-TATTTAATCC
757425 TTATTATTT-ATCC
1 TTATTATTTAATCC
757438 TTGATTATTT
1 TT-ATTATTT
757448 CTTTTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (14 bp):
TTATTATTTAATCC
Found at i:757948 original size:3 final size:3
Alignment explanation
Indices: 757940--757965 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
757930 TTTCATTTTC
757940 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
757966 CTTACTAACT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:768379 original size:20 final size:21
Alignment explanation
Indices: 768341--768379 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
768331 CATCAAGGTC
*
768341 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
768362 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
768380 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:771524 original size:13 final size:13
Alignment explanation
Indices: 771502--771565 Score: 101
Period size: 13 Copynumber: 4.9 Consensus size: 13
771492 TCATAAATCC
771502 ATGACGCGCATTT
1 ATGACGCGCATTT
*
771515 ATGACACGCATTT
1 ATGACGCGCATTT
* *
771528 ATGACTCACATTT
1 ATGACGCGCATTT
771541 ATGACGCGCATTT
1 ATGACGCGCATTT
771554 ATGACGCGCATT
1 ATGACGCGCATT
771566 GAGCATCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (13 bp):
ATGACGCGCATTT
Found at i:784084 original size:2 final size:2
Alignment explanation
Indices: 784077--784109 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
784067 TAAATTTCAA
784077 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 A
784110 ACGTTTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:785728 original size:23 final size:22
Alignment explanation
Indices: 785695--785746 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
785685 AAATATAGTT
785695 TTTG-AAAGTAT-ATAGTATAGG
1 TTTGAAAAGTATAATA-TATAGG
*
785716 TTTGAAAACGTATAATATATAGT
1 TTTGAAAA-GTATAATATATAGG
*
785739 TTTAAAAA
1 TTTGAAAA
785747 AAAGGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 3 0.12
23 16 0.62
24 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.38
Consensus pattern (22 bp):
TTTGAAAAGTATAATATATAGG
Found at i:785745 original size:22 final size:20
Alignment explanation
Indices: 785687--785745 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 20
785677 ATAATTTCAA
*
785687 ATATAGTTTTTGAAAGTATAT
1 ATATAG-TTTTAAAAGTATAT
*
785708 AGTATAGGTTTGAAAACGTATAAT
1 A-TATA-GTTTTAAAA-GTAT-AT
785732 ATATAGTTTTAAAA
1 ATATAGTTTTAAAA
785746 AAAAGGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 1 0.03
22 18 0.58
23 9 0.29
24 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (20 bp):
ATATAGTTTTAAAAGTATAT
Found at i:785790 original size:20 final size:19
Alignment explanation
Indices: 785765--785816 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
785755 TTGAAAACGC
785765 ATATAATATAGTTTTTGAAA
1 ATATAATATAGTTTTT-AAA
785785 ATATAATATATAGTTTTTAAA
1 ATAT-A-ATATAGTTTTTAAA
785806 ATA-AATATAGT
1 ATATAATATAGT
785817 GTACGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.23
19 1 0.03
20 4 0.13
21 7 0.23
22 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
ATATAATATAGTTTTTAAA
Found at i:785795 original size:60 final size:58
Alignment explanation
Indices: 785692--785806 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 58
785682 TTCAAATATA
* *
785692 GTTTTTGAAAGTATATAGTATAGGTTTGAAAACGTATAATATATAGTTTTAAAAAAAAG
1 GTTTTTGAAAGCATATAATATAGGTTTGAAAAC-TATAATATATAGTTTTAAAAAAAAG
* *
785751 GTTTTTGAAAACGCATATAATATAGTTTTTGAAAA-TATAATATATAGTTTTTAAAA
1 GTTTTTG-AAA-GCATATAATATAG-GTTTGAAAACTATAATATATAGTTTTAAAAA
785807 TAAATATAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 7 0.14
60 23 0.47
61 11 0.22
62 8 0.16
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (58 bp):
GTTTTTGAAAGCATATAATATAGGTTTGAAAACTATAATATATAGTTTTAAAAAAAAG
Found at i:785798 original size:22 final size:20
Alignment explanation
Indices: 785770--785814 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
785760 AACGCATATA
785770 ATATAGTTTTTGAAAATATAAT
1 ATATAGTTTTT-AAAATA-AAT
785792 ATATAGTTTTTAAAATAAAT
1 ATATAGTTTTTAAAATAAAT
785812 ATA
1 ATA
785815 GTGTACGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATAGTTTTTAAAATAAAT
Found at i:785832 original size:5 final size:5
Alignment explanation
Indices: 785822--785901 Score: 94
Period size: 5 Copynumber: 16.2 Consensus size: 5
785812 ATAGTGTACG
* * *
785822 TATTA TATTA TATATA TATTA TATTA T-TTA TAATA TTATT- TATAA TTTTA
1 TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA
785872 TATT- TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
785902 TATAAATATT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
4 11 0.17
5 45 0.70
6 8 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:785859 original size:12 final size:12
Alignment explanation
Indices: 785842--785915 Score: 69
Period size: 12 Copynumber: 5.8 Consensus size: 12
785832 TATATATATT
785842 ATATTATTTATA
1 ATATTATTTATA
785854 ATATTATTTATA
1 ATATTATTTATA
* *
785866 ATTTTATATTTATT
1 A-TAT-TATTTATA
785880 ATATTATATTATA
1 ATATTAT-TTATA
785893 TTATATTA-TTATAA
1 --ATATTATTTAT-A
785907 ATATTATTT
1 ATATTATTT
785916 TTCGATTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 22 0.43
13 14 0.27
14 9 0.18
15 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATTTATA
Found at i:785880 original size:38 final size:39
Alignment explanation
Indices: 785822--785906 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
785812 ATAGTGTACG
785822 TATTAT-ATTATATATATATTATATTAT-TTATA-ATAT
1 TATTATAATTATATATATATTATATTATATTATATATAT
* *
785858 TATTTATAATTTTATATTTATTATATTATATTATATTATAT
1 TA-TTATAATTATATATATATTATATTATATTATA-TATAT
785899 TATTATAA
1 TATTATAA
785907 ATATTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 2 0.05
37 4 0.10
38 19 0.45
39 5 0.12
40 6 0.14
41 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (39 bp):
TATTATAATTATATATATATTATATTATATTATATATAT
Found at i:785914 original size:15 final size:14
Alignment explanation
Indices: 785826--785914 Score: 57
Period size: 14 Copynumber: 6.6 Consensus size: 14
785816 TGTACGTATT
785826 ATATTA-TATATATA
1 ATATTATTAT-TATA
*
785840 TTA-TATTATTTATA
1 ATATTATTA-TTATA
785854 ATATTA-T-TTATA
1 ATATTATTATTATA
* *
785866 ATTTTA-TATTTATT
1 ATATTATTA-TTATA
785880 ATATTA-TATTATA
1 ATATTATTATTATA
*
785893 TTA-TATTATTATAA
1 ATATTATTATTAT-A
785907 ATATTATT
1 ATATTATT
785915 TTTCGATTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
12 13 0.22
13 14 0.24
14 25 0.42
15 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTATTATTATA
Found at i:787225 original size:28 final size:30
Alignment explanation
Indices: 787176--787231 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
787166 ATTTAAATCC
787176 TTTTAATTTAAAGTTTTCTTTTACTTTATA
1 TTTTAATTTAAAGTTTTCTTTTACTTTATA
*
787206 TTTTAATTT-AA-TTTTGTTTTACTTTA
1 TTTTAATTTAAAGTTTTCTTTTACTTTA
787232 ACGATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
29 2 0.08
30 9 0.36
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (30 bp):
TTTTAATTTAAAGTTTTCTTTTACTTTATA
Found at i:787849 original size:19 final size:20
Alignment explanation
Indices: 787825--787873 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
787815 CTATTTTTGC
*
787825 TATCGATACTCA-GGGTGAG
1 TATCGATACTCATGGGTCAG
*
787844 TATCGATACCCATGGGTCAG
1 TATCGATACTCATGGGTCAG
*
787864 CATCGATACT
1 TATCGATACT
787874 ACTGGCAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
TATCGATACTCATGGGTCAG
Found at i:793886 original size:11 final size:11
Alignment explanation
Indices: 793870--793904 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
793860 TGGAGAATAG
*
793870 CAATTTTGTTC
1 CAATTTTATTC
793881 CAATTTTATTC
1 CAATTTTATTC
*
793892 CAATTTTACTC
1 CAATTTTATTC
793903 CA
1 CA
793905 TAATGTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (11 bp):
CAATTTTATTC
Found at i:800863 original size:18 final size:18
Alignment explanation
Indices: 800840--800874 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
800830 AATGATAGGG
800840 GGTATCGATTCTATGAGT
1 GGTATCGATTCTATGAGT
800858 GGTATCGATTCTATGAG
1 GGTATCGATTCTATGAG
800875 GAAGGCATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (18 bp):
GGTATCGATTCTATGAGT
Found at i:800886 original size:20 final size:18
Alignment explanation
Indices: 800843--800886 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
800833 GATAGGGGGT
* *
800843 ATCGATTCTATGAGTGGT
1 ATCGATTCTATGAGAGGC
800861 ATCGATTCTATGAGGAAGGC
1 ATCGATTCTATGA-G-AGGC
800881 ATCGAT
1 ATCGAT
800887 ACCATTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 1 0.05
20 8 0.36
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (18 bp):
ATCGATTCTATGAGAGGC
Found at i:801455 original size:56 final size:56
Alignment explanation
Indices: 801312--801541 Score: 306
Period size: 56 Copynumber: 4.3 Consensus size: 56
801302 ATGACACATA
* * **
801312 TGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATGAATTTCTATACAGGCAC-T
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
801367 T-TGTGC--AAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
801420 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAA------T-T--GCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
* * *
801467 TGTGTGCAAAAACTAAGAAATTCGTAATGAGTTTATGAATTCCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
801523 TGTGTGCAAAAACTAAGAA
1 TGTGTGCAAAAACTAAGAA
801542 GTAAGAAGTT
Statistics
Matches: 157, Mismatches: 5, Indels: 25
0.84 0.03 0.13
Matches are distributed among these distances:
47 44 0.28
49 1 0.01
50 1 0.01
52 41 0.26
53 3 0.02
54 11 0.07
55 1 0.01
56 55 0.35
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTT
Found at i:801483 original size:47 final size:47
Alignment explanation
Indices: 801414--801507 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
801404 TTCTGTATGG
801414 GCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
1 GCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
*
801461 GCACTTTGTGTGCAAAAACTAAGAAATTCGTAATGAGTTTATGAATT
1 GCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
801508 CCCGTATGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (47 bp):
GCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
Found at i:808638 original size:21 final size:21
Alignment explanation
Indices: 808570--808644 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
808560 TTGGTGCAGA
*
808570 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
808590 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
808614 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
*
808635 GGGAATCGAT
1 GGGAACCGAT
808645 ACCTCCCTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.02
21 19 0.43
22 6 0.14
23 16 0.36
24 1 0.02
25 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:817467 original size:56 final size:56
Alignment explanation
Indices: 817379--817686 Score: 438
Period size: 56 Copynumber: 5.5 Consensus size: 56
817369 ATTACTGAAC
* * * *
817379 GACACTATATGTGTGCAAAAACAAAGAAATTCATAATTAGTTTATGAATTTTCGTATA
1 GACACT-T-TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* *
817437 GACACTTTGTGTGTAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT-G
* *
817494 GA-ACTTTATGTGCAAAAACTAAGAAATTCATAATGATTTTATGAATTTCCGTATG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
817549 GGCACTTTGTGTGAAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCATATG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* * *
817605 GTCACTTTGTGTGCAAAAACTGAGAAATTCATAATGAATTTATGAATTTCCGTATG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
* *
817661 GGCACTTTGTGTGAAAAAACTAAGAA
1 GACACTTTGTGTGCAAAAACTAAGAA
817687 GTGAGAAGTT
Statistics
Matches: 225, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
55 2 0.01
56 214 0.95
57 3 0.01
58 6 0.03
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (56 bp):
GACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
Found at i:817587 original size:112 final size:112
Alignment explanation
Indices: 817390--817686 Score: 486
Period size: 112 Copynumber: 2.7 Consensus size: 112
817380 ACACTATATG
* * * * * * *
817390 TGTGCAAAAACAAAGAAATTCATAATTAGTTTATGAATTTTCGTATAGACACTTTGTGTGTAAAA
1 TGTGCAAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
817455 ACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGAACTTTA
66 ACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGAACTTTA
*
817502 TGTGCAAAAACTAAGAAATTCATAATGATTTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
1 TGTGCAAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
** *
817567 ACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGTCACTTTG
66 ACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGAACTTTA
*
817614 TGTGCAAAAACTGAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
1 TGTGCAAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
817679 ACTAAGAA
66 ACTAAGAA
817687 GTGAGAAGTT
Statistics
Matches: 173, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 173 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (112 bp):
TGTGCAAAAACTAAGAAATTCATAATGAATTTATGAATTTCCGTATGGGCACTTTGTGTGAAAAA
ACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGAACTTTA
Found at i:821477 original size:21 final size:20
Alignment explanation
Indices: 821432--821474 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
821422 GTTGTGATCG
821432 TTTCTAGCATTTGGGGATGA
1 TTTCTAGCATTTGGGGATGA
*
821452 TTTCTAGCCGTTTGGGGAT-A
1 TTTCTAG-CATTTGGGGATGA
821472 TTT
1 TTT
821475 TCTCTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (20 bp):
TTTCTAGCATTTGGGGATGA
Found at i:827244 original size:21 final size:21
Alignment explanation
Indices: 827220--827264 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
827210 TTTCAATTTC
827220 TTTTATATT-ATATTTCTATAA
1 TTTTATATTCA-ATTTCTATAA
* *
827241 TTTTTTATTCAATTTCTATTA
1 TTTTATATTCAATTTCTATAA
827262 TTT
1 TTT
827265 AAGCTATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATTCAATTTCTATAA
Found at i:827500 original size:23 final size:23
Alignment explanation
Indices: 827465--827530 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
827455 GTGAGGGTTT
* * *
827465 TATGTTGTTCTTCGGGTCAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
*
827488 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAC
* *
827511 TATGTGGTCATTCAGGACAA
1 TATGTGGTCCTTCGGGACAA
827531 TTATGTGGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAC
Found at i:827537 original size:21 final size:21
Alignment explanation
Indices: 827488--827555 Score: 57
Period size: 23 Copynumber: 3.1 Consensus size: 21
827478 GGGTCAAAAC
* * *
827488 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCATTCAGGAC-AA-T
827511 TATGTGGTCATTCAGGACAAT
1 TATGTGGTCATTCAGGACAAT
*
827532 TATGTGG-CACTTCAGTGAAAAT
1 TATGTGGTCA-TTCAG-GACAAT
827554 TA
1 TA
827556 AGCGAGATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 12 0.31
22 9 0.23
23 16 0.41
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (21 bp):
TATGTGGTCATTCAGGACAAT
Found at i:830454 original size:21 final size:21
Alignment explanation
Indices: 830404--830468 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
830394 GAGGGTCTAC
*
830404 GTGGTCCTTCGG-ACATATAT
1 GTGGTCCTTTGGAACATATAT
** *
830424 GTAATACTTTGGAACATATAT
1 GTGGTCCTTTGGAACATATAT
830445 GTGGTCCTTTGAGACACATATAT
1 GTGGTCCTTTG-GA-ACATATAT
830468 G
1 G
830469 GTCTTTTGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 8 0.23
21 16 0.46
22 2 0.06
23 9 0.26
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTTGGAACATATAT
Found at i:837596 original size:23 final size:23
Alignment explanation
Indices: 837569--837631 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
837559 CATTTTATAT
*
837569 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACAC
* *
837592 GGCACTTCGGTGCATTTCTATAT
1 GGCACTTCGGTGCATTTCTACAC
837615 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
837632 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:838259 original size:21 final size:21
Alignment explanation
Indices: 838233--838309 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
838223 ATATGTTCAC
*
838233 TAATTTTTCAAATTGATCATT
1 TAATTTTTCAAATTGACCATT
*
838254 TAATTTTTCAAATTGACCTTT
1 TAATTTTTCAAATTGACCATT
** *
838275 TAATTTTTTGAATTGACCACT
1 TAATTTTTCAAATTGACCATT
838296 T-ATTTTATCAAATT
1 TAATTTT-TCAAATT
838310 TTTTCCAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 5 0.11
21 42 0.89
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (21 bp):
TAATTTTTCAAATTGACCATT
Found at i:838991 original size:13 final size:13
Alignment explanation
Indices: 838973--839000 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
838963 AATTAAAAAA
838973 TTAGGGTTAGGGT
1 TTAGGGTTAGGGT
838986 TTAGGGTTAGGGT
1 TTAGGGTTAGGGT
838999 TT
1 TT
839001 GAGAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (13 bp):
TTAGGGTTAGGGT
Found at i:853482 original size:2 final size:2
Alignment explanation
Indices: 853475--853509 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
853465 ACAGTAGTTG
853475 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
853510 CACACGTTTC
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:853760 original size:3 final size:3
Alignment explanation
Indices: 853752--853789 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
853742 AAAAGTGTTT
*
853752 ATC ATC ATC ATC ATC ATC AAC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
853790 GGAGATCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:854182 original size:22 final size:21
Alignment explanation
Indices: 854147--854188 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
854137 CATAATTATT
854147 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
854168 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
854189 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:855569 original size:2 final size:2
Alignment explanation
Indices: 855562--855626 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
855552 GAAAAGGCGC
*
855562 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
855604 CT CT CT CT CT CT CT CC CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
855627 ACGGTAGGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:856203 original size:45 final size:45
Alignment explanation
Indices: 856153--856238 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
856143 TTTAATTATC
* **
856153 CTTTAAT-TTGAAATATTTAAAATGAT-ATTGATATCTTTTAAATAA
1 CTTTAATATT-AAA-ATTTAAAAAGATAATAAATATCTTTTAAATAA
*
856198 CTTTAATATTTAAATTTAAAAAGATAATAAATATCTTTTAA
1 CTTTAATATTAAAATTTAAAAAGATAATAAATATCTTTTAA
856239 TTTTTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 11 0.31
45 22 0.63
46 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (45 bp):
CTTTAATATTAAAATTTAAAAAGATAATAAATATCTTTTAAATAA
Found at i:856245 original size:35 final size:33
Alignment explanation
Indices: 856191--856262 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
856181 TGATATCTTT
856191 TAAATAACTTTAATATTTAA-ATTTAAAAAGATAA
1 TAAATAACTTTAATATTTAATA-TTAAAAAGAT-A
* * *
856225 TAAATATCTTTTAATTTTTAATATTCAAAAGATA
1 TAAATAAC-TTTAATATTTAATATTAAAAAGATA
856259 TAAA
1 TAAA
856263 CTCCTTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 12 0.36
35 20 0.61
36 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (33 bp):
TAAATAACTTTAATATTTAATATTAAAAAGATA
Found at i:856262 original size:34 final size:34
Alignment explanation
Indices: 856191--856262 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
856181 TGATATCTTT
856191 TAAATAACTTTAATATTTAAATTTAAAAAGATAA
1 TAAATAACTTTAATATTTAAATTTAAAAAGATAA
* * *
856225 TAAATATCTTTTAAT-TTTTAATATTCAAAAGAT-A
1 TAAATAAC-TTTAATATTTAAAT-TTAAAAAGATAA
856259 TAAA
1 TAAA
856263 CTCCTTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (34 bp):
TAAATAACTTTAATATTTAAATTTAAAAAGATAA
Found at i:859014 original size:18 final size:18
Alignment explanation
Indices: 858978--859015 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
858968 ATATATCATG
*
858978 TATAATTTTAAATTAATA
1 TATAATTTTAAAGTAATA
858996 TATAATTTTTAAAGT-ATA
1 TATAA-TTTTAAAGTAATA
859014 TA
1 TA
859016 ATATATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAATTTTAAAGTAATA
Found at i:859231 original size:2 final size:2
Alignment explanation
Indices: 859153--859211 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
859143 TATAGTTTTG
859153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
859195 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
859212 GTTTTATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:859942 original size:21 final size:20
Alignment explanation
Indices: 859898--859972 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
859888 TTCATTATGC
*
859898 AAAGTTTCGAAACTCTTACT
1 AAAGTTTCGAAACTCTTACA
859918 AAAGTTTCGAAACTCTTTACA
1 AAAGTTTCGAAACTC-TTACA
*
859939 AAAGTTTTC-ATACTCTTACA
1 AAAG-TTTCGAAACTCTTACA
* *
859959 GAAGTTTCCAAACT
1 AAAGTTTCGAAACT
859973 ATGAACAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.08
20 27 0.56
21 13 0.27
22 4 0.08
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTACA
Found at i:863445 original size:20 final size:19
Alignment explanation
Indices: 863420--863472 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
863410 CTACACATGC
863420 AGTTTCAAAACTTTGGAGAA
1 AGTTTCAAAACTTTGGAG-A
*
863440 AGTTTCGAAAA-TTTGTAGA
1 AGTTTC-AAAACTTTGGAGA
* *
863459 AGTATCGAAACTTT
1 AGTTTCAAAACTTT
863473 TAAACACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 12 0.43
21 4 0.14
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (19 bp):
AGTTTCAAAACTTTGGAGA
Found at i:863614 original size:21 final size:21
Alignment explanation
Indices: 863584--863637 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
863574 AGGATGATAT
* *
863584 GTTTCGAAACTATTTACAAAC
1 GTTTCCAAACTATTTACAAAA
*
863605 GTTTCCAAACT-CTTACAAAA
1 GTTTCCAAACTATTTACAAAA
*
863625 GTTTACAAACTAT
1 GTTTCCAAACTAT
863638 GAACATTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.33
Consensus pattern (21 bp):
GTTTCCAAACTATTTACAAAA
Found at i:863883 original size:20 final size:21
Alignment explanation
Indices: 863854--863900 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
863844 TTATATCAAA
* * *
863854 ATATAATTCAACAATAT-TAT
1 ATATATTTCAAAAACATATAT
863874 ATATATTTCAAAAACATATAT
1 ATATATTTCAAAAACATATAT
863895 ATATAT
1 ATATAT
863901 ATATATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATATTTCAAAAACATATAT
Found at i:867401 original size:10 final size:10
Alignment explanation
Indices: 867388--867435 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
867378 CGAATTTAAC
867388 ATTATTTATT
1 ATTATTTATT
*
867398 ATTATTTAAT
1 ATTATTTATT
867408 ATTATTAGTATT
1 ATTATT--TATT
*
867420 ATTATTAATT
1 ATTATTTATT
867430 -TTATTT
1 ATTATTT
867436 TCTTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.16
10 18 0.56
12 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTATTTATT
Found at i:874956 original size:21 final size:23
Alignment explanation
Indices: 874932--874976 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
874922 CTCTCGTGCA
874932 TATTTTTCATTATTT-ATT-TAT
1 TATTTTTCATTATTTCATTATAT
*
874953 TATTTTTTATTATTTCATTATAT
1 TATTTTTCATTATTTCATTATAT
874976 T
1 T
874977 TTGATATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTTTTCATTATTTCATTATAT
Found at i:874961 original size:10 final size:10
Alignment explanation
Indices: 874932--874967 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
874922 CTCTCGTGCA
*
874932 TATTTTTCAT
1 TATTTTTTAT
874942 TATTTATTTAT
1 TATTT-TTTAT
874953 TATTTTTTAT
1 TATTTTTTAT
874963 TATTT
1 TATTT
874968 CATTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:876554 original size:64 final size:62
Alignment explanation
Indices: 876486--876605 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 62
876476 ATGCACATGC
*
876486 AGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGCATCGATGTATAAGG
1 AGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAA-AGGATTTATGCATCGATGTATAAGG
* * *
876550 AGTGCATCGATGCATCCCCATTAAATACAAACATCGAAAGGATTTATGCATCGATG
1 AGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAAAGGATTTATGCATCGATG
876606 CAGGGTGTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 18 0.36
64 25 0.50
65 6 0.12
66 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (62 bp):
AGTGCATCGATGCATCCAATTAAAAAAAAACATCGAAAGGATTTATGCATCGATGTATAAGG
Found at i:877633 original size:15 final size:15
Alignment explanation
Indices: 877614--877649 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
877604 GGAGAATTGA
*
877614 AATAAGGTATGTGAT
1 AATAAGATATGTGAT
*
877629 TATAAGATATGTGAT
1 AATAAGATATGTGAT
877644 AATAAG
1 AATAAG
877650 TTATATGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
AATAAGATATGTGAT
Found at i:878139 original size:103 final size:103
Alignment explanation
Indices: 877959--878180 Score: 410
Period size: 103 Copynumber: 2.2 Consensus size: 103
877949 AGGGTCTATA
877959 TGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
878024 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATG
*
878062 TGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
878127 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATG
878165 TGGTCCTT-ATGGACAT
1 TGGTCCTTCA-GGACAT
878181 TATTATATGG
Statistics
Matches: 115, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (103 bp):
TGGTCCTTCAGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATG
Found at i:878233 original size:23 final size:23
Alignment explanation
Indices: 878188--878233 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
878178 CATTATTATA
*
878188 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
878211 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
878234 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:881833 original size:13 final size:14
Alignment explanation
Indices: 881808--881860 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
881798 TTCTTTGCCT
881808 AAAGAATGAAAAAGA
1 AAAGAA-GAAAAAGA
881823 AAA-AAGAAAAAGA
1 AAAGAAGAAAAAGA
*
881836 AAAGAA-AGAAAGA
1 AAAGAAGAAAAAGA
881849 AAATGAA-AAAAA
1 AAA-GAAGAAAAA
881861 AATATGGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 20 0.59
14 11 0.32
15 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAGAAGAAAAAGA
Found at i:881847 original size:19 final size:18
Alignment explanation
Indices: 881817--881862 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
881807 TAAAGAATGA
881817 AAAAGAAAAAAGAAAAAG
1 AAAAGAAAAAAGAAAAAG
*
881835 AAAAGAAAGAAAGAAAATG
1 AAAAGAAA-AAAGAAAAAG
881854 AAAA-AAAAA
1 AAAAGAAAAA
881863 TATGGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 11 0.42
19 13 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAG
Found at i:883658 original size:132 final size:130
Alignment explanation
Indices: 883122--883824 Score: 692
Period size: 132 Copynumber: 5.3 Consensus size: 130
883112 GATAATTGAA
* * *
883122 CTCGATTCAATCTTCCATGAAGAACA-ATGGAATGAAACAACATCCCCAGATATAATTTTCCCTC
1 CTCGATTCAATCTTCC-TGAAGAACAGA-GGAATGAATCAACATCCCCAGATCTGATTTTCCCTC
* * * *
883186 AAGAAGAAATGGAGCAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAG
64 AAGAAG-AA-GG-GAAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
*
883251 TATAC
126 TCTAC
* * *
883256 CTCGATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCAA
1 CTCGATTCAATCTTCCTGAAGAACAGAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
* * * * *
883321 GAAGAA-AGAACAGATCC-TCTCTTTCAAGATTT-ATATT-CTTGAAGAT-A-AG-AGAAGTAAA
66 GAAGAAGGGAA-A-ATCCATCTCTTTCAAGATTTGATATTCCCTG-AG-TGACAGTGGAA-CAAG
* *
883379 TCGAA
126 TCTAC
* * * *
883384 CTCGATTCAATATTCTCTGAAGAATAGTA-GAATGAATCAACATCCCAATATCTGATTTTCCCTC
1 CTCGATTCAATCTTC-CTGAAGAACAG-AGGAATGAATCAACATCCCCAGATCTGATTTTCCCTC
* * ** *
883448 AAAAAGAAGCGGAACAAATCTATCTCTTTCAAGATTTGATATTGTCTGAGTGACAGAGGAACAAG
64 AAGAAGAAG-GG-A-AAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
883513 TCTAC
126 TCTAC
* *
883518 CTCGATTCAATCTTCGCTGAAGAACAGAGGAATGAATCAACGTCCCCAGATCTGATTTTCTCTCA
1 CTCGATTCAATCTTC-CTGAAGAACAGAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
*
883583 AGATA-AAGCGGAAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAACTC
65 AGA-AGAAG-GGAAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTC
883647 TAC
128 TAC
* * * * * * *
883650 CCCAATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAAAATCCTCATAT-TGATTTT-CCTCA
1 CTCGATTCAATCTT-CCTGAAGAACAGAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * * * **
883713 ACAAGAAGTAGAACAAATCCCTCTCTTGCAAGATTTGACGTTCCCTGAGTGACAGTGGAACAAGT
65 AGAAGAAG--GGA-AAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
883778 CTAC
127 CTAC
* * * *
883782 CTTGATTTAATCTTCCCTGAAGAACAGTGGAATGAGTCAACAT
1 CTCGATTCAATCTT-CCTGAAGAACAGAGGAATGAATCAACAT
883825 TTCTTGATCT
Statistics
Matches: 476, Mismatches: 69, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
127 3 0.01
128 23 0.05
129 59 0.12
130 25 0.05
131 17 0.04
132 197 0.41
133 59 0.12
134 89 0.19
135 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (130 bp):
CTCGATTCAATCTTCCTGAAGAACAGAGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
GAAGAAGGGAAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTAC
Found at i:883839 original size:264 final size:262
Alignment explanation
Indices: 883126--883822 Score: 811
Period size: 262 Copynumber: 2.6 Consensus size: 262
883116 ATTGAACTCG
* * * * * * *
883126 ATTCAATCTTCCATGAAGAACAATGGAATGAAACAACATCCCCAGATATAATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACAT-CCCATATATGATTTTCCCTCAAAAA
* * * * *
883191 GAAATGGAGCAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAGTATAC
65 GAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTAC
*
883256 CTCGATTCAATCTT-CCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCA
130 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCA
* *
883320 AGAAGAAAGAACAGATCCTCTCTTTCAAGATTTATATTCTTGAAGATAAGAGAAGTAAATCGAAC
195 AGAAGAAAGAACAGATCCTCTCTTTCAAGATTTATATTCCTGAAGATAAGAGAAGCAAATCGAAC
* *
883385 TCG
260 CCA
* * * *
883388 ATTCAATATTCTCTGAAGAATAGT-AGAATGAATCAACATCCCAATATCTGATTTTCCCTCAAAA
1 ATTCAATCTTCCCTGAAGAACAGTGA-AATGAATCAACATCCC-ATATATGATTTTCCCTCAAAA
* ** ** *
883452 AGAAGCGGAACAAATCTATCTCTTTCAAGATTTGATATTGTCTGAGTGACAGAGGAACAAGTCTA
64 AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTA
* * *
883517 CCTCGATTCAATCTTCGCTGAAGAACAGAGGAATGAATCAACGTCCCCAGATCTGATTTTCTCTC
129 CCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC
* *
883582 AAGATA-AAGCGGAA-A-ATCCATCTCTTTCAAGATTTGATATTCCCTG-AG-TGACAGTGGAA-
194 AAGA-AGAA--AGAACAGATCC-TCTCTTTCAAGATTT-ATATT-CCTGAAGAT-A-AG-AGAAG
* * *
883641 CAACTCTACCCCA
250 CAAATCGAACCCA
* *
883654 ATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAAAATCCTCATAT-TGATTTT-CCTCAACAA
1 ATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACATCC-CATATATGATTTTCCCTCAAAAA
* * **
883717 GAAGTAGAACAAATCCCTCTCTTGCAAGATTTGACGTTCCCTGAGTGACAGTGGAACAAGTCTAC
65 GAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTAC
* * *
883782 CTTGATTTAATCTTCCCTGAAGAACAGTGGAATGAGTCAAC
130 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAAC
883823 ATTTCTTGAT
Statistics
Matches: 366, Mismatches: 55, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
261 3 0.01
262 117 0.32
263 55 0.15
264 117 0.32
265 18 0.05
266 51 0.14
267 5 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (262 bp):
ATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACATCCCATATATGATTTTCCCTCAAAAAG
AAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACC
TCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAA
GAAGAAAGAACAGATCCTCTCTTTCAAGATTTATATTCCTGAAGATAAGAGAAGCAAATCGAACC
CA
Found at i:884016 original size:3 final size:3
Alignment explanation
Indices: 884003--884067 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
883993 CGAATTTAAC
* *
884003 ATT ATTT ATT ATT ATTT AAT ATT ATT ATTT AAT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
884051 AATT -TT ATT -TT ATT ATT
1 -ATT ATT ATT ATT ATT ATT
884068 TTTAGATTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 4 0.08
3 36 0.69
4 12 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:884027 original size:13 final size:13
Alignment explanation
Indices: 884009--884044 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
883999 TAACATTATT
884009 TATTATTATTTAA
1 TATTATTATTTAA
884022 TATTATTATTTAA
1 TATTATTATTTAA
884035 TATTATTATT
1 TATTATTATT
884045 ATTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTTAA
Found at i:884029 original size:16 final size:14
Alignment explanation
Indices: 884008--884068 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 14
883998 TTAACATTAT
884008 TTATTATTATTTAA
1 TTATTATTATTTAA
884022 -TATTATTATTTAA
1 TTATTATTATTTAA
884035 -TATTATTA-TT-A
1 TTATTATTATTTAA
*
884046 TTATTA--ATTTTA
1 TTATTATTATTTAA
884058 TT-TTATTATTT
1 TTATTATTATTT
884069 TTAGATTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 10 0.24
13 25 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTAA
Found at i:884065 original size:14 final size:15
Alignment explanation
Indices: 884007--884071 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
883997 TTTAACATTA
884007 TTTATTATTATTTAAT
1 TTTATTATTA-TTAAT
* *
884023 ATTATTATT-TAATAT
1 TTTATTATTATTA-AT
884038 TATTATTATTATTAAT
1 T-TTATTATTATTAAT
*
884054 TTTATT-TTATTATT
1 TTTATTATTATTAAT
884068 TTTA
1 TTTA
884072 GATTACAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 13 0.32
15 7 0.17
16 19 0.46
17 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTATTATTAAT
Found at i:885731 original size:21 final size:20
Alignment explanation
Indices: 885706--885752 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
885696 TCAATATATG
* *
885706 TATATTAGTATTTTTTAAATA
1 TATATTA-TATATATTAAATA
885727 TATATATATATATATTAAATA
1 TATAT-TATATATATTAAATA
885748 T-TATT
1 TATATT
885753 TTGTGCGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.13
21 17 0.74
22 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATATTATATATATTAAATA
Found at i:891721 original size:22 final size:21
Alignment explanation
Indices: 891679--891731 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
891669 ATTCTGACTA
891679 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
891700 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
891721 TCGCAATGCGA
1 TCGCATTGCGA
891732 ATTAGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:891764 original size:20 final size:21
Alignment explanation
Indices: 891717--891767 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
891707 GCGATTTTCC
891717 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
* *
891738 AAAATCGCAATGCGATTTA-G
1 TAAATCGCAATGCGAATTAGG
891758 TAAATCGCAA
1 TAAATCGCAA
891768 CGAGATTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (21 bp):
TAAATCGCAATGCGAATTAGG
Found at i:895245 original size:19 final size:19
Alignment explanation
Indices: 895223--895350 Score: 70
Period size: 19 Copynumber: 7.5 Consensus size: 19
895213 AATGACTATT
895223 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
895242 GCAAT--G--A-GAGAATC
1 GCAATGCGAAATGAAAATC
*
895256 GCAATGCGAAATGAAAATT
1 GCAATGCGAAATGAAAATC
*
895275 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
*
895289 GTAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
* **
895308 GTAA--CG--A-GGGAATC
1 GCAATGCGAAATGAAAATC
*
895322 GCAAAGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
895341 GCAACGCGAA
1 GCAATGCGAA
895351 TTTAGTTTCG
Statistics
Matches: 81, Mismatches: 13, Indels: 30
0.65 0.10 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 38 0.47
ACGTcount: A:0.45, C:0.16, G:0.25, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:895260 original size:33 final size:33
Alignment explanation
Indices: 895223--895346 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
895213 AATGACTATT
*
895223 GCAATGCGAAATGAAAATCGCAATGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
*
895256 GCAATGCGAAATGAAAATTGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
* * *
895289 GTAATGCGAAATGAAAATCGTAACGAGGGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
*
895322 GCAAAGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
895347 CGAATTTAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:895368 original size:19 final size:19
Alignment explanation
Indices: 895346--895387 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
895336 AAATCGCAAC
*
895346 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCATT
*
895365 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
895384 GCGA
1 GCGA
895388 TAGTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:895394 original size:19 final size:19
Alignment explanation
Indices: 895356--895396 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
895346 GCGAATTTAG
* **
895356 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATAGTCA
895375 TTTCGCATTGCGATAGTCA
1 TTTCGCATTGCGATAGTCA
895394 TTT
1 TTT
895397 TTGCCTTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATAGTCA
Found at i:895514 original size:14 final size:14
Alignment explanation
Indices: 895495--895531 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
895485 CATCAATTAA
895495 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
895509 ACAAATCATCTTTT
1 ACAAATCAACTTTT
895523 ACAAATCAA
1 ACAAATCAA
895532 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:896950 original size:21 final size:21
Alignment explanation
Indices: 896884--896950 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
896874 GTGAATCGGG
*
896884 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * * * *
896904 CCTCTTCAACGATGGCAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
896926 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
896947 CTCT
1 CTCT
896951 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:897442 original size:19 final size:19
Alignment explanation
Indices: 897426--897528 Score: 92
Period size: 19 Copynumber: 5.6 Consensus size: 19
897416 AAAAATGACT
897426 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
897445 ATCACAACGAGAGAATGAAA
1 ATCGCAACGCGA-AATGAAA
*
897465 ATCGCAACGCAAAAT-AAGA
1 ATCGCAACGCGAAATGAA-A
*
897484 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
* *
897498 ATCGCAATGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
897517 ATCGCAACGCGA
1 ATCGCAACGCGA
897529 TTATAGTTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 8 0.12
15 2 0.03
16 2 0.03
17 1 0.02
18 3 0.05
19 34 0.52
20 16 0.24
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:897547 original size:19 final size:19
Alignment explanation
Indices: 897525--897609 Score: 102
Period size: 19 Copynumber: 4.4 Consensus size: 19
897515 AAATCGCAAC
*
897525 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
897544 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
897563 GCGATTTTCGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
897582 GCGATTTTCA-TTCTCTCGTT
1 GCGATTTT-AGTT-TCGCGTT
897602 GCGATTTT
1 GCGATTTT
897610 CATTTCAACC
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
19 43 0.74
20 15 0.26
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:897567 original size:38 final size:39
Alignment explanation
Indices: 897525--897607 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 39
897515 AAATCGCAAC
897525 GCGATTATAGTTTCGCGTTGCGATTTTCATT-TCGCGTT
1 GCGATTATAGTTTCGCGTTGCGATTTTCATTCTCGCGTT
* * *
897563 GCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTT
1 GCGATTATAGTTTCGCGTTGCGATTTTCATTCTCGCGTT
897602 GCGATT
1 GCGATT
897608 TTCATTTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 29 0.71
39 12 0.29
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (39 bp):
GCGATTATAGTTTCGCGTTGCGATTTTCATTCTCGCGTT
Found at i:897603 original size:20 final size:19
Alignment explanation
Indices: 897535--897615 Score: 135
Period size: 19 Copynumber: 4.2 Consensus size: 19
897525 GCGATTATAG
897535 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
897554 TTTCGCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
897573 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
897592 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
897612 TTTC
1 TTTC
897616 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 40 0.69
20 18 0.31
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:897946 original size:94 final size:94
Alignment explanation
Indices: 897718--898069 Score: 554
Period size: 93 Copynumber: 3.8 Consensus size: 94
897708 ACTTCAACCA
* * * *
897718 AAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAATTTAGCAGAATTGGCAGCAAACGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
*
897783 CAAATTTACTTTCAATCAAAAGA-AAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
897811 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
897876 CAAATTTACTTTCAACCAAAAGACAAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
* *
897905 AAAGACAAATCCTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGAAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
*
897970 TAAATTTAC-TTCAACCAAAAGACAAAAC
66 CAAATTTACTTTCAACCAAAAGACAAAAC
* *
897998 AAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAGTATTGGCAGCAACCGA
1 -AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGA
*
898059 ATAAATTTACT
65 ACAAATTTACT
898070 AAGCAATCTA
Statistics
Matches: 244, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
90 40 0.16
93 102 0.42
94 102 0.42
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
CAAATTTACTTTCAACCAAAAGACAAAAC
Found at i:899855 original size:33 final size:33
Alignment explanation
Indices: 899807--899886 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
899797 AAAATCGCAA
**
899807 TGCGATTTTGGTTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
* *
899840 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
899873 TGCGATTTTCATTT
1 TGCGATTTTCATTT
899887 TCGTGTTGCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:899896 original size:20 final size:20
Alignment explanation
Indices: 899871--899921 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
899861 CGATTCTCTC
*
899871 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
899891 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
*
899911 GTTACGATTTT
1 GTTGCGATTTT
899922 AAGTTTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:900494 original size:20 final size:20
Alignment explanation
Indices: 900471--900564 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
900461 CGATAGTCAG
900471 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
900491 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
900511 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
900532 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
900552 ATTCGCATTGCGA
1 ATTCGCATTGCGA
900565 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:900578 original size:41 final size:41
Alignment explanation
Indices: 900471--900564 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
900461 CGATAGTCAG
* *
900471 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTA
* *
900512 ATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTA
900552 ATTCGCATTGCGA
1 ATTCGCATTGCGA
900565 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTA
Found at i:900585 original size:21 final size:21
Alignment explanation
Indices: 900561--900606 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
900551 TATTCGCATT
900561 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
900582 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
900603 GCGA
1 GCGA
900607 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:903386 original size:16 final size:16
Alignment explanation
Indices: 903367--903420 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
903357 GTTATTTTTT
*
903367 GTTTGAGTTACTTTCG
1 GTTTGGGTTACTTTCG
*
903383 GTTTGGGTTAGTTTCG
1 GTTTGGGTTACTTTCG
* *
903399 GTTCGGGTTACTTTTG
1 GTTTGGGTTACTTTCG
903415 GTTTGG
1 GTTTGG
903421 CTAAAATTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.07, C:0.09, G:0.33, T:0.50
Consensus pattern (16 bp):
GTTTGGGTTACTTTCG
Found at i:905482 original size:97 final size:97
Alignment explanation
Indices: 905316--905512 Score: 385
Period size: 97 Copynumber: 2.0 Consensus size: 97
905306 GGGATCGCCG
*
905316 TCTAAATCTGGGTATAATACGATATGATTCACTGATTTTCAGAAATATAAACATAATCCGAACCG
1 TCTAAATCTGGGTATAAAACGATATGATTCACTGATTTTCAGAAATATAAACATAATCCGAACCG
905381 AATCATGAGAATCAATTCATAATAATAAATCC
66 AATCATGAGAATCAATTCATAATAATAAATCC
905413 TCTAAATCTGGGTATAAAACGATATGATTCACTGATTTTCAGAAATATAAACATAATCCGAACCG
1 TCTAAATCTGGGTATAAAACGATATGATTCACTGATTTTCAGAAATATAAACATAATCCGAACCG
905478 AATCATGAGAATCAATTCATAATAATAAATCC
66 AATCATGAGAATCAATTCATAATAATAAATCC
905510 TCT
1 TCT
905513 CAAAGCACTA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (97 bp):
TCTAAATCTGGGTATAAAACGATATGATTCACTGATTTTCAGAAATATAAACATAATCCGAACCG
AATCATGAGAATCAATTCATAATAATAAATCC
Found at i:906486 original size:31 final size:31
Alignment explanation
Indices: 906449--906514 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
906439 TTAAAATAAT
906449 AAATTATCACTAACA-TTATCGATTTGTAACA
1 AAATTATCACTAA-AGTTATCGATTTGTAACA
*
906480 AAATTATCACTAAAGTTATCTATTTGTAACA
1 AAATTATCACTAAAGTTATCGATTTGTAACA
906511 AAAT
1 AAAT
906515 GACATTCCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (31 bp):
AAATTATCACTAAAGTTATCGATTTGTAACA
Found at i:914555 original size:3 final size:3
Alignment explanation
Indices: 914547--914598 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
914537 GCTTTTATCA
914547 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
914595 CTT C
1 CTT C
914599 CTCCTCCTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Done.