Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 30
Found at i:2953430 original size:21 final size:22
Alignment explanation
Indices: 2953380--2953430 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2953370 TTACTTATTT
2953380 GCATTGCG-AATTGGGAAAATC
1 GCATTGCGAAATTGGGAAAATC
**
2953401 GCAACGCGAAATT-GGAAAATC
1 GCATTGCGAAATTGGGAAAATC
2953422 GCATTGCGA
1 GCATTGCGA
2953431 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (22 bp):
GCATTGCGAAATTGGGAAAATC
Found at i:2953488 original size:20 final size:20
Alignment explanation
Indices: 2953465--2953510 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2953455 GGAAACTGAT
*
2953465 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
2953485 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
2953504 TTGCGAT
1 TTGCGAT
2953511 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:2953793 original size:15 final size:16
Alignment explanation
Indices: 2953742--2953786 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
2953732 TCACGAAATG
2953742 TAAGATTACCAGTGGAAA
1 TAAGATTACCAG-GG-AA
2953760 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
2953778 TAAGATTAC
1 TAAGATTAC
2953787 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:2957520 original size:13 final size:13
Alignment explanation
Indices: 2957502--2957533 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2957492 CCAATCGTCC
2957502 CCTTGTTGTGAAG
1 CCTTGTTGTGAAG
2957515 CCTTGTTGTGAAG
1 CCTTGTTGTGAAG
2957528 CCTTGT
1 CCTTGT
2957534 CGTTTTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.28, T:0.41
Consensus pattern (13 bp):
CCTTGTTGTGAAG
Found at i:2962662 original size:136 final size:136
Alignment explanation
Indices: 2962409--2962692 Score: 417
Period size: 136 Copynumber: 2.1 Consensus size: 136
2962399 ACTTCAATTC
* *
2962409 AGTGATATATCATACCATTGAATAATGTTTTTGACTTGTTTCCCTTTAATGAAAAATGTCATTTT
1 AGTGATATATCATACCACTAAATAATGTTTTTGACTTGTTTCCCTTTAATGAAAAATGTCATTTT
* * *
2962474 CTTATAAACCATTTAATACAAAATGACAAAAAACTTTTTAATGCTCAATCACTTCATTTCAAAAA
66 CTCATAAACCATTTAATACAAAATGACAAAAAACATTTTAATGCCCAATCACTTCATTTCAAAAA
2962539 CCTTTT
131 CCTTTT
* *
2962545 AGTGATATATCATACCACTAAATGATGTTTTTGACTTGTTTCCCTTTAATGAAAAA-GTTCTTTT
1 AGTGATATATCATACCACTAAATAATGTTTTTGACTTGTTTCCCTTTAATGAAAAATG-TCATTT
* * * * * **
2962609 TCTCATAGACCATTTAATATATAATGACAAAAAACATTTTAGTTCCCGGTCACTTCATTTCAAAA
65 TCTCATAAACCATTTAATACAAAATGACAAAAAACATTTTAATGCCCAATCACTTCATTTCAAAA
*
2962674 ACGTTTT
130 ACCTTTT
2962681 AGTGATATATCA
1 AGTGATATATCA
2962693 CTTCATTTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
135 1 0.01
136 131 0.99
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (136 bp):
AGTGATATATCATACCACTAAATAATGTTTTTGACTTGTTTCCCTTTAATGAAAAATGTCATTTT
CTCATAAACCATTTAATACAAAATGACAAAAAACATTTTAATGCCCAATCACTTCATTTCAAAAA
CCTTTT
Found at i:2963509 original size:33 final size:33
Alignment explanation
Indices: 2963462--2963532 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
2963452 ACAAAATTTA
* *
2963462 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
2963494 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
2963527 CGATAA
1 CGATAA
2963533 TTGAAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:2963552 original size:21 final size:21
Alignment explanation
Indices: 2963527--2963568 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2963517 CTTCCAAGTT
2963527 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2963548 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
2963569 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2966067 original size:26 final size:26
Alignment explanation
Indices: 2966028--2966088 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
2966018 TTCTATTGTA
*
2966028 TTATAATATAATGTATGAGTTAAAGT
1 TTATAATGTAATGTATGAGTTAAAGT
* *
2966054 TTCTAATGTAATGTATGAGTTAATGT
1 TTATAATGTAATGTATGAGTTAAAGT
2966080 TTATAATGT
1 TTATAATGT
2966089 GTGGGTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (26 bp):
TTATAATGTAATGTATGAGTTAAAGT
Found at i:2968683 original size:97 final size:97
Alignment explanation
Indices: 2968517--2968714 Score: 369
Period size: 97 Copynumber: 2.0 Consensus size: 97
2968507 ATCCAATAAA
2968517 ATATAATTTCTTATGAAACTTGTCATGTTAGCATGACGAGTTCAACGAATATTGTAGCATTTGCC
1 ATATAATTTCTTATGAAACTTGTCATGTTAGCATGACGAGTTCAACGAATATTGTAGCATTTGCC
2968582 ATATATTCCTAAATAAAGTTTTCTTAGCTGGT
66 ATATATTCCTAAATAAAGTTTTCTTAGCTGGT
* * *
2968614 ATATAATTTCTTGTGAAACTTGTCATGTTAGCATGACGGGTTCAACGAATATTGTAGCATTTGTC
1 ATATAATTTCTTATGAAACTTGTCATGTTAGCATGACGAGTTCAACGAATATTGTAGCATTTGCC
2968679 ATATATTCCTAAATAAAGTTTTCTTAGCTGGT
66 ATATATTCCTAAATAAAGTTTTCTTAGCTGGT
2968711 ATAT
1 ATAT
2968715 GGCTAATATT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (97 bp):
ATATAATTTCTTATGAAACTTGTCATGTTAGCATGACGAGTTCAACGAATATTGTAGCATTTGCC
ATATATTCCTAAATAAAGTTTTCTTAGCTGGT
Found at i:2968889 original size:16 final size:16
Alignment explanation
Indices: 2968859--2968888 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2968849 AATCTTCGAT
2968859 AAATCAATAATTTTTA
1 AAATCAATAATTTTTA
2968875 AAAT-AATAATTTTT
1 AAATCAATAATTTTT
2968889 TTTGGTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATCAATAATTTTTA
Found at i:2969262 original size:16 final size:16
Alignment explanation
Indices: 2969236--2969294 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
2969226 TAACTAGAAC
2969236 CGAAA-TAACCCCAAT
1 CGAAAGTAACCCCAAT
2969251 CGAAAGTAACCCCAAT
1 CGAAAGTAACCCCAAT
* **
2969267 CAAAAGTAACTCGAAAT
1 CGAAAGTAAC-CCCAAT
2969284 -GAAAGTAACCC
1 CGAAAGTAACCC
2969295 GAATATGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 6 0.16
16 27 0.73
17 4 0.11
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.14
Consensus pattern (16 bp):
CGAAAGTAACCCCAAT
Found at i:2969297 original size:16 final size:17
Alignment explanation
Indices: 2969252--2969302 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2969242 AACCCCAATC
*
2969252 GAAAGTAACCCCAATCA-
1 GAAAGTAACCCGAAT-AT
*
2969269 -AAAGTAACTCGAA-AT
1 GAAAGTAACCCGAATAT
2969284 GAAAGTAACCCGAATAT
1 GAAAGTAACCCGAATAT
2969301 GA
1 GA
2969303 TTTATCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 1 0.04
16 23 0.82
17 4 0.14
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.16
Consensus pattern (17 bp):
GAAAGTAACCCGAATAT
Found at i:2969403 original size:22 final size:22
Alignment explanation
Indices: 2969372--2969413 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2969362 AAGTGAATGA
* *
2969372 ATCATTTATTTATAATATTATT
1 ATCATCTATTTATAACATTATT
*
2969394 ATCATCTATTTTTAACATTA
1 ATCATCTATTTATAACATTA
2969414 AAAAATAATA
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:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
ATCATCTATTTATAACATTATT
Found at i:2976905 original size:17 final size:19
Alignment explanation
Indices: 2976868--2976909 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2976858 CACTAGACTC
2976868 ATTAAATTATTAATACCTA
1 ATTAAATTATTAATACCTA
*
2976887 ATTAAATT-TTAA-CCCTA
1 ATTAAATTATTAATACCTA
2976904 ATTAAA
1 ATTAAA
2976910 AAATACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAATTATTAATACCTA
Found at i:2978054 original size:21 final size:21
Alignment explanation
Indices: 2977966--2978055 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 21
2977956 CCTTAAGGAT
*
2977966 CACATATATATTCCAAATGAC
1 CACATATATATCCCAAATGAC
* * * *
2977987 CAAATATGTTTCCCGAA-GAAC
1 CACATATATATCCCAAATG-AC
* * * * *
2978008 CGCATATATGTTCCAAAGGAT
1 CACATATATATCCCAAATGAC
* *
2978029 TACATATATATCCCGAATGAC
1 CACATATATATCCCAAATGAC
2978050 CACATA
1 CACATA
2978056 GAACCCTCGA
Statistics
Matches: 47, Mismatches: 20, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (21 bp):
CACATATATATCCCAAATGAC
Found at i:2986430 original size:14 final size:14
Alignment explanation
Indices: 2986408--2986438 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2986398 TGATAATTCG
2986408 ACTTAACTCAAATA
1 ACTTAACTCAAATA
*
2986422 ACTTGACTCAAATA
1 ACTTAACTCAAATA
2986436 ACT
1 ACT
2986439 CGAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (14 bp):
ACTTAACTCAAATA
Found at i:2989819 original size:10 final size:10
Alignment explanation
Indices: 2989804--2989828 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2989794 AGGAATTGAC
2989804 AATTATTTAA
1 AATTATTTAA
2989814 AATTATTTAA
1 AATTATTTAA
2989824 AATTA
1 AATTA
2989829 ATTGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTATTTAA
Found at i:2992360 original size:64 final size:64
Alignment explanation
Indices: 2992152--2992361 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
2992142 TTTTTCAAAG
* **
2992152 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGG-ATATTTTGAAACATCGAATGCA
2992215 TT
63 TT
* * **
2992217 TCATGCATCGATGCA-TATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
2992280 TT
63 TT
* * * *
2992282 TGATGCATCAATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
2992346 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
2992362 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 49 0.40
65 64 0.52
66 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:2992361 original size:17 final size:19
Alignment explanation
Indices: 2992333--2992381 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2992323 TATTTTGAAA
2992333 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2992351 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2992370 CACCGATGCACT
1 CATCGATGCACT
2992382 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:2998705 original size:65 final size:63
Alignment explanation
Indices: 2998586--2998795 Score: 237
Period size: 65 Copynumber: 3.3 Consensus size: 63
2998576 TTTTTCAAAG
* * * **
2998586 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTA-GGACTATTTTGAAACATCGAATGCAT
2998650 T
63 T
*
2998651 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGA-T-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACT-AGGACTATTT-TG-AAACATCGAATGCA
2998714 TT
62 TT
* ** *
2998716 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTAGGACTATTTTGAAACATCGAATGCATT
2998780 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
2998796 TAAGTGTCCA
Statistics
Matches: 127, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 53 0.42
65 64 0.50
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTAGGACTATTTTGAAACATCGAATGCATT
Found at i:3000720 original size:20 final size:20
Alignment explanation
Indices: 3000695--3000813 Score: 141
Period size: 20 Copynumber: 5.8 Consensus size: 20
3000685 CGGTGTTTGA
*
3000695 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
* *
3000715 GTGCATCGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
3000735 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
3000757 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
3000777 GATGCATGAATGCACTGCAAGG
1 G-TGCATGGATGCACTGC-AGG
3000799 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3000814 TTGACACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 11
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.04
20 35 0.39
21 28 0.31
22 18 0.20
23 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:3000770 original size:42 final size:41
Alignment explanation
Indices: 3000696--3000813 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 41
3000686 GGTGTTTGAG
* * * *
3000696 TGCATGGATGCACTGCATGGTGCATCGATGCACTGCATGG-
1 TGCATGAATGCACTGCAGGGTGCATGGATGCACTGCAGGGA
3000736 TGCATCG-ATGCACTAGTGCA-GGTGCATGGATGCACTGCAGGGA
1 TGCAT-GAATGCAC---TGCAGGGTGCATGGATGCACTGCAGGGA
3000779 TGCATGAATGCACTGCAAGGGTGCATGGATGCACT
1 TGCATGAATGCACTGC-AGGGTGCATGGATGCACT
3000814 TTGACACCCT
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
40 14 0.21
41 2 0.03
42 37 0.54
43 15 0.22
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (41 bp):
TGCATGAATGCACTGCAGGGTGCATGGATGCACTGCAGGGA
Found at i:3000914 original size:29 final size:29
Alignment explanation
Indices: 3000893--3000950 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
3000883 AAACTTTGAA
3000893 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
3000922 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
3000951 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:3000940 original size:30 final size:30
Alignment explanation
Indices: 3000893--3000952 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
3000883 AAACTTTGAA
3000893 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
3000922 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
3000953 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3002270 original size:19 final size:20
Alignment explanation
Indices: 3002227--3002274 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3002217 TCTAAATCCT
*
3002227 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3002247 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3002266 TTTTCAAAA
1 TTTTCAAAA
3002275 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3003196 original size:34 final size:32
Alignment explanation
Indices: 3003134--3003198 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
3003124 CCTTACAACT
* *
3003134 CCCTAGTTTTTCCGGGCTAAACTAGAACCTTA
1 CCCTAGTTTTACCGGGATAAACTAGAACCTTA
*
3003166 CCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 CCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
3003199 TCCCCTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 5 0.18
34 17 0.61
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (32 bp):
CCCTAGTTTTACCGGGATAAACTAGAACCTTA
Found at i:3003442 original size:20 final size:21
Alignment explanation
Indices: 3003417--3003456 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3003407 TGTTGTATAT
*
3003417 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGATTTGG
3003437 AGCCGTTTGGGGATGATTTG
1 AGCCGTTTGGGGATGATTTG
3003457 TATACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.35
Consensus pattern (21 bp):
AGCCGTTTGGGGATGATTTGG
Found at i:3003600 original size:20 final size:21
Alignment explanation
Indices: 3003575--3003642 Score: 88
Period size: 20 Copynumber: 3.3 Consensus size: 21
3003565 TTCGTGAATG
3003575 GATGCACA-ATAGGATGCATC
1 GATGCACAGATAGGATGCATC
* *
3003595 GATGCACAGCCT-TGATGCATC
1 GATGCACAG-ATAGGATGCATC
3003616 GATGCACAGA-AGGATGCATC
1 GATGCACAGATAGGATGCATC
3003636 GATGCAC
1 GATGCAC
3003643 TAATTGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 23 0.56
21 17 0.41
22 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
GATGCACAGATAGGATGCATC
Found at i:3003605 original size:41 final size:41
Alignment explanation
Indices: 3003560--3003642 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
3003550 CTAGCCGCTG
*
3003560 CAGCCTTCG-TGAATGGATGCACA-ATAGGATGCATCGATGCA
1 CAGCCTT-GATGAATCGATGCACAGA-AGGATGCATCGATGCA
*
3003601 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGAATCGATGCACAGAAGGATGCATCGATGCA
3003642 C
1 C
3003643 TAATTGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.03
41 36 0.95
42 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (41 bp):
CAGCCTTGATGAATCGATGCACAGAAGGATGCATCGATGCA
Found at i:3003732 original size:21 final size:20
Alignment explanation
Indices: 3003663--3003782 Score: 152
Period size: 21 Copynumber: 5.8 Consensus size: 20
3003653 CGGTGTTTGA
*
3003663 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
3003683 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
3003705 GTGCATGGATGCATTGCAGG
1 GTGCATGGATGCACTGCAGG
3003725 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
3003746 GATGCATGGATGCACTGCAAGG
1 G-TGCATGGATGCACTGC-AGG
3003768 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3003783 TTGACACCCT
Statistics
Matches: 90, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
19 4 0.04
20 15 0.17
21 50 0.56
22 17 0.19
23 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:3003909 original size:30 final size:31
Alignment explanation
Indices: 3003862--3003923 Score: 101
Period size: 29 Copynumber: 2.0 Consensus size: 31
3003852 AAACTTTGAA
3003862 TAAATTCAATTAAGTCC-AAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAAACCATTTTG
3003891 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAAACCATTTTG
3003923 T
1 T
3003924 CTTAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.37
30 6 0.20
31 5 0.17
32 8 0.27
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTAAGTCCAAAAAACCATTTTG
Found at i:3004007 original size:21 final size:20
Alignment explanation
Indices: 3003979--3004036 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
3003969 AATTGCACAT
*
3003979 AGGATGCATCGATGCACAGCC
1 AGGATGCATCGATGCACAG-A
**
3004000 TTGATGCATCGATGCACAGA
1 AGGATGCATCGATGCACAGA
3004020 AGGATGCATCGATGCAC
1 AGGATGCATCGATGCAC
3004037 TAATTGCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (20 bp):
AGGATGCATCGATGCACAGA
Found at i:3004126 original size:21 final size:20
Alignment explanation
Indices: 3004057--3004197 Score: 185
Period size: 21 Copynumber: 6.8 Consensus size: 20
3004047 CGGTGTTTGA
*
3004057 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
3004077 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
3004099 GTGCATGGATGCATTGCAGG
1 GTGCATGGATGCACTGCAGG
3004119 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
3004140 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
3004161 GATGCATGGATGCACTGCAAGG
1 G-TGCATGGATGCACTGC-AGG
3004183 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3004198 TTGACACCCT
Statistics
Matches: 111, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.04
20 15 0.14
21 71 0.64
22 17 0.15
23 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:3004179 original size:13 final size:13
Alignment explanation
Indices: 3004058--3004166 Score: 53
Period size: 13 Copynumber: 8.9 Consensus size: 13
3004048 GGTGTTTGAG
3004058 TGCATGGATGCAC
1 TGCATGGATGCAC
3004071 TGCATGG-TGCATC
1 TGCATGGATGCA-C
* *
3004084 GATGCACTAG-TGCAGG
1 --TGCA-TGGATGCA-C
*
3004100 TGCATGGATGCAT
1 TGCATGGATGCAC
3004113 TGCA-GG--G-A-
1 TGCATGGATGCAC
3004121 TGCATGGATGCAC
1 TGCATGGATGCAC
3004134 TGCA-GG--G-A-
1 TGCATGGATGCAC
3004142 TGCATGGATGCAC
1 TGCATGGATGCAC
*
3004155 TGCAGGGATGCA
1 TGCATGGATGCA
3004167 TGGATGCACT
Statistics
Matches: 75, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
8 8 0.11
9 6 0.08
10 2 0.03
11 2 0.03
12 10 0.13
13 29 0.39
14 8 0.11
15 4 0.05
16 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:3004324 original size:30 final size:31
Alignment explanation
Indices: 3004277--3004338 Score: 101
Period size: 29 Copynumber: 2.0 Consensus size: 31
3004267 AAACTTTGAA
3004277 TAAATTCAATTAAGTCC-AAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAAACCATTTTG
3004306 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAAACCATTTTG
3004338 T
1 T
3004339 CTTAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.37
30 6 0.20
31 5 0.17
32 8 0.27
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTAAGTCCAAAAAACCATTTTG
Found at i:3004803 original size:21 final size:21
Alignment explanation
Indices: 3004777--3004986 Score: 208
Period size: 21 Copynumber: 9.9 Consensus size: 21
3004767 TCGAGGGTTC
3004777 TATGTGGT-ACTTCGGGACATA
1 TATGTGGTCA-TTCGGGACATA
* * * *
3004798 TATGTGATCCTTTGGAACATA
1 TATGTGGTCATTCGGGACATA
* *
3004819 TATGAGGTCTTTCGGGACATA
1 TATGTGGTCATTCGGGACATA
* * *
3004840 TATTTGGTCATTTGGAACATA
1 TATGTGGTCATTCGGGACATA
*
3004861 TATGTGGTCATTAGGGACAATTA
1 TATGTGGTCATTCGGGAC-A-TA
* * * *
3004884 TATATGATCCTTCGGAACATA
1 TATGTGGTCATTCGGGACATA
3004905 TATGTGGTTC-TTCGGGACATA
1 TATGTGG-TCATTCGGGACATA
* *
3004926 TATATGGTCTTTCGGGACATA
1 TATGTGGTCATTCGGGACATA
*
3004947 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCATTCGGGACATA
*
3004968 TATGAGGTCATTCGGGACA
1 TATGTGGTCATTCGGGACA
3004987 ATTTTATACG
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
20 2 0.01
21 133 0.86
22 4 0.03
23 15 0.10
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATA
Found at i:3004920 original size:86 final size:86
Alignment explanation
Indices: 3004796--3004965 Score: 245
Period size: 86 Copynumber: 2.0 Consensus size: 86
3004786 CTTCGGGACA
* * *
3004796 TATATGTGATCCTTTGGAACATATATGAGGTCTTTCGGGACATATATTTGGTCATTT-GGAACAT
1 TATATATGATCCTTCGGAACATATATGAGGTCTTTCGGGACATATATATGGTC-TTTCGGAACAT
3004860 ATATGTGGTCATTAGGGACAAT
65 ATATGTGGTCATTAGGGACAAT
* *
3004882 TATATATGATCCTTCGGAACATATATGTGGT-TCTTCGGGACATATATATGGTCTTTCGGGACAT
1 TATATATGATCCTTCGGAACATATATGAGGTCT-TTCGGGACATATATATGGTCTTTCGGAACAT
* *
3004946 ATATGTGGTCCTTCGGGACA
65 ATATGTGGTCATTAGGGACA
3004966 TATATGAGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 4 0.05
86 71 0.95
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (86 bp):
TATATATGATCCTTCGGAACATATATGAGGTCTTTCGGGACATATATATGGTCTTTCGGAACATA
TATGTGGTCATTAGGGACAAT
Found at i:3004977 original size:107 final size:107
Alignment explanation
Indices: 3004786--3004994 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 107
3004776 CTATGTGGTA
* * *
3004786 CTTCGGGACATATATGTGATCCTTTGGAACATATATGAGGTCTTTCGGGACATATATTTGGTCAT
1 CTTCGGAACATATATGTGATCCTTCGGAACATATATGAGGTCTTTCGGGACATATATGTGGTCAT
* *
3004851 TTGGAACATATATGTGGTCATTAGGGACAATTATATATGATC
66 TCGGAACATATATGAGGTCATTAGGGACAATTATATATGATC
* * * *
3004893 CTTCGGAACATATATGTGGTTCTTCGGGACATATAT-ATGGTCTTTCGGGACATATATGTGGTCC
1 CTTCGGAACATATATGTGATCCTTCGGAACATATATGA-GGTCTTTCGGGACATATATGTGGTCA
* * *
3004957 TTCGGGACATATATGAGGTCATTCGGGACAATTTTATA
65 TTCGGAACATATATGAGGTCATTAGGGACAATTATATA
3004995 CGAGCACTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 1 0.01
107 88 0.99
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (107 bp):
CTTCGGAACATATATGTGATCCTTCGGAACATATATGAGGTCTTTCGGGACATATATGTGGTCAT
TCGGAACATATATGAGGTCATTAGGGACAATTATATATGATC
Found at i:3005221 original size:21 final size:21
Alignment explanation
Indices: 3005187--3005248 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
3005177 GTAGTTATAT
*
3005187 AATGACTGTGATTACATGTTGA
1 AATGATTG-GATTACATGTTGA
*
3005209 AATGATTGGATTACATGCTGA
1 AATGATTGGATTACATGTTGA
3005230 AATGATTGGATTACATGTT
1 AATGATTGGATTACATGTT
3005249 TATGACTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (21 bp):
AATGATTGGATTACATGTTGA
Found at i:3010314 original size:20 final size:22
Alignment explanation
Indices: 3010289--3010340 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
3010279 AGAATAATTA
3010289 TGTCTTTGTG-ACATGT-TCTC
1 TGTCTTTGTGAACATGTATCTC
* *
3010309 TGTCTTTATGATACATTTATCTC
1 TGTCTTTGTGA-ACATGTATCTC
3010332 TGTCTTTGT
1 TGTCTTTGT
3010341 AGCCTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 9 0.35
22 5 0.19
23 12 0.46
ACGTcount: A:0.13, C:0.17, G:0.15, T:0.54
Consensus pattern (22 bp):
TGTCTTTGTGAACATGTATCTC
Found at i:3011699 original size:28 final size:28
Alignment explanation
Indices: 3011651--3011715 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
3011641 TTTAAAAACA
3011651 TTTT-AAAA-ATATATATAATATATAAT
1 TTTTGAAAACATATATATAATATATAAT
* *
3011677 TTTTGAAAACATATGTATAATATATAGT
1 TTTTGAAAACATATATATAATATATAAT
3011705 TTTTGAAAACA
1 TTTTGAAAACA
3011716 CTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 27 0.77
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAAT
Found at i:3011848 original size:11 final size:11
Alignment explanation
Indices: 3011796--3011845 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
3011786 ATTATATTGG
3011796 TTTATTTATTA
1 TTTATTTATTA
*
3011807 TTTACTTATTA
1 TTTATTTATTA
* *
3011818 TTTA-ATATCTT
1 TTTATTTAT-TA
3011829 TTTATTT-TTA
1 TTTATTTATTA
3011839 TTTATTT
1 TTTATTT
3011846 TTTGTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 11 0.34
11 20 0.62
12 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:3020376 original size:32 final size:32
Alignment explanation
Indices: 3020306--3020387 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 32
3020296 GGAATTACTT
** *
3020306 TACATTATCTAAATGTGACACTAACACTATTT
1 TACATTATCTAAATGCAACACTAACACTATTG
* * *
3020338 TACATTATCTAAATGCAACACTGACTCTGTTG
1 TACATTATCTAAATGCAACACTAACACTATTG
* * *
3020370 TGCATTATTTGAATGCAA
1 TACATTATCTAAATGCAA
3020388 TATTACTAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (32 bp):
TACATTATCTAAATGCAACACTAACACTATTG
Found at i:3023140 original size:47 final size:48
Alignment explanation
Indices: 3023089--3023180 Score: 109
Period size: 49 Copynumber: 1.9 Consensus size: 48
3023079 ATTTTCTATA
*
3023089 TTTC-TTATTA-T-TTTCGTTTTTATTCATTATTATTATATTATATTATT
1 TTTCTTTATTAGTCTTTCGTCTTTATT-ATTATT-TTATATTATATTATT
* *
3023136 TTTCTTTTTTTAGTCTTTTGTCTTTATTATTATTTTATATTATAT
1 TTTC-TTTATTAGTCTTTCGTCTTTATTATTATTTTATATTATAT
3023181 ATATATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
47 4 0.11
49 16 0.42
50 7 0.18
51 11 0.29
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.70
Consensus pattern (48 bp):
TTTCTTTATTAGTCTTTCGTCTTTATTATTATTTTATATTATATTATT
Found at i:3023344 original size:2 final size:2
Alignment explanation
Indices: 3023337--3023394 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3023327 ATTTATATGC
3023337 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
3023379 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3023395 TGTTCTACAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3034132 original size:20 final size:21
Alignment explanation
Indices: 3034094--3034137 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3034084 CCTAAATTGT
3034094 AAAAAGAAAAAGAAAAAGAGA
1 AAAAAGAAAAAGAAAAAGAGA
* *
3034115 AAAAAGAACAA-AAGAAGAGA
1 AAAAAGAAAAAGAAAAAGAGA
3034135 AAA
1 AAA
3034138 TAAGGGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAAGAGA
Found at i:3035070 original size:105 final size:105
Alignment explanation
Indices: 3034888--3035618 Score: 1327
Period size: 105 Copynumber: 7.0 Consensus size: 105
3034878 TACCCAGGGA
*
3034888 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
3034953 GGACCGCTGGTTGTCAACAAACATTTTTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
*
3034993 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3035058 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
*
3035098 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3035163 GGACCGTTGGTTGTCAATAAACATTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
*
3035203 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
3035268 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
* *
3035308 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3035373 GGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
3035413 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
3035478 GGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
*
3035518 CAATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
3035583 GGACCGCTGGTTGTCAACAAACATTTCCCAATTTCA
66 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCA
3035619 ACTTCACAAC
Statistics
Matches: 608, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 608 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGC
Found at i:3037372 original size:13 final size:13
Alignment explanation
Indices: 3037354--3037398 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3037344 CTTTAGTCTT
*
3037354 TATTATTATTTTA
1 TATTATTATTATA
3037367 TATTATTATTATA
1 TATTATTATTATA
3037380 TATATATATATATATA
1 TAT-TAT-TAT-TATA
3037396 TAT
1 TAT
3037399 ATCTAACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 15 0.54
14 3 0.11
15 3 0.11
16 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:3037383 original size:2 final size:2
Alignment explanation
Indices: 3037365--3037400 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3037355 ATTATTATTT
3037365 TA TA T- TA T- TA T- 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 TA TA T
3037401 CTAACCTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3037547 original size:2 final size:2
Alignment explanation
Indices: 3037540--3037575 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3037530 ATTTATATGC
3037540 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
3037576 TTGTTATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3041042 original size:20 final size:21
Alignment explanation
Indices: 3041005--3041043 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3040995 AAATTATTTT
3041005 TTAAATAATTTGTAAAAATAA
1 TTAAATAATTTGTAAAAATAA
3041026 TTAAATAATTT-TAAAAAT
1 TTAAATAATTTGTAAAAAT
3041044 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TTAAATAATTTGTAAAAATAA
Found at i:3043262 original size:17 final size:19
Alignment explanation
Indices: 3043226--3043264 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3043216 TAATATCTAT
3043226 TTATAGAGATAATTATTTGA
1 TTATAGAGATAA-TATTTGA
3043246 TTATAGAGA-AA-ATTTGA
1 TTATAGAGATAATATTTGA
3043263 TT
1 TT
3043265 TTGATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATAGAGATAATATTTGA
Found at i:3044253 original size:18 final size:18
Alignment explanation
Indices: 3044230--3044269 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3044220 CTTATATCAT
*
3044230 AAAAGAAATCGTTATGTG
1 AAAAGAAATCGTTAGGTG
*
3044248 AAAAGAAGTCGTTAGGTG
1 AAAAGAAATCGTTAGGTG
3044266 AAAA
1 AAAA
3044270 CTAGAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (18 bp):
AAAAGAAATCGTTAGGTG
Found at i:3045832 original size:27 final size:27
Alignment explanation
Indices: 3045788--3045839 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
3045778 ATTTTATGGC
*
3045788 ACGATCTAAAAAATATAAAAATAAAAA
1 ACGATCTAAAAAAGATAAAAATAAAAA
3045815 ACGAT-TAAAAAGAGATAAAAATAAA
1 ACGATCTAAAAA-AGATAAAAATAAA
3045840 TTAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (27 bp):
ACGATCTAAAAAAGATAAAAATAAAAA
Found at i:3049303 original size:18 final size:18
Alignment explanation
Indices: 3049280--3049315 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3049270 AGTTTTGCAG
* *
3049280 AGATTCTTGATGTGGCAA
1 AGATTCCTGAAGTGGCAA
3049298 AGATTCCTGAAGTGGCAA
1 AGATTCCTGAAGTGGCAA
3049316 CACGATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (18 bp):
AGATTCCTGAAGTGGCAA
Found at i:3049941 original size:20 final size:21
Alignment explanation
Indices: 3049916--3049958 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
3049906 TCATAAAATC
*
3049916 ATTTATGAGTA-CAAAATAAA
1 ATTTATCAGTATCAAAATAAA
3049936 ATTTATCAGTATTCAAAATAAA
1 ATTTATCAGTA-TCAAAATAAA
3049958 A
1 A
3049959 CAGATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTTATCAGTATCAAAATAAA
Found at i:3050574 original size:12 final size:12
Alignment explanation
Indices: 3050549--3050603 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
3050539 ACGGAGATAT
* *
3050549 CAGAAATCAAAA
1 CAGAATTCAGAA
3050561 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
3050573 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
3050585 CAGAAATCATAA
1 CAGAATTCAGAA
3050597 CAGAATT
1 CAGAATT
3050604 TAGGTCATGT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3050641 original size:24 final size:24
Alignment explanation
Indices: 3050561--3050643 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
3050551 GAAATCAAAA
* *
3050561 CAGAATTCAGAACAGAA-TCCAGAT
1 CAGAAATCAGAACAGAATTCAAG-T
* * *
3050585 CAGAAATCATAACAGAATTTAGGT
1 CAGAAATCAGAACAGAATTCAAGT
*
3050609 CATG-TATCAGAACAGAATTCAAGT
1 CA-GAAATCAGAACAGAATTCAAGT
*
3050633 TAGAAATCAGA
1 CAGAAATCAGA
3050644 TAAAATATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
23 1 0.02
24 41 0.91
25 3 0.07
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.22
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAAGT
Found at i:3053084 original size:18 final size:18
Alignment explanation
Indices: 3053063--3053137 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
3053053 GGTCAACTAC
3053063 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
* **
3053081 GGTCAACTGGTCAAGTCG
1 GGTCAACGGGTCGGGTCG
* * *
3053099 GGTCATCTGGTCGGGTCA
1 GGTCAACGGGTCGGGTCG
* *
3053117 GGTAAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
3053135 GGT
1 GGT
3053138 TGGAACCGGT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.15, C:0.19, G:0.44, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:3054114 original size:17 final size:17
Alignment explanation
Indices: 3054089--3054139 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
3054079 TTGTTAAAGG
*
3054089 ATAACTTAAACAAATTA
1 ATAATTTAAACAAATTA
3054106 ATAATTTAAA-ATTAATTA
1 ATAATTTAAACA--AATTA
3054124 ATAATTTAAACAAATT
1 ATAATTTAAACAAATT
3054140 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.03
17 13 0.43
18 15 0.50
19 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTTAAACAAATTA
Found at i:3054214 original size:27 final size:27
Alignment explanation
Indices: 3054178--3054236 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
3054168 TACTATTTAT
*
3054178 AAAAAGAAAATAGAGTTCGATTAACTA
1 AAAAAGAAAATAGAGTTCGACTAACTA
*
3054205 AAAAAGAAAATGGAGTTCGACTAACTA
1 AAAAAGAAAATAGAGTTCGACTAACTA
3054232 AAAAA
1 AAAAA
3054237 ATACAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (27 bp):
AAAAAGAAAATAGAGTTCGACTAACTA
Found at i:3057703 original size:4 final size:4
Alignment explanation
Indices: 3057694--3057808 Score: 63
Period size: 4 Copynumber: 27.8 Consensus size: 4
3057684 ATACCCCTTC
* ** * * *
3057694 AAAT AAAT AAAT AAA- ATAT TCA- AAAT AAAT AAAT AATT TATT CAAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT
* * ** *
3057742 AAAT GAAT ACAT AAAT AAAT AAATT ATTT GAAAT AAAT AAAT AATT CAAAGT
1 AAAT AAAT AAAT AAAT AAAT AAA-T AAAT -AAAT AAAT AAAT AAAT -AAA-T
3057794 AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAA
3057809 AATTACATCC
Statistics
Matches: 84, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
3 3 0.04
4 69 0.82
5 9 0.11
6 3 0.04
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:3057721 original size:22 final size:22
Alignment explanation
Indices: 3057694--3057750 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
3057684 ATACCCCTTC
3057694 AAATAAATAAATAAAATATTCA
1 AAATAAATAAATAAAATATTCA
**
3057716 AAATAAATAAATAATTTATTCA
1 AAATAAATAAATAAAATATTCA
*
3057738 AAATAAATGAATA
1 AAATAAATAAATA
3057751 CATAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAAATAAATAAAATATTCA
Found at i:3057759 original size:34 final size:34
Alignment explanation
Indices: 3057718--3057801 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
3057708 AATATTCAAA
* *
3057718 ATAAATAAATAATTTATTCAAAATAAATGAATAC
1 ATAAATAAATAAATTATTCAAAATAAATAAATAC
**
3057752 ATAAATAAATAAATTATTTGAAATAAATAAATA-
1 ATAAATAAATAAATTATTCAAAATAAATAAATAC
3057785 ATTCAAAGTAAATAAAT
1 A-T-AAA-TAAATAAAT
3057802 AAATAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 1 0.02
34 30 0.70
35 3 0.07
36 9 0.21
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (34 bp):
ATAAATAAATAAATTATTCAAAATAAATAAATAC
Found at i:3057798 original size:56 final size:56
Alignment explanation
Indices: 3057696--3057806 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
3057686 ACCCCTTCAA
* ** *
3057696 ATAAATAAATAAAATATTCAAAATAAATAAATAATTTATTCAAAATAAATGAATAC
1 ATAAATAAATAAAATATTCAAAATAAATAAATAATTCAAACAAAATAAATAAATAC
* ** **
3057752 ATAAATAAATAAATTATTTGAAATAAATAAATAATTCAAAGTAAATAAATAAATA
1 ATAAATAAATAAAATATTCAAAATAAATAAATAATTCAAACAAAATAAATAAATA
3057807 AAAATTACAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (56 bp):
ATAAATAAATAAAATATTCAAAATAAATAAATAATTCAAACAAAATAAATAAATAC
Found at i:3057801 original size:18 final size:18
Alignment explanation
Indices: 3057698--3057803 Score: 90
Period size: 18 Copynumber: 5.8 Consensus size: 18
3057688 CCCTTCAAAT
3057698 AAATAAATAAA-ATATTCA
1 AAATAAATAAATA-ATTCA
*
3057716 AAATAAATAAATAATTTA
1 AAATAAATAAATAATTCA
** *
3057734 TTCA-AAATAAATGAATACA
1 -AAATAAATAAAT-AATTCA
* **
3057753 TAAATAAATAAATTATTTG
1 -AAATAAATAAATAATTCA
3057772 AAATAAATAAATAATTCA
1 AAATAAATAAATAATTCA
*
3057790 AAGTAAATAAATAA
1 AAATAAATAAATAA
3057804 ATAAAAATTA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
18 51 0.74
19 10 0.14
20 8 0.12
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATAAATAAATAATTCA
Found at i:3060546 original size:28 final size:29
Alignment explanation
Indices: 3060504--3060561 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
3060494 GTATCATCTA
3060504 TGAAATCCCATTTAAGCCGATCATAGGCT
1 TGAAATCCCATTTAAGCCGATCATAGGCT
*
3060533 TGAAAT-CCATTTAATCCGATCATAGGCT
1 TGAAATCCCATTTAAGCCGATCATAGGCT
3060561 T
1 T
3060562 TCTCCAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (29 bp):
TGAAATCCCATTTAAGCCGATCATAGGCT
Found at i:3070335 original size:24 final size:24
Alignment explanation
Indices: 3070308--3070363 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
3070298 TTATGAATTA
3070308 TATTTATTATTTATGATACTTCAG
1 TATTTATTATTTATGATACTTCAG
3070332 TATTTATTATTTATGATACTTCAG
1 TATTTATTATTTATGATACTTCAG
*
3070356 GATTTATT
1 TATTTATT
3070364 TTGTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (24 bp):
TATTTATTATTTATGATACTTCAG
Found at i:3077350 original size:10 final size:10
Alignment explanation
Indices: 3077335--3077383 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 10
3077325 AACATAAATG
3077335 AACGAACATA
1 AACGAACATA
3077345 AACGAACATAA
1 AACGAACAT-A
3077356 CCTAACGAACATA
1 ---AACGAACATA
3077369 AACGAACATA
1 AACGAACATA
3077379 AACGA
1 AACGA
3077384 GATCTATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 24 0.69
11 1 0.03
13 1 0.03
14 9 0.26
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:3080948 original size:18 final size:16
Alignment explanation
Indices: 3080909--3080940 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3080899 TACAAAATCT
3080909 AATAATTCATAATATA
1 AATAATTCATAATATA
*
3080925 AATAATTCATTATATA
1 AATAATTCATAATATA
3080941 TATATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:3081382 original size:23 final size:23
Alignment explanation
Indices: 3081356--3081403 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3081346 ATAAAGTACA
*
3081356 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
3081379 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
3081402 AT
1 AT
3081404 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:3081842 original size:23 final size:22
Alignment explanation
Indices: 3081781--3081851 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
3081771 ACACTTTACA
*
3081781 ATATAACCATTACCTA-TACATT
1 ATATAACGA-TACCTATTACATT
3081803 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
3081825 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
3081848 ATAT
1 ATAT
3081852 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 6 0.14
22 20 0.47
23 17 0.40
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:3082270 original size:23 final size:22
Alignment explanation
Indices: 3082208--3082279 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
3082198 ACACTTTACA
*
3082208 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
3082231 ATATAACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
3082253 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
3082276 ATAT
1 ATAT
3082280 GTTTACCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:3082308 original size:428 final size:423
Alignment explanation
Indices: 3081515--3082376 Score: 1647
Period size: 428 Copynumber: 2.0 Consensus size: 423
3081505 GGATCGATAC
3081515 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
3081580 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTA
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTA
3081645 ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
131 ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
3081710 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
196 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
3081775 TTTACAATATAACCATTACCTATACATTATATAACGATACCTATTACATTATATAAGGGCTACCT
261 TTTACAATATAACCATTACCTATACATTATATAACGATACCTATTACATTATATAAGGGCTACCT
3081840 ATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACT
326 ATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-
3081904 TTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
390 TTTTTT-AAACTTATGTAATTTATGTTTCAATTTT
3081939 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
3082004 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAA-TT--TAATAATATATACC
3082069 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
128 GTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
3082134 AAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGATAG
192 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
3082198 ACACTTTACAATATAACCATTACCTATTACATTATATAACGATACCTATTACATTATATAAGGGC
257 ACACTTTACAATATAACCATTACCTA-TACATTATATAACGATACCTATTACATTATATAAGGGC
3082263 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
321 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
3082328 ATACTTTTTTAAACTTATGTAATTTATGTTTCAATTTT
386 ATACTTTTTTAAACTTATGTAATTTATGTTTCAATTTT
3082366 TTTAACAGTGT
1 TTTAACAGTGT
3082377 ACTGCGAATT
Statistics
Matches: 432, Mismatches: 0, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
424 111 0.26
425 2 0.00
427 118 0.27
428 180 0.42
429 21 0.05
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (423 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATACCGTA
ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
TTTACAATATAACCATTACCTATACATTATATAACGATACCTATTACATTATATAAGGGCTACCT
ATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACT
TTTTTAAACTTATGTAATTTATGTTTCAATTTT
Found at i:3085415 original size:184 final size:184
Alignment explanation
Indices: 3084834--3085504 Score: 1281
Period size: 184 Copynumber: 3.7 Consensus size: 184
3084824 TTTTAAATGG
*
3084834 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
3084899 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
3084964 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
3085018 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
3085083 TAAGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
3085147 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
*
3085201 TATGGACATAAAGTACCGACACAATATTAAAACGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
3085266 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
3085331 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
3085385 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
3085450 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
3085505 ATGTTGAAAG
Statistics
Matches: 479, Mismatches: 7, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
183 182 0.38
184 297 0.62
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:3085812 original size:200 final size:199
Alignment explanation
Indices: 3085586--3086019 Score: 787
Period size: 200 Copynumber: 2.2 Consensus size: 199
3085576 ATATTTTTTT
3085586 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
1 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
*
3085651 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
66 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
* ***
3085716 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
131 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TAAAAATTCATTC
*
3085781 TGGGA
195 TGGAA
3085786 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
1 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
3085851 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
66 GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
*
3085916 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCT
131 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCT
3085981 GGAA
196 GGAA
*
3085985 AAAAAATATCGACACAAACTATATTAGTATCGACA
1 AAAAAATATCGACACAAACTATATTAGTGTCGACA
3086020 TGACCCTTAA
Statistics
Matches: 226, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
199 48 0.21
200 178 0.79
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (199 bp):
AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
GGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCT
GGAA
Found at i:3086126 original size:37 final size:38
Alignment explanation
Indices: 3086085--3086160 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
3086075 TCTCATTCAT
*
3086085 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
3086122 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
3086160 A
1 A
3086161 TTAACTCGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 6 0.19
38 26 0.81
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:3086128 original size:19 final size:19
Alignment explanation
Indices: 3086101--3086160 Score: 102
Period size: 19 Copynumber: 3.2 Consensus size: 19
3086091 ATTCACATAA
*
3086101 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
3086120 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
3086139 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
3086158 AAA
1 AAA
3086161 TTAACTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:3087993 original size:33 final size:33
Alignment explanation
Indices: 3087956--3088021 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3087946 CATCTTAATA
*
3087956 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
3087989 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
3088022 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:3090170 original size:24 final size:24
Alignment explanation
Indices: 3090133--3090185 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3090123 CCGTTCTATC
3090133 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
3090157 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
3090181 TATTT
1 TATTT
3090186 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:3090376 original size:20 final size:19
Alignment explanation
Indices: 3090330--3090376 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3090320 TCCGGTATCA
*
3090330 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
3090349 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
3090370 TTTTACC
1 TTTTACC
3090377 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:3090541 original size:20 final size:20
Alignment explanation
Indices: 3090493--3090542 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3090483 TCGACACTTT
3090493 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
3090513 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
3090533 TAATTTTACC
1 TAATTTTACC
3090543 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:3091533 original size:14 final size:15
Alignment explanation
Indices: 3091510--3091550 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3091500 TTTTGTTACG
*
3091510 AATAATATAAATAA-
1 AATAAAATAAATAAT
3091524 AATAAAATAAATAATT
1 AATAAAATAAATAA-T
3091540 AATAAAA-AAAT
1 AATAAAATAAAT
3091551 TGAATCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 4 0.17
16 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAATAAATAAT
Found at i:3092188 original size:17 final size:17
Alignment explanation
Indices: 3092154--3092205 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3092144 ACCGGACAAA
*
3092154 TTTATTATTTTAGAGAG
1 TTTATTAATTTAGAGAG
**
3092171 TTTATTAATTTATCGAG
1 TTTATTAATTTAGAGAG
*
3092188 --TATTAATTTAAAGAG
1 TTTATTAATTTAGAGAG
3092203 TTT
1 TTT
3092206 CTACTGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTAGAGAG
Found at i:3092581 original size:5 final size:5
Alignment explanation
Indices: 3092569--3092697 Score: 204
Period size: 5 Copynumber: 25.8 Consensus size: 5
3092559 AAAAGAATCA
* * * * * *
3092569 ATAGT ACAGT ACAGT ACAGT ACAGT ATAAT ACAGT ATAGT ATAGT ATAGT
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
3092619 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
3092669 ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
1 ATAGT ATAGT ATAGT ATAGT ATAGT ATAG
3092698 GAACTAATAT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 118 1.00
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (5 bp):
ATAGT
Found at i:3094664 original size:36 final size:37
Alignment explanation
Indices: 3094611--3094682 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
3094601 GTCCTACTAT
3094611 GATTCAAACTCTCAAAAAT-AGTATAGAATTATGCTAG
1 GATTCAAACTCTCAAAAATAAG-ATAGAATTATGCTAG
*
3094648 GATTC-AACTC-CTAAAAATAAGATAGAATTTTGCTA
1 GATTCAAACTCTC-AAAAATAAGATAGAATTATGCTA
3094683 TGTTTTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 1 0.03
36 24 0.75
37 7 0.22
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
GATTCAAACTCTCAAAAATAAGATAGAATTATGCTAG
Found at i:3095248 original size:25 final size:25
Alignment explanation
Indices: 3095186--3095299 Score: 69
Period size: 25 Copynumber: 4.6 Consensus size: 25
3095176 TAAAGTTATC
3095186 ATATATATATATTTATAACTATTATA-TT
1 ATATA-ATATATTT-T-ACTATTA-ACTT
*
3095214 -TATTAT-TATTTTACTATTAACTT
1 ATATAATATATTTTACTATTAACTT
* * **
3095237 ATATAATATATTTTTCTCTTTTGC-T
1 ATATAATATATTTTACT-ATTAACTT
* *
3095262 ACTATTAT-TATTTTACTATTAACGT
1 A-TATAATATATTTTACTATTAACTT
3095287 ATATAA-ATATTTT
1 ATATAATATATTTT
3095300 TCTCTTTTGC
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
22 1 0.01
23 9 0.13
24 19 0.28
25 25 0.37
26 10 0.15
27 3 0.04
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATAATATATTTTACTATTAACTT
Found at i:3095316 original size:49 final size:50
Alignment explanation
Indices: 3095214--3095321 Score: 200
Period size: 49 Copynumber: 2.2 Consensus size: 50
3095204 CTATTATATT
*
3095214 TATTATTATTTTACTATTAACTTATATAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAATATATTTTTCTCTTTTGCTAC
3095264 TATTATTATTTTACTATTAACGTATATAA-ATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACGTATATAATATATTTTTCTCTTTTGCTAC
3095313 TATTATTAT
1 TATTATTAT
3095322 CATTATATGT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 29 0.51
50 28 0.49
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (50 bp):
TATTATTATTTTACTATTAACGTATATAATATATTTTTCTCTTTTGCTAC
Found at i:3095467 original size:16 final size:16
Alignment explanation
Indices: 3095446--3095479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3095436 CATGTATTTA
3095446 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
3095462 TATTATTTTACTTTAT
1 TATTATATTACATTAT
3095478 TA
1 TA
3095480 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:3098828 original size:8 final size:8
Alignment explanation
Indices: 3098817--3098886 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
3098807 CAAAAAGGGC
3098817 AAAAAGAA
1 AAAAAGAA
3098825 AAAAAGAA
1 AAAAAGAA
* *
3098833 AAGAAGCA
1 AAAAAGAA
*
3098841 AAAAAGGA
1 AAAAAGAA
*
3098849 AAAAACAA
1 AAAAAGAA
3098857 GAACAAA-AA
1 -AA-AAAGAA
*
3098866 AGAAAGAA
1 AAAAAGAA
*
3098874 CAAAAATAA
1 -AAAAAGAA
3098883 AAAA
1 AAAA
3098887 GGGAACAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
7 3 0.06
8 33 0.67
9 10 0.20
10 3 0.06
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3098851 original size:22 final size:21
Alignment explanation
Indices: 3098833--3098888 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3098823 AAAAAAAGAA
3098833 AAGAAGCAAAAAAGGAAAAAAC
1 AAGAA-CAAAAAAGGAAAAAAC
*
3098855 AAGAACAAAAAA-GAAAGAAC
1 AAGAACAAAAAAGGAAAAAAC
* *
3098875 AAAAATAAAAAAGG
1 AAGAACAAAAAAGG
3098889 GAACAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 8 0.27
22 5 0.17
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (21 bp):
AAGAACAAAAAAGGAAAAAAC
Found at i:3100434 original size:36 final size:36
Alignment explanation
Indices: 3100384--3100488 Score: 156
Period size: 37 Copynumber: 2.9 Consensus size: 36
3100374 GTGCTCACCA
*
3100384 TTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
3100420 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
3100457 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
3100489 TAAACATTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 31 0.49
37 32 0.51
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:3100582 original size:102 final size:102
Alignment explanation
Indices: 3100402--3100793 Score: 660
Period size: 102 Copynumber: 3.9 Consensus size: 102
3100392 CTTGAGACAG
** * * *
3100402 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3100467 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
3100504 TTTTCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
3100569 CGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
3100606 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3100671 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
3100708 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3100772 TGAGACAGTTTCTCTTAAAACA
66 TGAGACAGTTTCTCTTGAAACA
3100794 CAAAACCTTT
Statistics
Matches: 273, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
101 35 0.13
102 238 0.87
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3100673 original size:37 final size:37
Alignment explanation
Indices: 3100606--3100692 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
3100596 ATTGGAAACA
** * *
3100606 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3100642 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3100679 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
3100693 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3100752 original size:204 final size:203
Alignment explanation
Indices: 3100402--3100860 Score: 684
Period size: 204 Copynumber: 2.2 Consensus size: 203
3100392 CTTGAGACAG
*
3100402 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * *
3100467 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTGAAATGAGTTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
* * *
3100532 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTCGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTCGAGACAGTTTCTCTTAAAACATAAACA
3100597 TTGGAAACA
195 TTGGAAACA
** * *
3100606 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
3100671 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
* * *
3100736 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTAAAACA-TAAACA
* ***
3100801 TTTGAGATTG
195 TTGGA-AACA
* * * * *
3100811 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
3100861 CAAAATCTTT
Statistics
Matches: 228, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 34 0.15
204 150 0.66
205 44 0.19
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTAAAACATAAACAT
TGGAAACA
Found at i:3100754 original size:36 final size:36
Alignment explanation
Indices: 3100707--3100776 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3100697 CATTGAAAAC
** *
3100707 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
3100743 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
3100777 CAGTTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
Found at i:3100793 original size:36 final size:36
Alignment explanation
Indices: 3100707--3100793 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
3100697 CATTGAAAAC
* ** * *
3100707 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACA
*
3100743 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACA
* *
3100779 GTTTCTCTTAAAACA
1 ATTTCCCTTAAAACA
3100794 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (36 bp):
ATTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACA
Found at i:3100884 original size:67 final size:67
Alignment explanation
Indices: 3100735--3100893 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
3100725 TTTGTCTCTC
** *
3100735 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTAAAACACAAAAC
3100800 CT
66 CT
* * *
3100802 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTAAAACACAAAAC
3100867 CT
66 CT
*
3100869 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
3100894 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTAAAACACAAAAC
CT
Found at i:3101662 original size:109 final size:109
Alignment explanation
Indices: 3101472--3101942 Score: 603
Period size: 109 Copynumber: 4.4 Consensus size: 109
3101462 TAGCTAGAGT
* * * *
3101472 CAAGTTCAACTTCACAACGAAGGGACGTCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
3101536 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* *
3101580 CAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
*
3101645 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGAAAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * ** * **
3101689 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-C
* *
3101753 GATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
65 GATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * * ** * * * *
3101798 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
* * * *
3101863 ATTTCAACTTCAC-AGCGAAGGATAT--TG-AACTCGAGACAACA
66 ATTTCAACTCCACGA-CGGAGGATATCGTGCTACCCGAGACAACA
* *
3101904 CAAGTTCAACTTCACAACGAAGGGACGTCTGATTGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA
3101943 TAAGATTTCG
Statistics
Matches: 320, Mismatches: 39, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
106 48 0.15
107 2 0.01
108 39 0.12
109 230 0.72
110 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (109 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
Found at i:3101940 original size:106 final size:108
Alignment explanation
Indices: 3101472--3102093 Score: 569
Period size: 109 Copynumber: 5.8 Consensus size: 108
3101462 TAGCTAGAGT
* * * *
3101472 CAAGTTCAACTTCACAACGAAGGGACGTCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* *
3101536 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
66 ATTTCAACTCCACGACGGAGGATATC-TGCAACTCGAGACAACA
* * * * *
3101580 CAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* * *
3101645 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGAAAACA
66 ATTTCAACTCCACGACGGAGGATATC-TGCAACTCGAGACAACA
* ** * * **
3101689 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTT-TCAGTTTCA-TCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCAATTTCAGAAC-
* *
3101752 CGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
64 CAATTTCAACTCCACGACGGAGGATATC-TGCAACTCGAGACAACA
* * * * * *
3101798 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* *
3101863 ATTTCAACTTCAC-AGCGAAGGATAT-TG-AACTCGAGACAACA
66 ATTTCAACTCCACGA-CGGAGGATATCTGCAACTCGAGACAACA
* * * * * **
3101904 CAAGTTCAACTTCACAACGAAGGGACGTCTGATTGTCAA-TAA-GATTT--C--GTTCAGAGTCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* * * *
3101963 ATTTCAACTTCAC-AGCGAAAGATAT-T--AGACTCGAGACAGCA
66 ATTTCAACTCCACGA-CGGAGGATATCTGCA-ACTCGAGACAACA
* * ** * ** *
3102004 CAAGCTCAACTTCACAGCGAATGGG-CGGCTGACTGTCATCAAACAATTTCCCGGTTCCAGAACC
1 CAAGTTCAACTTCACAACGAA-GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACC
*
3102068 AATTTCAACTTCAC-AGCGGAGGATAT
65 AATTTCAACTCCACGA-CGGAGGATAT
3102094 TGGACTCGGA
Statistics
Matches: 441, Mismatches: 59, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
99 1 0.00
100 76 0.17
101 5 0.01
102 4 0.01
104 4 0.01
105 2 0.00
106 78 0.18
107 2 0.00
108 42 0.10
109 224 0.51
110 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (108 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
ATTTCAACTCCACGACGGAGGATATCTGCAACTCGAGACAACA
Found at i:3102660 original size:37 final size:36
Alignment explanation
Indices: 3102562--3102662 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
3102552 TTTCGTCCTA
3102562 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
* *
3102599 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** *
3102635 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
3102663 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.46
37 30 0.54
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:3103397 original size:21 final size:22
Alignment explanation
Indices: 3103373--3103423 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3103363 ATATTACATT
*
3103373 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
3103394 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
3103416 TTTATTAT
1 ATTATTAT
3103424 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:3116386 original size:2 final size:2
Alignment explanation
Indices: 3116375--3116409 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3116365 AATCACTTTC
3116375 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3116410 GAAGCGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3119178 original size:2 final size:2
Alignment explanation
Indices: 3119171--3119269 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
3119161 GACTTAACTT
3119171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3119213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3119255 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3119270 GTTTTGGATA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3121481 original size:21 final size:21
Alignment explanation
Indices: 3121397--3121474 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
3121387 CAAATCGAAA
* *
3121397 AGGGTGTACCGGTACGCTGGC
1 AGGGTGTACCAGTACACTGGC
* *
3121418 ATGGTGTACCGGTACACTGGC
1 AGGGTGTACCAGTACACTGGC
3121439 AGGGTGTACCAGTACACTGGC
1 AGGGTGTACCAGTACACTGGC
*
3121460 AGTGTGTACCAGTAC
1 AGGGTGTACCAGTAC
3121475 TCAGGCACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.22
Consensus pattern (21 bp):
AGGGTGTACCAGTACACTGGC
Found at i:3124763 original size:17 final size:17
Alignment explanation
Indices: 3124741--3124784 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
3124731 AAACGATCGA
3124741 TTTTTCATTCTTTTTCT
1 TTTTTCATTCTTTTTCT
3124758 TTTTTCATTCTTTTTCT
1 TTTTTCATTCTTTTTCT
3124775 TTTTTCATTC
1 TTTTTCATTC
3124785 GAACGAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATTCTTTTTCT
Found at i:3127650 original size:5 final size:5
Alignment explanation
Indices: 3127640--3127761 Score: 70
Period size: 5 Copynumber: 23.8 Consensus size: 5
3127630 TGTTCAAAGA
* * * *
3127640 AAAAT AAAAT AAAAT -TAAT CAAAAT AAAAT -AAAT AGAAT GAAACT AAAGT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
**** *
3127690 TTTCT AAAAAT AAAAT GAAAAT AAAAT AAAAT AAAACG AAAAT AAAAT
1 AAAAT A-AAAT AAAAT -AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
* *
3127738 AAAAT GAAATT AAAA- AAAAC AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAA
3127762 ATTATAATGA
Statistics
Matches: 90, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
4 11 0.12
5 58 0.64
6 21 0.23
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3127715 original size:16 final size:16
Alignment explanation
Indices: 3127696--3127756 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
3127686 AAGTTTTCTA
3127696 AAAATAAAATGAAAAT-
1 AAAATAAAAT-AAAATG
*
3127712 AAAATAAAATAAAACG
1 AAAATAAAATAAAATG
3127728 AAAATAAAATAAAATG
1 AAAATAAAATAAAATG
*
3127744 AAATTAAAA-AAAA
1 AAAATAAAATAAAA
3127757 CAAAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.20
16 33 0.80
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAAATG
Found at i:3127721 original size:21 final size:21
Alignment explanation
Indices: 3127696--3127761 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
3127686 AAGTTTTCTA
3127696 AAAATAAAATGAAAATAAAAT
1 AAAATAAAATGAAAATAAAAT
*
3127717 AAAATAAAACGAAAATAAAAT
1 AAAATAAAATGAAAATAAAAT
* * *
3127738 AAAATGAAATTAAAA-AAAAC
1 AAAATAAAATGAAAATAAAAT
3127758 AAAA
1 AAAA
3127762 ATTATAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 8 0.20
21 32 0.80
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAATAAAATGAAAATAAAAT
Found at i:3139955 original size:309 final size:309
Alignment explanation
Indices: 3139390--3140007 Score: 1182
Period size: 309 Copynumber: 2.0 Consensus size: 309
3139380 TCACGTCGGA
*
3139390 TACTACAATAACAATTCCTCGCTGTCGACTCAGATTTGTTTCAACAATAACTGATTTCGATCTCC
1 TACTACAATAACAATTCCTCGCTGTCGACTCAGATTTGTTTCAACAATAACTGATTCCGATCTCC
3139455 GTTTCCTCTTAGCAAATAATTTTGCTAAGTGTGTTCTCAGGAAGTTGAATGTGCTTCAATAAGCC
66 GTTTCCTCTTAGCAAATAATTTTGCTAAGTGTGTTCTCAGGAAGTTGAATGTGCTTCAATAAGCC
3139520 AATCATTCTTCTAACGTTAACCATAACAATATCCAGACCAATGTTGAAAATCGTTTTGATTTGAA
131 AATCATTCTTCTAACGTTAACCATAACAATATCCAGACCAATGTTGAAAATCGTTTTGATTTGAA
*
3139585 AAATAAACCCATAAAACAAAGAGAAAAATCCGAAGCGATTTAAGTACCTTACAATTCTCACGTTT
196 AAATAAACCAATAAAACAAAGAGAAAAATCCGAAGCGATTTAAGTACCTTACAATTCTCACGTTT
3139650 GGAATTGAGCCTTCGCTTTAGCCCTCGGCTTAAAAGAAATTTAGGTAAG
261 GGAATTGAGCCTTCGCTTTAGCCCTCGGCTTAAAAGAAATTTAGGTAAG
* *
3139699 TACTATAATAACAATTCCTCGCTGTCGACTCGGATTTGTTTCAACAATAACTGATTCCGATCTCC
1 TACTACAATAACAATTCCTCGCTGTCGACTCAGATTTGTTTCAACAATAACTGATTCCGATCTCC
3139764 GTTTCCTCTTAGCAAATAATTTTGCTAAGTGTGTTCTCAGGAAGTTGAATGTGCTTCAATAAGCC
66 GTTTCCTCTTAGCAAATAATTTTGCTAAGTGTGTTCTCAGGAAGTTGAATGTGCTTCAATAAGCC
3139829 AATCATTCTTCTAACGTTAACCATAACAATATCCAGACCAATGTTGAAAATCGTTTTGATTTGAA
131 AATCATTCTTCTAACGTTAACCATAACAATATCCAGACCAATGTTGAAAATCGTTTTGATTTGAA
*
3139894 AAATAAACCAATAAAATAAAGAGAAAAATCCGAAGCGATTTAAGTACCTTACAATTCTCACGTTT
196 AAATAAACCAATAAAACAAAGAGAAAAATCCGAAGCGATTTAAGTACCTTACAATTCTCACGTTT
*
3139959 GGAATTGAGCCTTCGCTTTAGCCCTCGGCTTAAAAGAAATTTTGGTAAG
261 GGAATTGAGCCTTCGCTTTAGCCCTCGGCTTAAAAGAAATTTAGGTAAG
3140008 CATGATCAAA
Statistics
Matches: 303, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
309 303 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (309 bp):
TACTACAATAACAATTCCTCGCTGTCGACTCAGATTTGTTTCAACAATAACTGATTCCGATCTCC
GTTTCCTCTTAGCAAATAATTTTGCTAAGTGTGTTCTCAGGAAGTTGAATGTGCTTCAATAAGCC
AATCATTCTTCTAACGTTAACCATAACAATATCCAGACCAATGTTGAAAATCGTTTTGATTTGAA
AAATAAACCAATAAAACAAAGAGAAAAATCCGAAGCGATTTAAGTACCTTACAATTCTCACGTTT
GGAATTGAGCCTTCGCTTTAGCCCTCGGCTTAAAAGAAATTTAGGTAAG
Found at i:3140296 original size:12 final size:12
Alignment explanation
Indices: 3140279--3140306 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3140269 AGATAAAATA
3140279 AAATATTATCCT
1 AAATATTATCCT
3140291 AAATATTATCCT
1 AAATATTATCCT
3140303 AAAT
1 AAAT
3140307 CCTAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATTATCCT
Found at i:3144125 original size:85 final size:85
Alignment explanation
Indices: 3143974--3144137 Score: 267
Period size: 85 Copynumber: 1.9 Consensus size: 85
3143964 TAAAGCGTAC
* *
3143974 CGGTACGCTCATTAAAGTGGTACCAGTACACCACTCGTATCGATACCAAAATATATTATTGAAAT
1 CGGTACGCTCATTAAAGTGGTACCAGTACACCAATCGTATCGATACCAAAATATATCATTGAAAT
3144039 TCATAATAAACCCATCGAAT
66 TCATAATAAACCCATCGAAT
* * *
3144059 CGGTACGCTCATTAAATTGGTACCAGTACACCAATCGTATC-ATTACTAAAATATATCATTGTAA
1 CGGTACGCTCATTAAAGTGGTACCAGTACACCAATCGTATCGA-TACCAAAATATATCATTGAAA
3144123 TTCATAATAAACCCA
65 TTCATAATAAACCCA
3144138 CATTATTGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
84 1 0.01
85 72 0.99
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (85 bp):
CGGTACGCTCATTAAAGTGGTACCAGTACACCAATCGTATCGATACCAAAATATATCATTGAAAT
TCATAATAAACCCATCGAAT
Found at i:3145655 original size:5 final size:5
Alignment explanation
Indices: 3145645--3145694 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
3145635 ACGGTCAACA
* * *
3145645 GTCGG GTCGG GTCAACG GTTGG GTCGA GTCGG GTCGG GTCGG GTCGG GTC
1 GTCGG GTCGG GTC--GG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTC
3145695 AGCCCGGTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 34 0.92
7 3 0.08
ACGTcount: A:0.06, C:0.20, G:0.52, T:0.22
Consensus pattern (5 bp):
GTCGG
Found at i:3145657 original size:17 final size:17
Alignment explanation
Indices: 3145637--3145670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3145627 GGAAGTCAAC
3145637 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
* *
3145654 GGTCAACGGTTGGGTCG
1 GGTCAACAGTCGGGTCG
3145671 AGTCGGGTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3152967 original size:22 final size:22
Alignment explanation
Indices: 3152940--3152987 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
3152930 AACAGTCAAC
3152940 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3152962 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3152984 GGTC
1 GGTC
3152988 GGTCGGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3152993 original size:4 final size:5
Alignment explanation
Indices: 3152947--3152996 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
3152937 AACGGTCAAC
*
3152947 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
3152997 AGTCAGACCG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
7 4 0.10
ACGTcount: A:0.04, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:3153010 original size:9 final size:9
Alignment explanation
Indices: 3152998--3153065 Score: 73
Period size: 9 Copynumber: 7.1 Consensus size: 9
3152988 GGTCGGGTCA
*
3152998 GTCAGACCG
1 GTCAAACCG
3153007 GTCAAACCG
1 GTCAAACCG
*
3153016 GTTCGAACCG
1 G-TCAAACCG
3153026 GTCAAACCG
1 GTCAAACCG
*
3153035 GTCAAAACTG
1 GTC-AAACCG
3153045 GTTCAAAACCG
1 G-TC-AAACCG
3153056 GTCAAACCG
1 GTCAAACCG
3153065 G
1 G
3153066 GTTTCAGCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
9 26 0.51
10 16 0.31
11 9 0.18
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (9 bp):
GTCAAACCG
Found at i:3153068 original size:21 final size:21
Alignment explanation
Indices: 3153029--3153068 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3153019 CGAACCGGTC
*
3153029 AAACCGGTCAAAACTGGTTCA
1 AAACCGGTCAAAACGGGTTCA
*
3153050 AAACCGGTCAAACCGGGTT
1 AAACCGGTCAAAACGGGTT
3153069 TCAGCCACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
AAACCGGTCAAAACGGGTTCA
Found at i:3153873 original size:127 final size:126
Alignment explanation
Indices: 3153742--3153984 Score: 324
Period size: 127 Copynumber: 1.9 Consensus size: 126
3153732 CTAGGATGTC
* * *
3153742 CCACCACATCGATACAGACCACGTATCGATACCCTGAATATATACTGGATTATGACTAGACTTAT
1 CCACCACATCGATACAGACCACGTATCGATACCCTCAATATATACTGGATTATGACTAGAATTAC
** * * *
3153807 AGGGTATCAATATGCATTGAGTATCGGTACTCTCGATTGTTTGTTGGATTTTCAAGGCAGTT
66 AGGGTATCAATACACATTG-GTATAGATACTCTCGATTGTTTGTTGAATTTTCAAGGCAGTT
* * * * * *
3153869 CCACCATATCGATACAGATCACGTATCGATACCCTCATTTTATACTGGATTATGACTTGAATTGC
1 CCACCACATCGATACAGACCACGTATCGATACCCTCAATATATACTGGATTATGACTAGAATTAC
* * *
3153934 ATGGTATCAATACACATTGGTATAGATATTGTCGATTGTTTGTTGAATTTT
66 AGGGTATCAATACACATTGGTATAGATACTCTCGATTGTTTGTTGAATTTT
3153985 TAAGATCATC
Statistics
Matches: 99, Mismatches: 17, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
126 27 0.27
127 72 0.73
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (126 bp):
CCACCACATCGATACAGACCACGTATCGATACCCTCAATATATACTGGATTATGACTAGAATTAC
AGGGTATCAATACACATTGGTATAGATACTCTCGATTGTTTGTTGAATTTTCAAGGCAGTT
Found at i:3155675 original size:31 final size:31
Alignment explanation
Indices: 3155640--3155699 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3155630 AATTCGGTGA
*
3155640 ATTCAATATGTCCTTCTCACTAGGAACTCGC
1 ATTCAATATGTCATTCTCACTAGGAACTCGC
*
3155671 ATTCAATATGTCATTCTCATTAGGAACTC
1 ATTCAATATGTCATTCTCACTAGGAACTC
3155700 CCAAGCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCGC
Done.