Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 7 of 202
Found at i:2327186 original size:24 final size:22
Alignment explanation
Indices: 2327159--2327206 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2327149 AATATATTAT
*
2327159 TTTTTAATTTAATATTTGTATATA
1 TTTTTAA-TTAAAATTT-TATATA
*
2327183 TTTTTTATTAAAATTTTATATA
1 TTTTTAATTAAAATTTTATATA
2327205 TT
1 TT
2327207 GTCATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAATTAAAATTTTATATA
Found at i:2333076 original size:29 final size:28
Alignment explanation
Indices: 2333037--2333161 Score: 99
Period size: 29 Copynumber: 4.2 Consensus size: 28
2333027 GGTTGCTCAC
* *
2333037 ATAATGGCCAAACATTTCAAAATGGTCAT
1 ATAA-GGCCAAACATTTCAAAATGATCAA
*
2333066 ATAAGGCCCAAACATTTACAAAAGTGCTCAA
1 ATAAGG-CCAAACATTT-CAAAA-TGATCAA
* * *
2333097 ATGAAGGCCAAACCTTTCTAAATGATCAG
1 AT-AAGGCCAAACATTTCAAAATGATCAA
* *
2333126 ATAAAAGCCAAACCTTTTCAAAATG-TACAA
1 AT-AAGGCCAAA-CATTTCAAAATGAT-CAA
2333156 ATAAGG
1 ATAAGG
2333162 GTTAAACCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 33 0.42
30 23 0.29
31 16 0.21
32 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (28 bp):
ATAAGGCCAAACATTTCAAAATGATCAA
Found at i:2341017 original size:6 final size:6
Alignment explanation
Indices: 2341008--2341072 Score: 78
Period size: 6 Copynumber: 10.7 Consensus size: 6
2340998 AATAATAAAT
* *
2341008 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA-A TAAATA TAAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
*
2341055 TAAATA TAATAATA TTAA
1 TTAATA T--TAATA TTAA
2341073 ATAAAACAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 4 0.07
6 45 0.83
8 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
TTAATA
Found at i:2341018 original size:18 final size:17
Alignment explanation
Indices: 2340997--2341065 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
2340987 TAAAAAATTA
2340997 TAATAATAAATTTAATAT
1 TAAT-ATAAATTTAATAT
*
2341015 TAATATTAATATTAATAT
1 TAATATAAAT-TTAATAT
*
2341033 TAATATTAAA-TAAATAT
1 TAATA-TAAATTTAATAT
* *
2341050 AAATATAAATATAATA
1 TAATATAAATTTAATA
2341066 ATATTAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.10
17 19 0.45
18 16 0.38
19 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATAAATTTAATAT
Found at i:2341071 original size:31 final size:31
Alignment explanation
Indices: 2340999--2341077 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
2340989 AAAAATTATA
* * *
2340999 ATAATAA-ATTTAATATTAATATTAATATTAAT
1 ATAATAATA-TTAA-ATAAATATAAATATAAAT
2341031 AT--TAATATTAAATAAATATAAATATAAAT
1 ATAATAATATTAAATAAATATAAATATAAAT
2341060 ATAATAATATTAAATAAA
1 ATAATAATATTAAATAAA
2341078 ACAAAAATCC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.41
30 7 0.17
31 15 0.37
32 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAATAATATTAAATAAATATAAATATAAAT
Found at i:2342970 original size:30 final size:28
Alignment explanation
Indices: 2342903--2342972 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2342893 TCCTCATAAA
*
2342903 TTGAAAATTTAGTCTCTATACTTTTATT
1 TTGAAAATTTAATCTCTATACTTTTATT
* *
2342931 TCT-AGAAATTTAATCTCTTTATTTTTTATAT
1 T-TGA-AAATTTAATCTCTATA-CTTTTAT-T
2342962 TTGAAAATTTA
1 TTGAAAATTTA
2342973 TGTCTAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 14 0.41
31 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (28 bp):
TTGAAAATTTAATCTCTATACTTTTATT
Found at i:2346049 original size:20 final size:19
Alignment explanation
Indices: 2346024--2346076 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
2346014 TTCATTATAT
2346024 ATTTTTAGAATTTTTATGAA
1 ATTTTTAGAATTTTTATG-A
* *
2346044 ATTTTTATAATTTGTTTTGA
1 ATTTTTAGAATTT-TTATGA
2346064 A-TTTT-GAATTTTT
1 ATTTTTAGAATTTTT
2346077 GTAATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 4 0.14
20 14 0.48
21 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
ATTTTTAGAATTTTTATGA
Found at i:2351624 original size:2 final size:2
Alignment explanation
Indices: 2351617--2351650 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2351607 TTTGATCAAG
2351617 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
2351651 GCCAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2370163 original size:20 final size:20
Alignment explanation
Indices: 2370138--2370178 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2370128 ATTTTAATAA
2370138 ATGAAA-ATTAATATAAAAAT
1 ATGAAATATTAA-ATAAAAAT
*
2370158 ATGAAATATTAAATTAAAAT
1 ATGAAATATTAAATAAAAAT
2370178 A
1 A
2370179 ATATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
ATGAAATATTAAATAAAAAT
Found at i:2373304 original size:2 final size:2
Alignment explanation
Indices: 2373297--2373321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2373287 CAATCAATCA
2373297 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 A
2373322 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2373326 original size:2 final size:2
Alignment explanation
Indices: 2373321--2373351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2373311 ATATATATAT
2373321 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2373352 CTGCAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2377611 original size:4 final size:4
Alignment explanation
Indices: 2377602--2377626 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2377592 TTATTAGGAA
2377602 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
2377627 TACACTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2377668 original size:18 final size:18
Alignment explanation
Indices: 2377645--2377680 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2377635 AAGTCACTGG
2377645 CAATTATAACCATCCATC
1 CAATTATAACCATCCATC
2377663 CAATTATAACCATCCATC
1 CAATTATAACCATCCATC
2377681 AAGACAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (18 bp):
CAATTATAACCATCCATC
Found at i:2383957 original size:26 final size:26
Alignment explanation
Indices: 2383928--2383993 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
2383918 TATGTAAATA
*
2383928 TAATAAATATAATTATTGATTATATT
1 TAATAAATATAATTATTAATTATATT
* * *
2383954 TAATAACT-TAATTTAGTAATTATGTT
1 TAATAAATATAA-TTATTAATTATATT
2383980 T-AT-AATATAATTAT
1 TAATAAATATAATTAT
2383994 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
24 5 0.16
25 8 0.25
26 19 0.59
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (26 bp):
TAATAAATATAATTATTAATTATATT
Found at i:2386161 original size:23 final size:23
Alignment explanation
Indices: 2386134--2386178 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2386124 CTCGTTACAC
2386134 GGCTCTTCCTGAGCTTCCCGATA
1 GGCTCTTCCTGAGCTTCCCGATA
*
2386157 GGCTCTTCGTGAGCTTCCCGAT
1 GGCTCTTCCTGAGCTTCCCGAT
2386179 CAAATGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.33, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCTCTTCCTGAGCTTCCCGATA
Found at i:2389104 original size:15 final size:15
Alignment explanation
Indices: 2389084--2389115 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2389074 TATATATGAA
2389084 TCTTCATGTAAGAGT
1 TCTTCATGTAAGAGT
2389099 TCTTCATGTAAGAGT
1 TCTTCATGTAAGAGT
2389114 TC
1 TC
2389116 GCCGAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (15 bp):
TCTTCATGTAAGAGT
Found at i:2391387 original size:14 final size:14
Alignment explanation
Indices: 2391368--2391394 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2391358 TGAAATGAAA
2391368 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
2391382 TCGAGTTAAATTA
1 TCGAGTTAAATTA
2391395 AAATTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:2399009 original size:24 final size:24
Alignment explanation
Indices: 2398956--2399017 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2398946 CACAGCTCGA
* *
2398956 ATGAGCATCCCGTTATTATCTCTC
1 ATGAGCATCCCGTTATTAGCCCTC
*
2398980 ATGAGCATCCTGTTATTAGCCCTC
1 ATGAGCATCCCGTTATTAGCCCTC
*
2399004 -TCGAGCTTCCCGTT
1 AT-GAGCATCCCGTT
2399018 GTGTGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (24 bp):
ATGAGCATCCCGTTATTAGCCCTC
Found at i:2400514 original size:41 final size:41
Alignment explanation
Indices: 2400467--2400584 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
2400457 TGGCGCTAAC
* * *
2400467 AGAAAAACGTCGCAATAGGTAAAGCAGTAGCAGG-GTTTATG
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGC-GGCGTTTATG
* *
2400508 AGAAAAACGCCTCAAAAAGTCAAGCAGTAGCGGCGTTTATG
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTTTATG
* ** * * *
2400549 AAAAAAATACCGCAAAAGGT-AAGCAATAGTGGCGTT
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTT
2400585 CAAAAACGTC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.25
41 48 0.75
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (41 bp):
AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTTTATG
Found at i:2401058 original size:33 final size:33
Alignment explanation
Indices: 2401021--2401089 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2401011 TATCATGCAT
2401021 CATCCTGTTTTGTTTATATTTGCATATAATCAA
1 CATCCTGTTTTGTTTATATTTGCATATAATCAA
2401054 CATCCTGTTTTGTTTATATTTGCATATAATCAA
1 CATCCTGTTTTGTTTATATTTGCATATAATCAA
2401087 CAT
1 CAT
2401090 TCTTTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.48
Consensus pattern (33 bp):
CATCCTGTTTTGTTTATATTTGCATATAATCAA
Found at i:2402244 original size:92 final size:92
Alignment explanation
Indices: 2402087--2402277 Score: 301
Period size: 92 Copynumber: 2.1 Consensus size: 92
2402077 TTTGAACCTG
* * * * *
2402087 TTGAATCGGTAGAGGTACCAATCTAGAGAGAGGCATCAAACTTATTAACTTGCAAATTGGTACGA
1 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
*
2402152 GCTGGTAGAACTAGACTAAAAAACCGA
66 GCTGGTAGAACTAAACTAAAAAACCGA
* *
2402179 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTGACTTGCAAGCTGGTACGA
1 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
*
2402244 GCTGGTAGAACTAAACTAAAAAATCGA
66 GCTGGTAGAACTAAACTAAAAAACCGA
2402271 TTGAACC
1 TTGAACC
2402278 CAAATTTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (92 bp):
TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
GCTGGTAGAACTAAACTAAAAAACCGA
Found at i:2408658 original size:85 final size:85
Alignment explanation
Indices: 2408515--2408682 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 85
2408505 GTCACTTCAC
* *
2408515 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCTTTGGGCCTTCTTTAGACATGTTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2408580 AGCTTGAACAATGATAGACT
66 AGCTTGAACAATGATAGACT
* *
2408600 TTAATCGCTAAAACCTAGTACTTCTGTTTATGTCTGATCCCTTGGGCCTTCTTTAGACATGCTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2408665 AGCTTGAACAATGATAGA
66 AGCTTGAACAATGATAGA
2408683 ATTGGGCTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (85 bp):
TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
AGCTTGAACAATGATAGACT
Found at i:2415031 original size:17 final size:17
Alignment explanation
Indices: 2415009--2415072 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2414999 AATCTTAGAG
2415009 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
2415026 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
2415045 TTTTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
2415062 TTTTAATTGTA
1 TTCTAATTGTA
2415073 GCCTTTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 22 0.58
18 4 0.11
19 10 0.26
20 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:2415052 original size:36 final size:36
Alignment explanation
Indices: 2415001--2415071 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2414991 GATTATGTAA
2415001 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
2415037 TCTTAGAGTTTTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
2415072 AGCCTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:2415340 original size:48 final size:48
Alignment explanation
Indices: 2415265--2415359 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
2415255 TGAAGGAATT
2415265 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
*
2415313 CTGTTGAATCATTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTT
2415360 AAGCAAAGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
Found at i:2415926 original size:21 final size:21
Alignment explanation
Indices: 2415900--2415952 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2415890 AACAGTGGCA
* *
2415900 GTGAGATTAGTTATTGTAACG
1 GTGAGATTAGATACTGTAACG
* *
2415921 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAACG
2415942 GTGAGATTAGA
1 GTGAGATTAGA
2415953 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAACG
Found at i:2419530 original size:30 final size:30
Alignment explanation
Indices: 2419462--2419610 Score: 255
Period size: 30 Copynumber: 4.9 Consensus size: 30
2419452 GAATATAAAC
2419462 TATA-TTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
2419491 TATATTTTTTTTATTTTTAAAATACACTACA
1 TATA-TTTTTTTATTTTTAAAATACACTACA
*
2419522 TATATTTTTTTATTTTTGAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
2419552 TATATTTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
*
2419582 TATATTTTTTTTATTTTTAAAATAAACTA
1 TATA-TTTTTTTATTTTTAAAATACACTA
2419611 ATACAGTGCA
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
29 4 0.04
30 58 0.51
31 52 0.46
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (30 bp):
TATATTTTTTTATTTTTAAAATACACTACA
Found at i:2419556 original size:61 final size:60
Alignment explanation
Indices: 2419462--2419610 Score: 255
Period size: 61 Copynumber: 2.5 Consensus size: 60
2419452 GAATATAAAC
2419462 TATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACATATA-TTTTTTTATTTTTAAAATACACTACA
*
2419522 TATATTTTTTTATTTTTGAAATACACTACATATATTTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACA
*
2419582 TATATTTTTTTTATTTTTAAAATAAACTA
1 TATA-TTTTTTTATTTTTAAAATACACTA
2419611 ATACAGTGCA
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
60 34 0.40
61 50 0.60
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (60 bp):
TATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACA
Found at i:2422135 original size:22 final size:21
Alignment explanation
Indices: 2422110--2422175 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2422100 CCAAGAACAA
2422110 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAAAGA-GGGAGAAACC
* * *
2422132 AGCAAAAACGAAGGACAAACC
1 AGCAAAAAAGAGGGAGAAACC
*
2422153 AGCAAGAACA-AGGGAGAAACC
1 AGCAA-AAAAGAGGGAGAAACC
2422174 AG
1 AG
2422176 TATGGGTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.55, C:0.18, G:0.27, T:0.00
Consensus pattern (21 bp):
AGCAAAAAAGAGGGAGAAACC
Found at i:2422698 original size:24 final size:24
Alignment explanation
Indices: 2422645--2422700 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2422635 ATGTATATGC
* *
2422645 AATTTAATATTTTTTATTCTTTAT
1 AATTTAATATTATTTATTATTTAT
*
2422669 ATTTTAATATTATTTATTA-TTAT
1 AATTTAATATTATTTATTATTTAT
2422692 AAATTTAAT
1 -AATTTAAT
2422701 TTTTATGTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTAATATTATTTATTATTTAT
Found at i:2423168 original size:22 final size:21
Alignment explanation
Indices: 2423124--2423168 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2423114 CATGTAATTC
*
2423124 ATAAAAAATTAAAATAAATAA
1 ATAAAAAATTAAAATAAACAA
* *
2423145 ATAAAAATTTAAAAATCAACAA
1 ATAAAAAATT-AAAATAAACAA
2423167 AT
1 AT
2423169 TCCAAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAAAAATTAAAATAAACAA
Found at i:2429965 original size:83 final size:83
Alignment explanation
Indices: 2429834--2430019 Score: 259
Period size: 83 Copynumber: 2.2 Consensus size: 83
2429824 CTATATGCAT
* * * *
2429834 AGTACAAG-ACTAGTAATTTAGTTTAATCAAATGGATTTAAGCATTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTA-AAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACT
* *
2429898 AAAATTTCAAATTTTGAAA
65 AAAATTTAAAAATTTGAAA
* *
2429917 AGTAGAGGAACTAAAATTGAGTTTAATCAAACGGATTTAA-CTACTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGC-ACTACTATTTTGGGTTAGGACT
2429981 AAAATTTAAAAATTTGAAA
65 AAAATTTAAAAATTTGAAA
*
2430000 AGTACAATAACTAAAATTGA
1 AGTACAAGAACTAAAATTGA
2430020 CTATTTCGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 85 0.94
84 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (83 bp):
AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACTA
AAATTTAAAAATTTGAAA
Found at i:2443140 original size:24 final size:25
Alignment explanation
Indices: 2443111--2443160 Score: 79
Period size: 22 Copynumber: 2.1 Consensus size: 25
2443101 TTCTTATGAA
2443111 TATTTTTTTA--TTTTGAAT-TTTT
1 TATTTTTTTATTTTTTGAATATTTT
2443133 TATTTTTTTATTTTTTGAATATTTT
1 TATTTTTTTATTTTTTGAATATTTT
2443158 TAT
1 TAT
2443161 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.40
24 8 0.32
25 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (25 bp):
TATTTTTTTATTTTTTGAATATTTT
Found at i:2443155 original size:19 final size:20
Alignment explanation
Indices: 2443132--2443179 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2443122 TTTGAATTTT
* *
2443132 TTATTTTTTTATTTTTTGAA
1 TTATTTTTTTAATTTTTAAA
*
2443152 -TATTTTTATAATTTTTAAA
1 TTATTTTTTTAATTTTTAAA
2443171 TTATTTTTT
1 TTATTTTTT
2443180 GGCGTGGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTTTTTTAATTTTTAAA
Found at i:2444945 original size:28 final size:28
Alignment explanation
Indices: 2444909--2444978 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
2444899 AAATAAAAAA
*
2444909 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
2444937 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
2444965 TTACCAAAATATAT
1 TTACCAAAATATAT
2444979 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:2445057 original size:27 final size:27
Alignment explanation
Indices: 2445016--2445094 Score: 117
Period size: 27 Copynumber: 2.9 Consensus size: 27
2445006 TTCCCTGGGT
2445016 CAAGGGAACAC-TGTTGGCGGCACCAAA
1 CAAGGGAAC-CTTGTTGGCGGCACCAAA
2445043 CAAGGGAACCTTGTTGGCGGCACCAAA
1 CAAGGGAACCTTGTTGGCGGCACCAAA
*
2445070 CAA-GGATTCCTTGTTGGCGGCACCA
1 CAAGGGA-ACCTTGTTGGCGGCACCA
2445095 CCTTAAATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.16
Consensus pattern (27 bp):
CAAGGGAACCTTGTTGGCGGCACCAAA
Found at i:2445164 original size:18 final size:18
Alignment explanation
Indices: 2445141--2445294 Score: 66
Period size: 18 Copynumber: 8.9 Consensus size: 18
2445131 GAAGGAGAGG
2445141 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAGAAA
2445159 GGAAGAAAGAAAAAG-AA
1 GGAAGAAAGAAAAAGAAA
* * * *
2445176 TG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGAAA
2445192 GGAAAGAAAGAAAAAG-AA
1 GG-AAGAAAGAAAAAGAAA
*
2445210 -G--GAAAGAAAAGGAAA
1 GGAAGAAAGAAAAAGAAA
*
2445225 GGGGAGGAAAGAAAGAA-AAA
1 --GGAAGAAAGAAA-AAGAAA
* *
2445245 -TAAGGAAAGAAAAGGAAA
1 GGAA-GAAAGAAAAAGAAA
2445263 GG-AGAAGAGAAAAA-AAA
1 GGAAGAA-AGAAAAAGAAA
*
2445280 --AAGAAAGAAGAAGAA
1 GGAAGAAAGAAAAAGAA
2445295 GAGGGAAGGA
Statistics
Matches: 102, Mismatches: 16, Indels: 38
0.65 0.10 0.24
Matches are distributed among these distances:
14 10 0.10
15 16 0.16
16 9 0.09
17 12 0.12
18 30 0.29
19 13 0.13
20 11 0.11
21 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (18 bp):
GGAAGAAAGAAAAAGAAA
Found at i:2445174 original size:10 final size:10
Alignment explanation
Indices: 2445143--2445214 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
2445133 AGGAGAGGGG
*
2445143 AAGAAGAAGA
1 AAGAAAAAGA
2445153 AAGAAAGGAAGA
1 AAGAAA--AAGA
2445165 AAGAAAAAGA
1 AAGAAAAAGA
* *
2445175 ATGAAAAGGA
1 AAGAAAAAGA
2445185 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
2445199 AAGAAAAAGA
1 AAGAAAAAGA
*
2445209 AGGAAA
1 AAGAAA
2445215 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:2445174 original size:22 final size:23
Alignment explanation
Indices: 2445143--2445244 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
2445133 AGGAGAGGGG
*
2445143 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
2445165 AAGAAAAAGAATGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
2445187 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
2445213 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
2445237 AAGAAAAA
1 AAGAAAAA
2445245 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:2445197 original size:38 final size:38
Alignment explanation
Indices: 2445155--2445318 Score: 174
Period size: 38 Copynumber: 4.3 Consensus size: 38
2445145 GAAGAAGAAA
* *
2445155 GAAAGGAAGAAAGAA-AAAGAATGAAAAGGAAAGGAGAG
1 GAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAAGGAGAG
* *
2445193 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAG
1 GAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAG
* * *
2445231 GAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAA
1 GAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAG
* *
2445269 GAGAA-AAA-AAAAAGAAAGAAGAAGAAGAGGGAAGGA-AG
1 GA-AAGAAAGAAAAAGAAAG-A-AAGAAAAGGAAAGGAGAG
*
2445307 GAAAAAAAGAAA
1 GAAAGAAAGAAA
2445319 CTAAGTTAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
37 12 0.11
38 78 0.72
39 18 0.17
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
GAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAG
Found at i:2445201 original size:28 final size:28
Alignment explanation
Indices: 2445146--2445225 Score: 76
Period size: 34 Copynumber: 2.8 Consensus size: 28
2445136 AGAGGGGAAG
2445146 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
*
2445171 AAGAATGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAA-GGAAA-G-AA--A-AGGAAAGAAAGAAA
2445205 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
2445226 GGGAGGAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
25 5 0.11
27 3 0.07
28 8 0.18
29 1 0.02
30 1 0.02
31 2 0.05
32 2 0.05
33 7 0.16
34 15 0.34
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:2445221 original size:10 final size:10
Alignment explanation
Indices: 2445163--2445263 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
2445153 AAGAAAGGAA
*
2445163 GAAAGAAAAA
1 GAAAGAAAAG
*
2445173 GAATGAAAAG
1 GAAAGAAAAG
* *
2445183 GAAAGGAGAG
1 GAAAGAAAAG
2445193 GAAAG-AAA-
1 GAAAGAAAAG
2445201 GAAA-AAGAAG
1 GAAAGAA-AAG
2445211 GAAAGAAAAG
1 GAAAGAAAAG
***
2445221 GAAAGGGGAG
1 GAAAGAAAAG
2445231 GAAAG-AAA-
1 GAAAGAAAAG
2445239 GAAA-AATAAG
1 GAAAGAA-AAG
2445249 GAAAGAAAAG
1 GAAAGAAAAG
2445259 GAAAG
1 GAAAG
2445264 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 7 0.10
10 51 0.71
11 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:2445221 original size:33 final size:33
Alignment explanation
Indices: 2445161--2445312 Score: 128
Period size: 34 Copynumber: 4.4 Consensus size: 33
2445151 GAAAGAAAGG
* *
2445161 AAGAAAGAAAAAGAATGAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAA-GGAAAGAAAAGGAGAGGA
2445195 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGG--A---GAGGA
* *
2445233 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAGAGGA
* *
2445266 GAAGAGAA-AAAAA-AAAGAAAGAAGAAGAAGAGGGA
1 -AAGA-AAGAAAAAGAAGGAAAGAA-AAGGAGA-GGA
* *
2445301 AGGAAGGAAAAA
1 AAGAAAGAAAAA
2445313 AAGAAACTAA
Statistics
Matches: 99, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
33 24 0.24
34 37 0.37
35 6 0.06
36 1 0.01
38 31 0.31
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (33 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAGAGGA
Found at i:2447289 original size:27 final size:27
Alignment explanation
Indices: 2447251--2447345 Score: 154
Period size: 27 Copynumber: 3.5 Consensus size: 27
2447241 ATAACATGAG
*
2447251 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
*
2447278 TGGTGCCGCCAACAAGGAATCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
**
2447305 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
2447332 TGGTGCCGCCAACA
1 TGGTGCCGCCAACA
2447346 GTGTTCCCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAACCCTTGTT
Found at i:2447440 original size:28 final size:29
Alignment explanation
Indices: 2447408--2447478 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
2447398 TTTAGTTTTT
*
2447408 TATATATTTTGGTAAAT-AAAAAAATTTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
2447436 TATATATTTTGGTAAATAAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
*
2447465 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
2447479 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 28 0.70
29 12 0.30
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAATGTA
Found at i:2452060 original size:2 final size:2
Alignment explanation
Indices: 2452053--2452091 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2452043 ATGAAATACC
2452053 TA TA 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 TA TA T
2452092 GACTGTCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2454883 original size:6 final size:6
Alignment explanation
Indices: 2454872--2454896 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2454862 TTTGGCCTCT
2454872 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
2454897 CAATTGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:2456132 original size:2 final size:2
Alignment explanation
Indices: 2456125--2456155 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2456115 ACTCTCAATT
2456125 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 T
2456156 CAAATTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2460080 original size:2 final size:2
Alignment explanation
Indices: 2460073--2460106 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2460063 TGATTCAAAG
2460073 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
2460107 GCTAACCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2460689 original size:288 final size:288
Alignment explanation
Indices: 2460173--2460751 Score: 1077
Period size: 288 Copynumber: 2.0 Consensus size: 288
2460163 GATCGATTGC
2460173 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
1 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
2460238 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
66 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
* * * *
2460303 GAAAAAATGTTAGAATCTAGGAGGTGCTTGTATTATAGGGACTGTATCAAGTAAATCCCCTTTTA
131 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
*
2460368 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAATCAAATAAGTCCAAATAAGATACTAT
196 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
*
2460433 TAACATATAAATATCTTAAATTAATAAT
261 TAACATATAAATATATTAAATTAATAAT
2460461 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
1 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
* *
2460526 GAAACAGCAAGAAAGGGCTTCATATCAACCGTAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
66 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
2460591 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
131 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
*
2460656 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATATGATACTAT
196 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
2460721 TAACATATAAATATATTAAATTAATAAT
261 TAACATATAAATATATTAAATTAATAAT
2460749 AAC
1 AAC
2460752 CATAAAATTA
Statistics
Matches: 282, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
288 282 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (288 bp):
AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
TAACATATAAATATATTAAATTAATAAT
Found at i:2463799 original size:2 final size:2
Alignment explanation
Indices: 2463792--2463828 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
2463782 AATCACAAAT
2463792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2463829 AAAGCTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2464508 original size:30 final size:30
Alignment explanation
Indices: 2464458--2464530 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2464448 TTAAATTAGT
* *
2464458 AAATT-TAAAAATATATTTTAATTTCTTTAA
1 AAATTATAAAAATATAGTTTAATAT-TTTAA
* *
2464488 AAA-TATGAAAATTTAGTTTAATATTTTAA
1 AAATTATAAAAATATAGTTTAATATTTTAA
2464517 AAATTATAAAAATA
1 AAATTATAAAAATA
2464531 GAATATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTATAAAAATATAGTTTAATATTTTAA
Found at i:2464635 original size:29 final size:33
Alignment explanation
Indices: 2464603--2464666 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 33
2464593 TAATGTTAAA
* *
2464603 TATTTTATTTAGTT-AT-TAAA-TAATA-TATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2464632 TATTTTATGTAATTAATATAAAGTAATATTATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2464665 TA
1 TA
2464667 ATGTTGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 4 0.14
32 5 0.17
33 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (33 bp):
TATTTTATGTAATTAATATAAAGTAATATTATT
Found at i:2464638 original size:25 final size:25
Alignment explanation
Indices: 2464601--2464652 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2464591 TTTAATGTTA
*
2464601 AATATTTTATTTA-GTTATTAA-AT
1 AATATTTTATTTATGTAATTAATAT
2464624 AATATATTTATTTTATGTAATTAATAT
1 AATAT-TTTA-TTTATGTAATTAATAT
2464651 AA
1 AA
2464653 AGTAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 4 0.17
26 7 0.29
27 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
AATATTTTATTTATGTAATTAATAT
Found at i:2465172 original size:2 final size:2
Alignment explanation
Indices: 2465165--2465191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2465155 TGTCTAATTT
2465165 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2465192 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2477234 original size:2 final size:2
Alignment explanation
Indices: 2477229--2477260 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2477219 GAAGAGTGTG
2477229 TA TA TA TA T- 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 T
2477261 GTTGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2477560 original size:5 final size:5
Alignment explanation
Indices: 2477552--2477577 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2477542 AATTCAATTG
2477552 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2477578 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2483850 original size:32 final size:31
Alignment explanation
Indices: 2483784--2483852 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
2483774 TTTGGCCCTT
*
2483784 ATTTTTTTAGCTAAATTTGACTAAAACATTA
1 ATTTTTTTAGCGAAATTTGACTAAAACATTA
2483815 ATTTTTTTAG-GAAATATTGACTAAAACATTA
1 ATTTTTTTAGCGAAAT-TTGACTAAAACATTA
*
2483846 AATTTTT
1 ATTTTTT
2483853 AAATGTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (31 bp):
ATTTTTTTAGCGAAATTTGACTAAAACATTA
Found at i:2493673 original size:19 final size:20
Alignment explanation
Indices: 2493634--2493673 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2493624 TCTTTAGGCC
* *
2493634 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
2493654 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
2493673 T
1 T
2493674 AAACACCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:2495616 original size:23 final size:23
Alignment explanation
Indices: 2495573--2495618 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2495563 TGAGCAAATG
*
2495573 TTCTTTCATTCTTTACTATTTTT
1 TTCTTTCATTCTTTACGATTTTT
**
2495596 TTCTTTCATTCTTTTGGATTTTT
1 TTCTTTCATTCTTTACGATTTTT
2495619 CTGCCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (23 bp):
TTCTTTCATTCTTTACGATTTTT
Found at i:2496601 original size:7 final size:7
Alignment explanation
Indices: 2496549--2496595 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
2496539 AGTGATGTGA
2496549 AAAAATG
1 AAAAATG
2496556 AAAAGATG
1 AAAA-ATG
2496564 -AAAATG
1 AAAAATG
2496570 AAAAATG
1 AAAAATG
2496577 AAAAATG
1 AAAAATG
*
2496584 AGAAATG
1 AAAAATG
2496591 AAAAA
1 AAAAA
2496596 ATAAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 3 0.08
7 30 0.83
8 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:2496601 original size:21 final size:22
Alignment explanation
Indices: 2496546--2496601 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
2496536 AGAAGTGATG
2496546 TGAAAAAATGAAAAGATGAAAA
1 TGAAAAAATGAAAAGATGAAAA
2496568 TG-AAAAATGAAAA-ATGAGAAA
1 TGAAAAAATGAAAAGATGA-AAA
2496589 TGAAAAAAT-AAAA
1 TGAAAAAATGAAAA
2496602 TAGAGAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (22 bp):
TGAAAAAATGAAAAGATGAAAA
Found at i:2498037 original size:43 final size:43
Alignment explanation
Indices: 2497988--2498313 Score: 133
Period size: 44 Copynumber: 7.4 Consensus size: 43
2497978 CCCTGAGGTT
*
2497988 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * * * **
2498031 GCAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCA
** * * * *** * * * **
2498075 ATAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 GCAGTGGAGTACATTGAAGCCAGT-AATTCTATCTCCCTG-GGCA
* *
2498120 GCAGTGGAGTACATTGAAGCCAGTAATTTTATCTTCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * **
2498163 GCAGTGG-G-ATCGATTGAAG--ATTACAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGTA-C-ATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCA
* * * * *** * * * **
2498207 GTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 GCAGTGGAGTACATTGAAGCCAGT-AATTCTATCTCCCTG-GGCA
2498252 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * *
2498295 ACAGTGGAATAGATTGAAG
1 GCAGTGGAGTACATTGAAG
2498314 ATTTCAGATC
Statistics
Matches: 196, Mismatches: 69, Indels: 36
0.65 0.23 0.12
Matches are distributed among these distances:
41 7 0.04
42 4 0.02
43 54 0.28
44 88 0.45
45 38 0.19
46 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
Found at i:2498086 original size:132 final size:132
Alignment explanation
Indices: 2497923--2500316 Score: 2710
Period size: 132 Copynumber: 17.9 Consensus size: 132
2497913 TGAAGATAGT
* * *
2497923 AGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* *
2497988 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
*
2498053 AC
131 TC
* * *
2498055 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * * *
2498120 GCAGTGGAGTACATTGAAGCCAGTAATTTTATCTTCCTGGGCAGCAGTGGGATCGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
*
2498185 AC
131 TC
* *
2498187 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* *
2498252 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2498317 TC
131 TC
* * * *
2498319 AGATCTTTTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
*
2498384 ACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCTCTGGGCAGCAGTGGAATAGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
*
2498448 TTT
130 TTC
* * * * *
2498451 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAATATAGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * *
2498516 ACAGTAGAGTACATTGAAGCTAGTAATTCTA-CTTCCCTAGGCAGCAGTAGAATAGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
2498580 TTC
130 TTC
* * * * * * *
2498583 AGATCTTGTCTCCCCAAGCAATAGTTGAGCAGATTAAAAATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* *
2498648 ACAGTGGAGTACATTGAAGCCAGCAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTAAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
2498712 TTC
130 TTC
* * * * *
2498715 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * ** *
2498780 ACAGTAGAGTACATTGAAGCCGGTAATTCTA-CTTCCCTAAGCAACAGTGGAATAGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
2498844 TTC
130 TTC
* * * * *
2498847 ATATATTGTCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * *
2498912 ACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAGCAGTGGAATAGACTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
*
2498977 TT
131 TC
* * * ** * ** *
2498979 AGATCTTGCCTTCCT--GCA-TAGACAGCGAAGCAGATTGAAGACGGCAGATTTTACCTCCCTGT
1 AGATCTTGTCTCCCTAAGCAGTAG--TG-G-AGCAGATCAAAGATGGTGGATTTTACCTCCCTGA
*
2499041 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGACTGAA
62 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
*
2499106 GATTTT
127 GATTTC
* * * * * *** *
2499112 AGATCTTGCCTTCCT--GCATAGATAGTGAAGCAG-TCGAAGACGGCATATTTTACCTCCCTGTG
1 AGATCTTGTCTCCCTAAGC--AG-TAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAG
* * * * *
2499174 GTTATAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTAGGCAGCAGTGGAATATACTGAAG
63 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAG
*
2499239 ATTTT
128 ATTTC
* * * * ** *
2499244 AGATCTTGCCTTCCT--GCA-TAGATAGCGAAGCAGATCGAAGACGGCAGATTTTACCTCCCTGT
1 AGATCTTGTCTCCCTAAGCAGTAG-T-G-G-AGCAGATCAAAGATGGTGGATTTTACCTCCCTGA
*
2499306 GGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGA
62 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGA
2499370 AGATTTC
126 AGATTTC
* * ** * ** *
2499377 ATATATTGTCTAGCTAAGCAGTAGTGGAGC-GATCAAAGATGGCGGATTTTACCTCATTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * *
2499441 ATAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCTCTAGGCAGCAGTGGAATAAATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
*
2499505 TAC
130 TTC
* **
2499508 AGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * *
2499573 ATAGTGGAGTACATTGAAGCCAGTAATTTTATCTCCCTAGGC-GACAGTGGAATAGATTGGAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAG-CAGTGGAATAGATTGAAGAT
2499637 TTC
130 TTC
* * * *
2499640 AGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * * *** **
2499705 GCAGTGGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTTGGC-GT-GAAGTAGATCAAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAA-TAGATTGAAGAT
**
2499768 AAC
130 TTC
* *
2499771 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCAAATATGGTGGATTT
1 AGATCTTGTC-TCCC-TA-----AGC--AGTAG-T-G--G--AGCAGATCAAAGATGGTGGATTT
* * *
2499836 TGCCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
51 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
*
2499901 AATAGATTGGAGATTTC
116 AATAGATTGAAGATTTC
* * ** * *
2499918 AGATCTTGCCTCCCTAAGTAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGAAGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * * * *** **
2499983 GCAGTGGAGTATATTAAAGCCAGTAATTCTACCTCCCCGGTTGGC-GT-GAAGTAGATCAAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAA-TAGATTGAAGAT
**
2500046 AGC
130 TTC
* *
2500049 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCAAAAATGGTGGATTT
1 AGATCTTGTC-TCCC-TA-----AGC--AGTAG-T-G--G--AGCAGATCAAAGATGGTGGATTT
*
2500114 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
51 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
*
2500179 AATAGATTGAATATTAT-
116 AATAGATTGAAGATT-TC
*
2500196 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
*
2500261 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC-GGAGCAACAGTGGAATAGA
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG-GCAGCAGTGGAATAGA
2500317 CAGAAGAAAT
Statistics
Matches: 1995, Mismatches: 206, Indels: 122
0.86 0.09 0.05
Matches are distributed among these distances:
128 3 0.00
129 4 0.00
130 10 0.01
131 162 0.08
132 1338 0.67
133 228 0.11
134 3 0.00
135 6 0.00
136 5 0.00
137 5 0.00
138 13 0.01
140 13 0.01
141 2 0.00
142 2 0.00
144 2 0.00
145 4 0.00
146 148 0.07
147 41 0.02
148 6 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
TC
Found at i:2498314 original size:88 final size:88
Alignment explanation
Indices: 2497953--2498315 Score: 229
Period size: 88 Copynumber: 4.1 Consensus size: 88
2497943 GTAGTGGAGC
*
2497953 AGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
*
2498018 ATCTTCCTGGGCAGCAGTGGAAT
66 ATCTCCCTGGGCAGCAGTGGAAT
**** * * * ** * * * *** *
2498041 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAAT--AGTGGAGCAGATCGAAGATGGTGGATT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAG-GTTGCAGTGGAGTACATTGAAGCCAGT-AATT
* * ** *
2498104 TTACCTCCCTGAGGTTGCAGTGGAGT
64 CTATCTCCCTG-GGCAGCAGTGGAAT
* *** * * * ** *
2498130 ACATTGAAGCCAGT-AATTTTATCTTCCTG-GGCAGCAGTGG-G-ATCGATTGAAG--ATTACAG
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTA-C-ATTGAAGCCAGTA-A-
* ** * **
2498189 ATCTTATCTCCCTAAGCAGTAGTGGAGC
62 TTC-TATCTCCCTGGGCAGCAGTGGAAT
*
2498217 AGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
*
2498282 ATCTCCCTGGGCAACAGTGGAAT
66 ATCTCCCTGGGCAGCAGTGGAAT
2498305 AGATTGAAGAT
1 AGATTGAAGAT
2498316 TTCAGATCTT
Statistics
Matches: 190, Mismatches: 69, Indels: 32
0.65 0.24 0.11
Matches are distributed among these distances:
86 3 0.02
87 37 0.19
88 105 0.55
89 38 0.20
90 3 0.02
91 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (88 bp):
AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
ATCTCCCTGGGCAGCAGTGGAAT
Found at i:2499696 original size:44 final size:44
Alignment explanation
Indices: 2499507--2499698 Score: 120
Period size: 44 Copynumber: 4.4 Consensus size: 44
2499497 TTGAAGATTA
* * *
2499507 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
1 CAGATTTTACCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * * * * ***
2499551 CAGATTTTACCTCCCTGAGGTTA-TAGTGGAGTACATTGAAGCCAG
1 CAGATTTTACCTCCCT-AAG-CAGTAGTGGAGCAGATCGAAGATGG
* * * * ** * * **
2499596 TA-ATTTTATCTCCCTAGGC-GACAGTGGAATAGATTGGAGATTT
1 CAGATTTTACCTCCCTAAGCAG-TAGTGGAGCAGATCGAAGATGG
* *
2499639 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATTTTACCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
*
2499683 CGGATTTTACCTCCCT
1 CAGATTTTACCTCCCT
2499699 GAAGTTGCAG
Statistics
Matches: 105, Mismatches: 37, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
43 18 0.17
44 67 0.64
45 19 0.18
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGATTTTACCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
Found at i:2500032 original size:278 final size:278
Alignment explanation
Indices: 2499535--2500297 Score: 1294
Period size: 278 Copynumber: 2.7 Consensus size: 278
2499525 GCAGTAGTGG
* ** *
2499535 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
2499600 TTTATCTCCCTAGGCGACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
2499665 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTA
131 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTA
2499730 ATTCTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTG
196 ATTCTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTG
2499795 GCGAAGTAGATCGAAGAA
261 GCGAAGTAGATCGAAGAA
* * *
2499813 AGCAGATCAAATATGGTGGATTTTGCCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
2499878 TCTATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGTAGTAGT
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
* *
2499943 GGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCAGTA
131 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTA
*
2500008 ATTCTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTG
196 ATTCTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTG
2500073 GCGAAGTAGATCGAAGAA
261 GCGAAGTAGATCGAAGAA
2500091 AGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * **
2500156 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAATATTAT-AGATCTTATCTCCCTAAGCAGTAG
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGGAGATT-TCAGATCTTGCCTCCCTAAGCAGTAG
* * * * *
2500220 TGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT
130 TGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGT
*
2500285 AATTCTATCTCCC
195 AATTCTACCTCCC
2500298 GGAGCAACAG
Statistics
Matches: 455, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
278 454 1.00
279 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (278 bp):
AGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTA
ATTCTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTG
GCGAAGTAGATCGAAGAA
Found at i:2500297 original size:44 final size:44
Alignment explanation
Indices: 2500117--2500297 Score: 104
Period size: 44 Copynumber: 4.1 Consensus size: 44
2500107 TGGATTTTAC
2500117 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
** * * * * *
2500161 CTCCCTG-GGCAACAGTGGAATAGATTGAA--TATTATAGATCTTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-TAT
* * * ** *** * * *
2500205 CTCCCTAAGCAG-T--AGTGGAGCAGATCAAAGATGGTGGATTTTAC
1 CTCCCTGAG--GTTACAGTGGAGTACATTGAAGCCAGT-AATTCTAT
2500249 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
2500293 CTCCC
1 CTCCC
2500298 GGAGCAACAG
Statistics
Matches: 95, Mismatches: 30, Indels: 24
0.64 0.20 0.16
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 21 0.22
44 48 0.51
45 17 0.18
46 3 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
Found at i:2503848 original size:9 final size:9
Alignment explanation
Indices: 2503834--2503860 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2503824 ATAAACTAAA
2503834 AAAATATTT
1 AAAATATTT
2503843 AAAATATTT
1 AAAATATTT
2503852 AAAATATTT
1 AAAATATTT
2503861 TTATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:2507914 original size:2 final size:2
Alignment explanation
Indices: 2507907--2507933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2507897 TTGAATTTAT
2507907 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2507934 CACAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2509592 original size:22 final size:22
Alignment explanation
Indices: 2509565--2509609 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2509555 ATAGTGTATG
2509565 TATATACAT-ATATTAAAAAATA
1 TATATACATGA-ATTAAAAAATA
**
2509587 TATATATTTGAATTAAAAAATA
1 TATATACATGAATTAAAAAATA
2509609 T
1 T
2509610 GAAAAACGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATACATGAATTAAAAAATA
Found at i:2509798 original size:10 final size:10
Alignment explanation
Indices: 2509783--2509807 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2509773 TGTATTGAAA
2509783 TAATAATAAT
1 TAATAATAAT
2509793 TAATAATAAT
1 TAATAATAAT
2509803 TAATA
1 TAATA
2509808 TAAAAGAATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATAATAAT
Found at i:2509823 original size:17 final size:18
Alignment explanation
Indices: 2509803--2509837 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2509793 TAATAATAAT
2509803 TAATATAAAAGA-ATTAA
1 TAATATAAAAGACATTAA
2509820 TAATATAAAAGACATTAA
1 TAATATAAAAGACATTAA
2509838 AAAAAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAATATAAAAGACATTAA
Found at i:2510342 original size:20 final size:20
Alignment explanation
Indices: 2510317--2510354 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2510307 TTTTTTAAAT
2510317 AAAAAAATGAGACAAAAAGC
1 AAAAAAATGAGACAAAAAGC
2510337 AAAAAAATGAGACAAAAA
1 AAAAAAATGAGACAAAAA
2510355 AAACAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAATGAGACAAAAAGC
Found at i:2511438 original size:100 final size:100
Alignment explanation
Indices: 2511253--2511612 Score: 453
Period size: 100 Copynumber: 3.6 Consensus size: 100
2511243 GCCATTGTGA
* *
2511253 CTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGAT-TCGCCG-T-TGGCTTCAATCTTTTTA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCT-GCCGTTGTGGCTTCAATCTTTTTA
* * *
2511315 ATTGCAATGTCTAGGAAACAAGATCTACCATCGTAG
65 ATTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
* * * * **
2511351 CTTCAATCTGTTCCATTGCCCCACTAGGGAAGTAAGATCTGTTGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAA
*
2511416 TTGCAATGTCTGGGAAATAAGATCCACCGTCGTAG
66 TTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
* * *
2511451 CTTTAATTTGTTCCACTGCACCGCCAGGG-AGATAAGATCTGCCGTTGTGGCTTCAATCTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAG-TAAGATCTGCCGTTGTGGCTTCAATCTTTTTA
* * *
2511515 ATTGCAATGTCGGGGAAATAAGAT-TCGCCGTCGTGG
65 ATTGCAATGTCTGGGAAATAAGATCT-ACCGTCGTAG
* * *
2511551 CTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGAT-TCACCGCTGTGGCTTCAATCTTTT
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCT-GCCGTTGTGGCTTCAATCTTTT
2511613 CCACTGTAAT
Statistics
Matches: 225, Mismatches: 30, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
98 34 0.15
99 5 0.02
100 184 0.82
101 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (100 bp):
CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAA
TTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
Found at i:2511581 original size:50 final size:50
Alignment explanation
Indices: 2511229--2511618 Score: 229
Period size: 50 Copynumber: 7.8 Consensus size: 50
2511219 TGCAATGTCG
* * * * * * *
2511229 GGGAAACAAGATTCGCCATTGTGACTTCAATCTATTCCACTACACCGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* ** * * *
2511279 GGGAAGTAAGATTCGCCGT--TGGCTTCAATCTTTTTAATTGCAATGTCTA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTG-CCA
* * * * * * * ** *
2511328 -GGAAACAAGA-TCTACCATCGTAGCTTCAATCTGTTCCATTGCCCCACTA
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* ** * ** * * * *
2511377 GGGAAGTAAGA-TCTGTTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCT
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* * * * *
2511427 GGGAAATAAGATCCACCGTCGTAGCTTTAAT-TTGTTCCACTGCACCGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTT-TTCCACTGCACTGCCA
* * ** * * * *
2511477 GGGAGATAAGA-TCTGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCG
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
*
2511527 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTGTTCCACTGCACTGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* *
2511577 GGGAAGTAAGATTCACCG-CTGTGGCTTCAATCTTTTCCACTG
1 GGGAAATAAGATTCGCCGTC-GTGGCTTCAATCTTTTCCACTG
2511619 TAATACCAAA
Statistics
Matches: 247, Mismatches: 82, Indels: 22
0.70 0.23 0.06
Matches are distributed among these distances:
47 2 0.01
48 29 0.12
49 9 0.04
50 202 0.82
51 5 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (50 bp):
GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
Found at i:2511871 original size:100 final size:100
Alignment explanation
Indices: 2511740--2511978 Score: 343
Period size: 100 Copynumber: 2.4 Consensus size: 100
2511730 CGCTGTGACG
* * * * *
2511740 CCAGGAAAATAAGATCCGCTATTGTGGCTTCAATCTTTTTAATTGCAATGTCTGGGAAATAAGAT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
*
2511805 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCG
66 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
* *
2511840 CCAGGGAGGTAAGATCTGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
* * * *
2511905 TCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTA
66 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
* **
2511940 CCAGGGAAGTAAGATCCGTCGCTGTGGCTTCAATCTTTT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTT
2511979 CCACTGTAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 122 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
Found at i:2511981 original size:50 final size:49
Alignment explanation
Indices: 2511712--2511984 Score: 161
Period size: 50 Copynumber: 5.5 Consensus size: 49
2511702 GACTTGCCCT
* * * * * * **
2511712 TGTGGCTTCAATTTGCTCCGCTGTGAC-GCCAGGAAAATAAGATCCGCTAT
1 TGTGGCTTCAATCTGTTCCACTG-CACTGCCAGGGAAGTAAGATCCGC-CG
* ** * * * * * *
2511762 TGTGGCTTCAATCTTTTTAATTGCAATGTCTGGGAAATAAGATCCACCG
1 TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
* * * * * *
2511811 TCATAGCTTCAATCTGTTCCACTGCACCGCCAGGGAGGTAAGATCTGCCAT
1 T-GTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCC-G
* ** * * * * * *
2511862 TGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGATTCGCCG
1 TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
* * *
2511911 TCGTAGCTTCAATCTGTTCCACTGCACTACCAGGGAAGTAAGATCCGTCG
1 T-GTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
*
2511961 CTGTGGCTTCAATCTTTTCCACTG
1 -TGTGGCTTCAATCTGTTCCACTG
2511985 TAATACCAAA
Statistics
Matches: 159, Mismatches: 59, Indels: 10
0.70 0.26 0.04
Matches are distributed among these distances:
49 3 0.02
50 154 0.97
51 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (49 bp):
TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
Found at i:2512289 original size:88 final size:88
Alignment explanation
Indices: 2512167--2512393 Score: 346
Period size: 88 Copynumber: 2.6 Consensus size: 88
2512157 TCATGGCGAT
* * * *
2512167 AAGACTGATGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
* *
2512232 ACTCCACTGCTGCCTAGGGAGAC
66 ACTCCACTACTGCCCAGGGAGAC
* * * * *
2512255 AAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAAGCT
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
2512320 ACTCCACTACTGCCCAGGGAGAC
66 ACTCCACTACTGCCCAGGGAGAC
*
2512343 AAGACTGGTATCTTCGGTCTGCTTCTCTGTCAGTACAGGAAGGCAATATCT
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCT
2512394 ACTATCTTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (88 bp):
AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
ACTCCACTACTGCCCAGGGAGAC
Found at i:2513598 original size:42 final size:42
Alignment explanation
Indices: 2513536--2513636 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
2513526 CCCCATTCCA
** *
2513536 ATCAAAAGCTGAGCCACTCTGATCACCTCCAACCCTATTCTG
1 ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
* *
2513578 ATCAAAATTTGAGCCGCTCTGATCACCTCTAGCCCTATTCTG
1 ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
2513620 ATCAAAATTTGAGCCGC
1 ATCAAAATTTGAGCCGC
2513637 CCTTTTCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.27
Consensus pattern (42 bp):
ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
Found at i:2519225 original size:22 final size:22
Alignment explanation
Indices: 2519198--2519242 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2519188 ATAGTGTATG
2519198 TATATACAT-ATATTAAAAAATA
1 TATATACATGA-ATTAAAAAATA
**
2519220 TATATATTTGAATTAAAAAATA
1 TATATACATGAATTAAAAAATA
2519242 T
1 T
2519243 GAAAAACGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATACATGAATTAAAAAATA
Found at i:2519431 original size:10 final size:10
Alignment explanation
Indices: 2519416--2519440 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2519406 TGTATTGAAA
2519416 TAATAATAAT
1 TAATAATAAT
2519426 TAATAATAAT
1 TAATAATAAT
2519436 TAATA
1 TAATA
2519441 TAAAAGAATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATAATAAT
Found at i:2519456 original size:17 final size:18
Alignment explanation
Indices: 2519436--2519470 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2519426 TAATAATAAT
2519436 TAATATAAAAGA-ATTAA
1 TAATATAAAAGACATTAA
2519453 TAATATAAAAGACATTAA
1 TAATATAAAAGACATTAA
2519471 AAAAAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAATATAAAAGACATTAA
Found at i:2521918 original size:16 final size:16
Alignment explanation
Indices: 2521887--2521919 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2521877 GTTTCAACCC
2521887 ATAATAGATGCGAAAA
1 ATAATAGATGCGAAAA
2521903 ATAA-AGATGCGAAAA
1 ATAATAGATGCGAAAA
2521918 AT
1 AT
2521920 CAAATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
ATAATAGATGCGAAAA
Found at i:2528764 original size:18 final size:19
Alignment explanation
Indices: 2528741--2528777 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2528731 TTTACAAAAT
*
2528741 ATGTATAAA-TTATATAAA
1 ATGTATAAACATATATAAA
2528759 ATGTATAAACATATATAAA
1 ATGTATAAACATATATAAA
2528778 TTATATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
ATGTATAAACATATATAAA
Found at i:2528965 original size:3 final size:3
Alignment explanation
Indices: 2528957--2529027 Score: 62
Period size: 3 Copynumber: 25.3 Consensus size: 3
2528947 TATATGTAAG
* * *
2528957 ATA ATA ATA AAA AT- ATA AT- ATA ACA ATA ATA GTA ATA ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
2529001 ATA ATA ATA ACA ATA TTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2529028 ACTAAAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 10 0.19
3 44 0.81
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:2528996 original size:31 final size:31
Alignment explanation
Indices: 2528957--2529028 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2528947 TATATGTAAG
2528957 ATAATAATAAAAATATAAT-ATAACAATAATA
1 ATAATAATAAAAA-ATAATAATAACAATAATA
* *
2528988 GTAATAATAAAAAATAATAATAACAATATTA
1 ATAATAATAAAAAATAATAATAACAATAATA
2529019 ATAA-AATAAA
1 ATAATAATAAA
2529029 CTAAAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (31 bp):
ATAATAATAAAAAATAATAATAACAATAATA
Found at i:2529006 original size:22 final size:23
Alignment explanation
Indices: 2528957--2529027 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 23
2528947 TATATGTAAG
* *
2528957 ATAATAATAAAAAT-ATAATATA
1 ATAATAATAACAATAATAATAAA
* **
2528979 ACAATAATAGTAATAATAA-AAA
1 ATAATAATAACAATAATAATAAA
*
2529001 ATAATAATAACAATATTAATAAA
1 ATAATAATAACAATAATAATAAA
2529024 ATAA
1 ATAA
2529028 ACTAAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 28 0.72
23 11 0.28
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (23 bp):
ATAATAATAACAATAATAATAAA
Found at i:2530856 original size:30 final size:30
Alignment explanation
Indices: 2530814--2530897 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
2530804 TCGCATTATT
2530814 TTTTTAGT-TTTATTTATTTACTTTTATAAA
1 TTTTTAGTATTTATTTATTTA-TTTTATAAA
* * *
2530844 TTTTTA-TATTTATATAGTTATTTTATTATA
1 TTTTTAGTATTTATTTATTTATTTTA-TAAA
*
2530874 TCATTTTATTATTTA-TTATTTATT
1 T--TTTTAGTATTTATTTATTTATT
2530898 ATTTATATCT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 6 0.14
30 20 0.45
32 12 0.27
33 6 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
TTTTTAGTATTTATTTATTTATTTTATAAA
Found at i:2530890 original size:7 final size:7
Alignment explanation
Indices: 2530878--2530903 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2530868 ATTATATCAT
2530878 TTTATTA
1 TTTATTA
2530885 TTTATTA
1 TTTATTA
2530892 TTTATTA
1 TTTATTA
2530899 TTTAT
1 TTTAT
2530904 ATCTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:2530913 original size:31 final size:33
Alignment explanation
Indices: 2530845--2530906 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
2530835 TTTTATAAAT
*
2530845 TTTTA-TATTTATATAGTTATTTTATTATATCA
1 TTTTATTATTTATATAGTTATTATATTATATCA
*
2530877 TTTTATTATTTAT-TATTTATTAT-TTATATC
1 TTTTATTATTTATATAGTTATTATATTATATC
2530907 TCTTTATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 7 0.26
32 13 0.48
33 7 0.26
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (33 bp):
TTTTATTATTTATATAGTTATTATATTATATCA
Found at i:2530936 original size:3 final size:3
Alignment explanation
Indices: 2530928--2530953 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2530918 TAAAAAATTC
2530928 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2530954 TATTATTATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2533364 original size:19 final size:19
Alignment explanation
Indices: 2533340--2533380 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2533330 TAGCAATCTA
2533340 AATAAAA-AAGAAAGCTACT
1 AATAAAACAAGAAAG-TACT
*
2533359 AATAAAACAAGAACGTACT
1 AATAAAACAAGAAAGTACT
2533378 AAT
1 AAT
2533381 TAGCAAGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (19 bp):
AATAAAACAAGAAAGTACT
Found at i:2556104 original size:260 final size:259
Alignment explanation
Indices: 2555634--2556156 Score: 915
Period size: 260 Copynumber: 2.0 Consensus size: 259
2555624 TCAGAGCTAG
* *
2555634 TAACTCTAAATTTTCTTTCATTAGAAAGACTACGATCTAGTAAGAAGAGAGTTTAGAATCATGGA
1 TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
* * * *
2555699 ATCCTCTAGATTATCTACCACAAAAGTACCTCTCTCATTACCTGAATCCCCATTTTGCTCTCACT
66 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
2555764 CTGCTAGAAAGATTTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACT
131 CTGCTAGAAAGA-TTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACT
2555829 AATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
195 AATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
* *
2555894 TAACTCCAGATTTTCTTTCATTAGAAATACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
1 TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
*
2555959 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACGTTTCGCTCTCACT
66 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
2556024 CTGCTAGAAAGA-T-TTCTCTTTATGAAGTAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTA
131 CTGCTAGAAAGATTCTTCTCTTTATG-A--AGAATATTTTACTGAAGAAGAGAAAGTACAAGCTA
2556087 CTAATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGT
193 CTAATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGT
2556152 AT
258 AT
2556154 TAA
1 TAA
2556157 GTCTCTTATT
Statistics
Matches: 251, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
257 11 0.04
258 2 0.01
260 238 0.95
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (259 bp):
TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
CTGCTAGAAAGATTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACTA
ATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
Found at i:2560832 original size:535 final size:535
Alignment explanation
Indices: 2559823--2560858 Score: 1883
Period size: 535 Copynumber: 1.9 Consensus size: 535
2559813 TTGATGGTTC
2559823 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
1 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
2559888 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
66 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
* *
2559953 GAATTTGCTGATCTTTCTGATTTCCCTGAAAATGATACTGAATCATCTTATTCTGGGATTTGTTC
131 GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
*
2560018 CAAATCTGGAATTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
196 CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
* *
2560083 TATGACTGTAATCCTTTAAAAACCTTGTTAAGGGATTAGAAGGATTTTTATAATTTTGCATCATA
261 TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTACATCATA
2560148 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
326 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
* *
2560213 TTCTTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTTCTTCTGCAGCTT
391 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
2560278 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
456 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
2560343 TTCATAGTAAATTGA
521 TTCATAGTAAATTGA
2560358 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
1 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
*
2560423 CTGGCAAATCCTCAATTCCTTCTTCTGAGGAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
66 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
* * *
2560488 GGATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTCTTTTGGGATTTGTTC
131 GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
* *
2560553 CCAATCTGGAACTGGGGTTGTTTCTGATTTATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
196 CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
* * *
2560618 TATGACTGTAATCCTTTAAAAGCCCTGTTAAGGGATTAGAATGATTTTTATCATTTTACATCATA
261 TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTACATCATA
* * *
2560683 AGAGACTTTGACATCAGTTTTGGTGGTGGAGATGTTGGTGGTGAAGAGAATTGGCTTTCTTCATC
326 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
* *
2560748 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAGCCTTTTCTCTTTTTCTTTTTCCTTCTGCAGTTT
391 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
2560813 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTC
456 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTC
2560859 ATAGACTGTG
Statistics
Matches: 480, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
535 480 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (535 bp):
TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTACATCATA
AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
TTCATAGTAAATTGA
Found at i:2564444 original size:500 final size:498
Alignment explanation
Indices: 2563429--2564457 Score: 1754
Period size: 497 Copynumber: 2.1 Consensus size: 498
2563419 TAATCCTACA
* *
2563429 ATATTGATGCCCTAAATGAAGGTTAGAACCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
1 ATATTGTTGCCCTAAATGAAGGTTAG-AGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
*
2563494 GTGACTGATTATGCATTTTCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
65 GTGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
* * * ** * *
2563559 GTGCTATCATAATTATTCCTACCCTTGTAAATTGACTTACTTTTCATTTGCTTGTACTGGTTGTC
130 GTGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTC
* * *
2563624 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTTCTTGTATAG
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAA
*
2563689 AACTTGAGTAATGCTAAGGTACAAAGAAGTCGAGTCATGTGTAAATGTCTTCCTTTTTCCAAGAT
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCATGTGTAAATGTCTTCCTTTTTCCAAGAT
*
2563754 GAATGAGTGGACTCAGTTTTGTTAGGACTGTGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTAC
325 GAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTAC
* * *
2563819 GAATCTCCTAGCACCTTTAGGGAACTAGAATTGAAGTTTGTTAGCTTTGGGCAGAGAATTTTAAC
390 GAAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTAAC
2563884 CAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
455 CAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
**
2563928 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTT-TATCCTTGGAAAG
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAAG
*
2563992 TGACTGATTATGCATTTGCCAATGTTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
66 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
* *
2564057 TGCCATCATAATTATTCCTATCCTTGTAAATTCACTGATTTTTCATTTGCCAGTAATGCTTGTCA
131 TGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTCA
2564122 TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
196 TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
*
2564187 ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCAAG
261 ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTC-ATGTGT--AAATGTCTTCCTTTTTCCAAG
* *
2564252 ATGAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTTTTCTTGTTGTTTTGAATGGGT
323 ATGAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGT
* *
2564317 ATGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTA
388 ACGAAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTA
*
2564382 ACCAAAGGCTTGTTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
453 ACCAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
2564428 ATATTGTTGCCCTAAATGAAGGTTAGAGCC
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCC
2564458 TCCTGTATAA
Statistics
Matches: 498, Mismatches: 29, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
497 228 0.46
498 27 0.05
499 25 0.05
500 218 0.44
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (498 bp):
ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAAG
TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
TGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTCA
TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCATGTGTAAATGTCTTCCTTTTTCCAAGATG
AATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTACG
AAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTAACC
AAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
Found at i:2570779 original size:14 final size:14
Alignment explanation
Indices: 2570760--2570786 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2570750 AAATTATAAT
2570760 ATCTAGATGTCTTA
1 ATCTAGATGTCTTA
2570774 ATCTAGATGTCTT
1 ATCTAGATGTCTT
2570787 CATCAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (14 bp):
ATCTAGATGTCTTA
Found at i:2575621 original size:18 final size:19
Alignment explanation
Indices: 2575598--2575633 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2575588 AATTTTAATA
*
2575598 TAATTAAA-ATTTAAATTT
1 TAATTAAATATATAAATTT
2575616 TAATTAAATATATAAATT
1 TAATTAAATATATAAATT
2575634 ATTTAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAATATATAAATTT
Found at i:2579465 original size:19 final size:18
Alignment explanation
Indices: 2579430--2579465 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2579420 TGTTTATATA
*
2579430 TTTTTTTTCTTTAAATAC
1 TTTTTTTTCTTAAAATAC
2579448 TTTTTTTTCTTAATAATA
1 TTTTTTTTCTTAA-AATA
2579466 AAAAGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTTCTTAAAATAC
Found at i:2579653 original size:19 final size:20
Alignment explanation
Indices: 2579615--2579653 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2579605 AATTTATATA
*
2579615 TTTAATTTAAATTTAAATTT
1 TTTAATTTAAATTGAAATTT
*
2579635 TTTAA-TTATATTGAAATTT
1 TTTAATTTAAATTGAAATTT
2579654 AAAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAATTTAAATTGAAATTT
Found at i:2583001 original size:14 final size:14
Alignment explanation
Indices: 2582982--2583010 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2582972 TCTTGTCATG
2582982 TTATTGATGTAATT
1 TTATTGATGTAATT
2582996 TTATTGATGTAATT
1 TTATTGATGTAATT
2583010 T
1 T
2583011 CTGTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTATTGATGTAATT
Found at i:2585683 original size:17 final size:20
Alignment explanation
Indices: 2585649--2585685 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
2585639 TTTACTTTTA
2585649 AAAAATATATAATATGAAAT
1 AAAAATATATAATATGAAAT
2585669 AAAAA-ATA-AAT-TGAAAT
1 AAAAATATATAATATGAAAT
2585686 TGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 3 0.18
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATATATAATATGAAAT
Found at i:2598764 original size:25 final size:25
Alignment explanation
Indices: 2598736--2598783 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2598726 AAAAGGAATC
2598736 TTTATGTTTTT-TTAATAATTATTTT
1 TTTA-GTTTTTCTTAATAATTATTTT
*
2598761 TTTAGTTTTTCTTAATTATTATT
1 TTTAGTTTTTCTTAATAATTATT
2598784 ATTCTTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTAGTTTTTCTTAATAATTATTTT
Found at i:2602018 original size:30 final size:30
Alignment explanation
Indices: 2601984--2602048 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2601974 TGTAATGAAC
* ** *
2601984 TTAAAAT-TAACAAATAATTGGATCTGAATT
1 TTAAAATCTAAAAAATAAAGGGA-CTAAATT
2602014 TTAAAATCTAAAAAATAAAGGGACTAAATT
1 TTAAAATCTAAAAAATAAAGGGACTAAATT
2602044 TTAAA
1 TTAAA
2602049 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.32
Consensus pattern (30 bp):
TTAAAATCTAAAAAATAAAGGGACTAAATT
Found at i:2602980 original size:4 final size:4
Alignment explanation
Indices: 2602971--2603003 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2602961 ATGTTATGTA
2602971 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
2603004 GAGAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:2606423 original size:2 final size:2
Alignment explanation
Indices: 2606416--2606442 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2606406 AGATTCATGC
2606416 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
2606443 AACAAACAAA
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:2606513 original size:4 final size:4
Alignment explanation
Indices: 2606506--2606535 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2606496 TGCATGCATG
2606506 CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
2606536 AACAAATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:2606589 original size:16 final size:17
Alignment explanation
Indices: 2606568--2606603 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2606558 TTATATAAAT
*
2606568 TTTGACAT-ATTATTTA
1 TTTGACATAATTATATA
2606584 TTTGACATAATTATATA
1 TTTGACATAATTATATA
2606601 TTT
1 TTT
2606604 TTATTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTGACATAATTATATA
Found at i:2607076 original size:31 final size:31
Alignment explanation
Indices: 2607022--2607082 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2607012 AAATAATCAC
* *
2607022 TGAACTATTCGAAAGTTTTCATTTATGTCAT
1 TGAACTATTCGAAAGTTTCCATTTAAGTCAT
*
2607053 TGAACTTTTC-AAATGTTTCCATTTAAGTCA
1 TGAACTATTCGAAA-GTTTCCATTTAAGTCA
2607083 CTGATTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (31 bp):
TGAACTATTCGAAAGTTTCCATTTAAGTCAT
Found at i:2609507 original size:24 final size:22
Alignment explanation
Indices: 2609457--2609507 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
2609447 GCAGAAAACT
2609457 AATA-CTAGAATTTAACCTAAA
1 AATATCTAGAATTTAACCTAAA
2609478 ATATATCTA-AATTTGAACCCTAATA
1 A-ATATCTAGAATTT-AA-CCTAA-A
2609503 AATAT
1 AATAT
2609508 GAAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.32
23 5 0.20
24 9 0.36
25 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATCTAGAATTTAACCTAAA
Found at i:2617296 original size:40 final size:40
Alignment explanation
Indices: 2617251--2617327 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
2617241 TTTAAAATTT
*
2617251 ATAATATTT-TTTCTTGTAGGTAACTGTCGATAAGATTTTC
1 ATAATATTTCTTT-TTGTAGGTAACTATCGATAAGATTTTC
*
2617291 ATAATATTTCTTTTTGTAGGTAATTATCGATAAGATT
1 ATAATATTTCTTTTTGTAGGTAACTATCGATAAGATT
2617328 AAAAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (40 bp):
ATAATATTTCTTTTTGTAGGTAACTATCGATAAGATTTTC
Found at i:2619186 original size:21 final size:20
Alignment explanation
Indices: 2619140--2619189 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
2619130 TCAGTTTTTC
*
2619140 TATAATTGACATTTTAACAA
1 TATAATTGTCATTTTAACAA
* **
2619160 TTTAATTGTCATATTTATTAA
1 TATAATTGTCAT-TTTAACAA
2619181 TATAATTGT
1 TATAATTGT
2619190 ATTCGTTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATAATTGTCATTTTAACAA
Found at i:2620689 original size:15 final size:15
Alignment explanation
Indices: 2620669--2620720 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
2620659 ACTACAAAAC
2620669 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
2620684 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
2620703 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
2620718 ATT
1 ATT
2620721 AATATTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:2620812 original size:18 final size:18
Alignment explanation
Indices: 2620774--2620809 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2620764 TTATTAGTTT
*
2620774 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
2620792 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
2620810 TAATGTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:2620825 original size:24 final size:24
Alignment explanation
Indices: 2620798--2620862 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
2620788 AAAATAAAAT
2620798 TTAAATATTAAATAATGTATTATA
1 TTAAATATTAAATAATGTATTATA
*
2620822 TTAATTATATT-AATAATTTATTATA
1 TTAA--ATATTAAATAATGTATTATA
*
2620847 TGACAATA-TAAATAAT
1 TTA-AATATTAAATAAT
2620863 TAAATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 1 0.03
24 13 0.37
25 15 0.43
26 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (24 bp):
TTAAATATTAAATAATGTATTATA
Found at i:2627599 original size:30 final size:31
Alignment explanation
Indices: 2627565--2627633 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
2627555 TTACCCAAGA
* **
2627565 GTAAATACT-AAAAAATTGAGGGGTTAA-AGT
1 GTAAATA-TGAAAAAATTGAAGGACTAATAGT
*
2627595 GTAAATATGAAAAAGTTGAAGGACTAATAGT
1 GTAAATATGAAAAAATTGAAGGACTAATAGT
2627626 GTAAATAT
1 GTAAATAT
2627634 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.64
31 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.28
Consensus pattern (31 bp):
GTAAATATGAAAAAATTGAAGGACTAATAGT
Found at i:2629798 original size:34 final size:34
Alignment explanation
Indices: 2629740--2629805 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
2629730 CAAACACCAG
* *
2629740 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
*
2629775 AAAACATTTTTCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
2629806 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:2631641 original size:14 final size:14
Alignment explanation
Indices: 2631622--2631652 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2631612 ATCCAAACAA
2631622 TAACAACAAAATAG
1 TAACAACAAAATAG
*
2631636 TAACAACATAATAG
1 TAACAACAAAATAG
2631650 TAA
1 TAA
2631653 AATGACAGTA
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:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:2633422 original size:30 final size:30
Alignment explanation
Indices: 2633386--2633447 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2633376 TAATAAGTGA
2633386 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
2633416 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
2633446 TT
1 TT
2633448 GATCTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (30 bp):
TTACCAATTTAGGGTCTTATTAAATGGAAC
Found at i:2647074 original size:9 final size:9
Alignment explanation
Indices: 2647057--2647093 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2647047 TGAGTTTTCG
2647057 AATTCGAAT
1 AATTCGAAT
*
2647066 AACTCGAAT
1 AATTCGAAT
2647075 AATTCGAAT
1 AATTCGAAT
2647084 AATTCGAAT
1 AATTCGAAT
2647093 A
1 A
2647094 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.