Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004599.1 Hibiscus syriacus cultivar Beakdansim tig00010275_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 185235
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1691 original size:23 final size:23
Alignment explanation
Indices: 1665--1709 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1655 AAATCCAGCA
1665 AAGAAATTCAAAGCACTCAAAAG
1 AAGAAATTCAAAGCACTCAAAAG
* *
1688 AAGAAATTGAAAGCACTTAAAA
1 AAGAAATTCAAAGCACTCAAAA
1710 AGGAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (23 bp):
AAGAAATTCAAAGCACTCAAAAG
Found at i:23897 original size:25 final size:25
Alignment explanation
Indices: 23868--23917 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
23858 ATCGCTTTAG
*
23868 TAAAATTGATCATATTGATGTAGAA
1 TAAAATTGATCATATTGATATAGAA
23893 TAAAATTGATCATATTGATATAGAA
1 TAAAATTGATCATATTGATATAGAA
23918 CTAGTGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (25 bp):
TAAAATTGATCATATTGATATAGAA
Found at i:26423 original size:20 final size:20
Alignment explanation
Indices: 26372--26443 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
26362 TGATATTGAG
26372 CCTTCGGTATGGATACTCA-T
1 CCTTCGGTATGGATACT-AGT
*
26392 -CTTCGGTGTGGATACTAGT
1 CCTTCGGTATGGATACTAGT
* * *
26411 CCTTCAGTATGGAGAATAGT
1 CCTTCGGTATGGATACTAGT
* *
26431 TCTTCTGTATGGA
1 CCTTCGGTATGGA
26444 GACCATTCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.02
19 16 0.37
20 26 0.60
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
CCTTCGGTATGGATACTAGT
Found at i:26556 original size:20 final size:20
Alignment explanation
Indices: 26531--26568 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26521 ATTACAACCT
26531 TCAGTATCGATACCAATTGG
1 TCAGTATCGATACCAATTGG
*
26551 TCAGTATCGATACTAATT
1 TCAGTATCGATACCAATT
26569 CCCTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TCAGTATCGATACCAATTGG
Found at i:30064 original size:41 final size:41
Alignment explanation
Indices: 30007--30248 Score: 236
Period size: 41 Copynumber: 5.8 Consensus size: 41
29997 AGGTTCATCC
*
30007 AGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTAA
1 AGACTTGTACTTTAGTGGCATTTTTATACAAACGCCGCTAA
* * ** *
30048 AGACTAGTACTTTAGTGGCATTTTTATATAAACGATGCAAA
1 AGACTTGTACTTTAGTGGCATTTTTATACAAACGCCGCTAA
* * * * *
30089 AGACTCGTACTTTAGTGGCGTTTTTTTTTCCAATAAATGCCGCTAA
1 AGACTTGTACTTTAGTGGC--ATTTTTAT---ACAAACGCCGCTAA
* *
30135 AGACTTGTACTTTAGTGGTATTTTTATACAAACGCCACTAA
1 AGACTTGTACTTTAGTGGCATTTTTATACAAACGCCGCTAA
* *
30176 AGGCTTGTAATTTAGTGG-AGTTTTT-TAACAAACGCCGCTAA
1 AGACTTGTACTTTAGTGGCA-TTTTTAT-ACAAACGCCGCTAA
* * * *
30217 AGAATTTTAGTTTAGTGGCGTTTTTATACAAA
1 AGACTTGTACTTTAGTGGCATTTTTATACAAA
30249 TGCCACAGTT
Statistics
Matches: 165, Mismatches: 27, Indels: 18
0.79 0.13 0.09
Matches are distributed among these distances:
40 2 0.01
41 123 0.75
42 1 0.01
43 6 0.04
44 6 0.04
46 27 0.16
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (41 bp):
AGACTTGTACTTTAGTGGCATTTTTATACAAACGCCGCTAA
Found at i:30190 original size:87 final size:87
Alignment explanation
Indices: 30040--30201 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
30030 TTATACAAAC
* ** *
30040 GCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATATAAACGATGCAAAAGACTCGTACTTTAGT
1 GCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATACAAACGACACAAAAGACTCGTAATTTAGT
*
30105 GGCGTTTTTTTTTCCAATAAAT
66 GGAGTTTTTTTTTCCAATAAAT
* * * * * *
30127 GCCGCTAAAGACTTGTACTTTAGTGGTATTTTTATACAAACGCCACTAAAGGCTTGTAATTTAGT
1 GCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATACAAACGACACAAAAGACTCGTAATTTAGT
30192 GGAGTTTTTT
66 GGAGTTTTTT
30202 AACAAACGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (87 bp):
GCCGCTAAAGACTAGTACTTTAGTGGCATTTTTATACAAACGACACAAAAGACTCGTAATTTAGT
GGAGTTTTTTTTTCCAATAAAT
Found at i:30235 original size:128 final size:128
Alignment explanation
Indices: 30007--30241 Score: 312
Period size: 128 Copynumber: 1.8 Consensus size: 128
29997 AGGTTCATCC
* *
30007 AGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACGCCACTAAAGACTAGTAATTTAGTGGCATTTT
* * *
30072 TATATAAACGATGCAAAAGACTCGTACTTTAGTGGCGTTTTTTTTTCCAATAAATGCCGCTAA
66 TATACAAACGACGCAAAAGAATCGTACTTTAGTGGCGTTTTTTTTTCCAATAAATGCCGCTAA
* * * *
30135 AGACTTGTACTTTAGTGGTATTTTTATACAAACGCCACTAAAGGCTTGTAATTTAGTGG-AGTTT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACGCCACTAAAGACTAGTAATTTAGTGGCA-TTT
* * ** *
30199 TT-TAACAAACGCCGCTAAAGAATTTTAGTTTAGTGGCGTTTTT
65 TTAT-ACAAACGACGCAAAAGAATCGTACTTTAGTGGCGTTTTT
30242 ATACAAATGC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
127 2 0.02
128 89 0.98
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (128 bp):
AGACTCGTACTTTAGTGGCATTTTTATACAAACGCCACTAAAGACTAGTAATTTAGTGGCATTTT
TATACAAACGACGCAAAAGAATCGTACTTTAGTGGCGTTTTTTTTTCCAATAAATGCCGCTAA
Found at i:33317 original size:43 final size:43
Alignment explanation
Indices: 33270--33378 Score: 191
Period size: 43 Copynumber: 2.5 Consensus size: 43
33260 CCAAAACGTT
*
33270 GCTATAGATCTGACCTTTTGCGGCATTTTTAGATACAAACGCC
1 GCTATAGATCTGACCTTTTACGGCATTTTTAGATACAAACGCC
*
33313 GCTATAGATCTGACCTTTTACGGCGTTTTTAGATACAAACGCC
1 GCTATAGATCTGACCTTTTACGGCATTTTTAGATACAAACGCC
*
33356 GCTATAGATCTAACCTTTTACGG
1 GCTATAGATCTGACCTTTTACGG
33379 TGTTTGTTCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (43 bp):
GCTATAGATCTGACCTTTTACGGCATTTTTAGATACAAACGCC
Found at i:33430 original size:43 final size:43
Alignment explanation
Indices: 33381--33534 Score: 129
Period size: 43 Copynumber: 3.7 Consensus size: 43
33371 TTTTACGGTG
*
33381 TTTGTTCAAAAAATGCCGCTACATATCTCGACATTTTGCGGCA
1 TTTGTTCAAAAAATGCCGCTATATATCTCGACATTTTGCGGCA
* * * * * * * **
33424 TTTGTTC--CAAA-GCCGCAATAGATCTTGACCTATGGCGGTG
1 TTTGTTCAAAAAATGCCGCTATATATCTCGACATTTTGCGGCA
* *
33464 TTTGTTCAAAAAACGCCGCTATATATCTCTACATTTTGCGGCGA
1 TTTGTTCAAAAAATGCCGCTATATATCTCGACATTTTGCGGC-A
* *
33508 -TTGTTCCAAAAACT-CCGCTATAGATCT
1 TTTGTT-CAAAAAATGCCGCTATATATCT
33535 TGACCTATGG
Statistics
Matches: 83, Mismatches: 23, Indels: 10
0.72 0.20 0.09
Matches are distributed among these distances:
40 27 0.33
41 3 0.04
42 3 0.04
43 44 0.53
44 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
TTTGTTCAAAAAATGCCGCTATATATCTCGACATTTTGCGGCA
Found at i:33471 original size:83 final size:85
Alignment explanation
Indices: 33349--33544 Score: 256
Period size: 83 Copynumber: 2.3 Consensus size: 85
33339 TTTTAGATAC
* * * ** *
33349 AAACGCCGCTATAGATC-TAACCTTTTACGGTGTTTGTTCAAAAAATGCCGCTACATATCTCGAC
1 AAACGCCGCAATAGATCTTGACCTATGGCGGTGTTTGTTCAAAAAACGCCGCTACATATCTCGAC
33413 ATTTTGCGGC-ATTTGTTCC-
66 ATTTTGCGGCGA-TTGTTCCA
* *
33432 AAA-GCCGCAATAGATCTTGACCTATGGCGGTGTTTGTTCAAAAAACGCCGCTATATATCTCTAC
1 AAACGCCGCAATAGATCTTGACCTATGGCGGTGTTTGTTCAAAAAACGCCGCTACATATCTCGAC
33496 ATTTTGCGGCGATTGTTCCAA
66 ATTTTGCGGCGATTGTTCC-A
* *
33517 AAACTCCGCTATAGATCTTGACCTATGG
1 AAACGCCGCAATAGATCTTGACCTATGG
33545 AGGCGTTTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
82 12 0.12
83 60 0.61
84 1 0.01
85 3 0.03
86 22 0.22
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (85 bp):
AAACGCCGCAATAGATCTTGACCTATGGCGGTGTTTGTTCAAAAAACGCCGCTACATATCTCGAC
ATTTTGCGGCGATTGTTCCA
Found at i:36525 original size:20 final size:20
Alignment explanation
Indices: 36500--36538 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36490 AGAGAAAATG
*
36500 AAAGAAGAAGATATGAAGAA
1 AAAGAAGAAGAAATGAAGAA
36520 AAAGAAGAAGAAATGAAGA
1 AAAGAAGAAGAAATGAAGA
36539 GAAGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.08
Consensus pattern (20 bp):
AAAGAAGAAGAAATGAAGAA
Found at i:39735 original size:25 final size:24
Alignment explanation
Indices: 39698--39744 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
39688 TATTTTATAT
* *
39698 CTTTTTGGATGGTTTTAAAAGGATG
1 CTTTTTAGATGG-TTAAAAAGGATG
*
39723 CTTTTTAGTTGGTTAAAAAGGA
1 CTTTTTAGATGGTTAAAAAGGA
39745 AAATTTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.43
Consensus pattern (24 bp):
CTTTTTAGATGGTTAAAAAGGATG
Found at i:43088 original size:23 final size:22
Alignment explanation
Indices: 43033--43075 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
43023 TAAACGACTG
*
43033 AAAAACATGCCA-AAAGGCAAA
1 AAAAACATGTCAGAAAGGCAAA
43054 AAAAACATGTCAGAAAGGCAAA
1 AAAAACATGTCAGAAAGGCAAA
43076 TGAAAACGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAAACATGTCAGAAAGGCAAA
Found at i:43643 original size:23 final size:25
Alignment explanation
Indices: 43602--43649 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
43592 TTTAGTAAAT
*
43602 AAAATACAAATAATGGTAAA-ATATG
1 AAAATAC-AATAATAGTAAATATATG
43627 AAAATAC-ATAATAGTAAATATAT
1 AAAATACAATAATAGTAAATATAT
43650 ATATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.27
Consensus pattern (25 bp):
AAAATACAATAATAGTAAATATATG
Found at i:57886 original size:16 final size:16
Alignment explanation
Indices: 57865--57897 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57855 AACCTCTATA
*
57865 AATTATATCCCAGTCT
1 AATTATATCCAAGTCT
57881 AATTATATCCAAGTCT
1 AATTATATCCAAGTCT
57897 A
1 A
57898 TAGACTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (16 bp):
AATTATATCCAAGTCT
Found at i:62328 original size:2 final size:2
Alignment explanation
Indices: 62321--62354 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
62311 AACGATAAAC
62321 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
62355 GCGCACACAC
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:74302 original size:21 final size:20
Alignment explanation
Indices: 74249--74309 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
74239 AGTCGAGGGT
* *
74249 TACATAGGTCCTTCAGGACATA
1 TACATAGGTCATTCGGGAC--A
74271 TACATAGGTCATTCGGGACA
1 TACATAGGTCATTCGGGACA
74291 TACATGAGGTCATTCGGGA
1 TACAT-AGGTCATTCGGGA
74310 TAAATTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 6 0.17
21 13 0.36
22 17 0.47
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (20 bp):
TACATAGGTCATTCGGGACA
Found at i:76444 original size:29 final size:30
Alignment explanation
Indices: 76411--76473 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
76401 GTGATATTAA
76411 ATTTAATAAGTTAAGA-AAAAATAAAATAT
1 ATTTAATAAGTTAAGACAAAAATAAAATAT
*
76440 ATTTAATAAGTTAATACAAAAATAAAATAT
1 ATTTAATAAGTTAAGACAAAAATAAAATAT
76470 ATTT
1 ATTT
76474 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTAATAAGTTAAGACAAAAATAAAATAT
Found at i:88008 original size:32 final size:32
Alignment explanation
Indices: 87948--88017 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
87938 GTTTTTGGTT
* * ** *
87948 AGATGAAAGGAGTTTTTTGTGTAGGAGATTGA
1 AGATGAAAGGAGTGTGTAATGTAAGAGATTGA
87980 AGATGAAAGGAGTGTGTAATGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTAATGTAAGAGATTGA
*
88012 CGATGA
1 AGATGA
88018 TGTGCACAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.01, G:0.34, T:0.29
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTAATGTAAGAGATTGA
Found at i:89211 original size:42 final size:42
Alignment explanation
Indices: 89109--89221 Score: 194
Period size: 41 Copynumber: 2.7 Consensus size: 42
89099 TTTCAAATTC
89109 CCGTGTTTGTTTCACGTAATTCGTTTTCC-AGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGAGAAAATGTTTT
89150 CCGTGTTTGTTTCACGTAATTCGTTTTCCGA-AAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGAGAAAATGTTTT
*
89191 CCTGTGTTTGTTTCACGTAATTGGTTTTCCG
1 CC-GTGTTTGTTTCACGTAATTCGTTTTCCG
89222 GAATGTAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
41 41 0.59
42 28 0.41
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.47
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGAGAAAATGTTTT
Found at i:89472 original size:30 final size:32
Alignment explanation
Indices: 89406--89485 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
89396 AAATATTATT
89406 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
89437 TATTATATTT-TTAATA-TTAT-ATAA-ATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
89465 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
89486 AAGATATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 5 0.12
29 4 0.10
30 12 0.29
31 11 0.26
32 10 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:89545 original size:27 final size:28
Alignment explanation
Indices: 89428--89582 Score: 86
Period size: 29 Copynumber: 5.4 Consensus size: 28
89418 AATATTTATA
* * *
89428 ATAATATAATATTATATTTTTAATATTAT
1 ATAATA-AAAATTATATATTTAATAATAT
* *
89457 ATAAATAATCAATTATAT-TATAATAATAT
1 AT-AATAA-AAATTATATATTTAATAATAT
* * *
89486 A-AGATATTATATT-TTTATTTTAATAATAT
1 ATA-ATA-AAAATTATATA-TTTAATAATAT
89515 ATAA-AAAAATTATATATTTAATAATGA-
1 ATAATAAAAATTATATATTTAATAAT-AT
** *
89542 ATAATATTATTTATATATTTAAATAATATT
1 ATAATAAAAATTATATATTT-AATAATA-T
*
89572 TTAATAAAAAT
1 ATAATAAAAAT
89583 ATTTAAAATA
Statistics
Matches: 94, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
27 20 0.21
28 24 0.26
29 31 0.33
30 19 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATAATAAAAATTATATATTTAATAATAT
Found at i:89549 original size:56 final size:56
Alignment explanation
Indices: 89425--89570 Score: 149
Period size: 56 Copynumber: 2.6 Consensus size: 56
89415 ATTAATATTT
* *
89425 ATAATAATATAATA-TTATATTTTTAATATTATATAAATAATCAATTATATTATAATA
1 ATAATAATATTATATTTATA-TTTTAATAATATATAAATAA-CAATTATATTATAATA
* *
89482 AT-ATAAGATATTATATTTTTATTTTAATAATATATAAA-AA-AATTATATATTTAATA
1 ATAAT-A-ATATTATATTTATATTTTAATAATATATAAATAACAATTATAT-TATAATA
*
89538 ATGAATAATATTAT-TTATATATTTAAATAATAT
1 AT-AATAATATTATATT-TATATTTTAATAATAT
89571 TTTAATAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
55 10 0.13
56 31 0.41
57 6 0.08
58 25 0.33
59 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (56 bp):
ATAATAATATTATATTTATATTTTAATAATATATAAATAACAATTATATTATAATA
Found at i:89599 original size:23 final size:22
Alignment explanation
Indices: 89573--89616 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
89563 AATAATATTT
89573 TAATAAAAATATTTAAAATATAC
1 TAATAAAAAT-TTTAAAATATAC
* * *
89596 TAATTAATATTTTTAAATATA
1 TAATAAAAATTTTAAAATATA
89617 ATATATACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAAAATTTTAAAATATAC
Found at i:89969 original size:20 final size:20
Alignment explanation
Indices: 89932--89970 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
89922 CCGTAAAATG
**
89932 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
89952 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
89971 CAGTAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:89986 original size:15 final size:15
Alignment explanation
Indices: 89944--89987 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
89934 TTCCAGAAAT
89944 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
89959 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
89973 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
89988 CTTCCACTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:90007 original size:21 final size:21
Alignment explanation
Indices: 89968--90008 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
89958 AGAATTCAAA
* **
89968 TTCCAGTAATTTATTTTCCAC
1 TTCCACTAATTTAAATTCCAC
89989 TTCCACTAATTTAAATTCCA
1 TTCCACTAATTTAAATTCCA
90009 GTATTTCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.44
Consensus pattern (21 bp):
TTCCACTAATTTAAATTCCAC
Found at i:90521 original size:37 final size:37
Alignment explanation
Indices: 90468--90572 Score: 149
Period size: 37 Copynumber: 2.8 Consensus size: 37
90458 CCTTTTCGTC
*
90468 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
90505 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
*
90542 CTACTATGATTTAAACTCC-AAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAA-ATAGGAT
90573 CCACAAACAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 4 0.07
37 56 0.93
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:91119 original size:2 final size:2
Alignment explanation
Indices: 91114--91145 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91104 GTTATTACCA
91114 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
91146 TTTCTTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91299 original size:12 final size:12
Alignment explanation
Indices: 91277--91318 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
91267 TCTTTCTTTT
91277 TATTATT-CTTG
1 TATTATTACTTG
91288 TATTATTACTTG
1 TATTATTACTTG
91300 TATTATTACTTG
1 TATTATTACTTG
91312 TATTATT
1 TATTATT
91319 TTTATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (12 bp):
TATTATTACTTG
Found at i:91336 original size:24 final size:24
Alignment explanation
Indices: 91277--91329 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
91267 TCTTTCTTTT
*
91277 TATTATT-CTTGTATTATTACTTG
1 TATTATTACTTGTATTATTACTTA
*
91300 TATTATTACTTGTATTATT-TTTA
1 TATTATTACTTGTATTATTACTTA
91323 TATTATT
1 TATTATT
91330 TATTTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (24 bp):
TATTATTACTTGTATTATTACTTA
Found at i:91546 original size:2 final size:2
Alignment explanation
Indices: 91539--91580 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
91529 TTACTATTAT
91539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91581 CACAAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91958 original size:18 final size:21
Alignment explanation
Indices: 91935--91982 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
91925 ATTTGTTTTT
91935 TTTACTTAC-T-ATTTTATC-
1 TTTACTTACTTCATTTTATCA
*
91953 TTTACTTTCTTCATTTTATCA
1 TTTACTTACTTCATTTTATCA
91974 TTTTACTTA
1 -TTTACTTA
91983 ATTTGTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 8 0.33
22 7 0.29
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTACTTACTTCATTTTATCA
Found at i:96302 original size:16 final size:16
Alignment explanation
Indices: 96283--96327 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 16
96273 GGGCAAAAAT
96283 AAAAAAGAAAAGAAACA
1 AAAAAAGAAAA-AAACA
96300 AAAAAAGAAAAAAACATA
1 AAAAAAGAAAAAAAC--A
96318 AAAAAAGAAA
1 AAAAAAGAAA
96328 GGACAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 11 0.42
18 11 0.42
ACGTcount: A:0.84, C:0.04, G:0.09, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAACA
Found at i:96336 original size:16 final size:17
Alignment explanation
Indices: 96283--96360 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
96273 GGGCAAAAAT
*
96283 AAAAAAGAAAAGAAACA
1 AAAAAAGAAAAGACACA
* *
96300 AAAAAAGAAAAAAACATA
1 AAAAAAG-AAAAGACACA
* *
96318 AAAAAAGAAAGGACAAAA
1 AAAAAAGAAAAGAC-ACA
*
96336 ATCAAAAAGAAAAAGAGACA
1 A--AAAAAG-AAAAGACACA
96356 AAAAA
1 AAAAA
96361 GAACATGCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 12 0.26
18 21 0.45
20 9 0.19
21 5 0.11
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAGACACA
Found at i:96343 original size:23 final size:24
Alignment explanation
Indices: 96299--96360 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
96289 GAAAAGAAAC
96299 AAAAAA-AGA-AAAAAACATAAAA
1 AAAAAAGAGACAAAAAACATAAAA
*
96321 AAAGAAAG-GACAAAAATCA-AAAA
1 AAA-AAAGAGACAAAAAACATAAAA
*
96344 GAAAAAGAGACAAAAAA
1 AAAAAAGAGACAAAAAA
96361 GAACATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 7 0.21
23 19 0.58
24 7 0.21
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.03
Consensus pattern (24 bp):
AAAAAAGAGACAAAAAACATAAAA
Found at i:97241 original size:18 final size:19
Alignment explanation
Indices: 97218--97254 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
97208 TTAACATCAA
*
97218 ATATTGGGGTAT-ATTTGG
1 ATATTGGGGCATCATTTGG
97236 ATATTGGGGCATCATTTGG
1 ATATTGGGGCATCATTTGG
97255 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (19 bp):
ATATTGGGGCATCATTTGG
Found at i:97831 original size:106 final size:106
Alignment explanation
Indices: 97630--99061 Score: 2039
Period size: 106 Copynumber: 13.6 Consensus size: 106
97620 ATATCGTGCC
* * * * * * *
97630 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGACAAT-AACAACTTT-T
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
* * *
97693 CAATTTCGGAGCCAACTTCAACTTCCCAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
97735 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
97800 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
97841 ACTCCAGATAACACAAGTTCAACTTCACGATGAAGGGACAGCTGGTTGTCAATAAACAACTTT-T
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
97905 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
97947 ACTCCAGACAACGCAAGTTTAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
98012 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
98053 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
98118 AATTTCAGAGCCAATTTCAACTTCACAGGGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
98159 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
98224 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
98265 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
98330 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
98371 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
98436 AATTTCTGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
98477 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
98542 AATTTCATAGCCAATTTAAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
98583 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * * *
98648 AATTTTAGAGCAAATTTCAATTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
98689 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
98754 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * **
98795 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCAATGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
* * *
98859 CAATTTCATAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
98901 AC-CCAAGAGAACACAAGCTCAACTTCACGACGAAAGGG-CGGCTGATTG-CAA-CAA-AATTT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACG-AAGGGACCGCTGGTTGTCAATAAACAATTTC
*
98960 -C-A-TTCAGAGTCAATTT-AACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
98999 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAATAAACAATTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTC
99062 AACACAAGTT
Statistics
Matches: 1201, Mismatches: 112, Indels: 31
0.89 0.08 0.02
Matches are distributed among these distances:
97 6 0.00
98 53 0.04
99 16 0.01
100 3 0.00
101 6 0.00
102 3 0.00
103 2 0.00
104 2 0.00
105 55 0.05
106 1044 0.87
107 11 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:99089 original size:54 final size:49
Alignment explanation
Indices: 99007--99110 Score: 163
Period size: 54 Copynumber: 2.0 Consensus size: 49
98997 GGACTCAAGA
99007 CAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAATAAACAATTT
1 CAACACAAGTTCAACTTCACAACGAA-GG--GAC-GGTT-TCAATAAACAATTT
99061 CAACACAAGTTCAACTTCACAACGAAGGGACGGTTTCAATAAACAATTT
1 CAACACAAGTTCAACTTCACAACGAAGGGACGGTTTCAATAAACAATTT
99110 C
1 C
99111 CCGTTCCAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
49 15 0.30
50 4 0.08
51 3 0.06
53 2 0.04
54 26 0.52
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.22
Consensus pattern (49 bp):
CAACACAAGTTCAACTTCACAACGAAGGGACGGTTTCAATAAACAATTT
Found at i:99938 original size:37 final size:37
Alignment explanation
Indices: 99885--99989 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
99875 CCTTTTCGTC
*
99885 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
99922 TTGCTAGGATTTAAACTCCTAAAAATATGATTGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
99959 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
99990 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:100628 original size:15 final size:15
Alignment explanation
Indices: 100569--100647 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 15
100559 TATTATTTAT
100569 TATTATTTTTACTATTA
1 TATT-TTTTTA-TATTA
100586 TATTTCCTTTTAT-TCTA
1 TATTT--TTTTATAT-TA
*
100603 CTATTTATTTATATTA
1 -TATTTTTTTATATTA
100619 TATTTTTTTATATT-
1 TATTTTTTTATATTA
*
100633 TATTATTATTATATT
1 TATT-TTTTTATATT
100648 TTTTTACTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.08
15 22 0.42
16 9 0.17
17 8 0.15
18 10 0.19
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTTTATATTA
Found at i:100642 original size:25 final size:25
Alignment explanation
Indices: 100604--100653 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
100594 TTTATTCTAC
100604 TATTTATTTATATTATATTTTTTTA
1 TATTTATTTATATTATATTTTTTTA
100629 TATTTA-TTATTATTATATTTTTTTA
1 TATTTATTTA-TATTATATTTTTTTA
100654 CTTTCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTTATTTATATTATATTTTTTTA
Found at i:100648 original size:15 final size:14
Alignment explanation
Indices: 100552--100653 Score: 54
Period size: 15 Copynumber: 7.2 Consensus size: 14
100542 TGCATTTTTA
100552 TTATTACTA-TTA-T
1 TTATTA-TATTTATT
100565 TTATTATTATTT-TT
1 TTATTA-TATTTATT
* *
100579 ACTATTATATTTCCTT
1 -TTATTATATTT-ATT
* *
100595 TTATTCTA-CTA-T
1 TTATTATATTTATT
100607 TTATTTATATTATATT
1 TTA-TTATATT-TATT
*
100623 TTTTTATATTTATT
1 TTATTATATTTATT
100637 ATTATTATATTT-TT
1 -TTATTATATTTATT
100651 TTA
1 TTA
100654 CTTTCTCTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.06
13 15 0.22
14 15 0.22
15 30 0.43
16 5 0.07
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATATTTATT
Found at i:100673 original size:55 final size:58
Alignment explanation
Indices: 100552--100705 Score: 140
Period size: 58 Copynumber: 2.6 Consensus size: 58
100542 TGCATTTTTA
*
100552 TTATTACTATTATTTATTATTATTT-TTACTATTATATTTCCTTTTATTCTACTATTTATTT
1 TTATTA-TATT-TTT-TTATTATTTATTATTATTATATTT-CTTTTATTCTACTATTTATTT
* * *
100613 ATATTATATTTTTTTA-TATTTATTATTATTATATTT-TTTTACTT-T-CTCTTTCTTT
1 TTATTATATTTTTTTATTATTTATTATTATTATATTTCTTTTA-TTCTACTATTTATTT
* *
100668 TTATTAT-TCTTGTATTATTACTTTATTATTTTTATATT
1 TTATTATAT-TT-TTTTATTA-TTTATTATTATTATATT
100706 ATTTATTTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
54 1 0.01
55 16 0.20
56 10 0.12
57 9 0.11
58 32 0.40
59 3 0.04
60 4 0.05
61 5 0.06
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (58 bp):
TTATTATATTTTTTTATTATTTATTATTATTATATTTCTTTTATTCTACTATTTATTT
Found at i:100685 original size:11 final size:10
Alignment explanation
Indices: 100667--100712 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
100657 TCTCTTTCTT
100667 TTTATTATTC
1 TTTATTATTC
100677 TTGTATTATTAC
1 TT-TATTATT-C
100689 TTTATTATT-
1 TTTATTATTC
*
100698 TTTA-TATTA
1 TTTATTATTC
100707 TTTATT
1 TTTATT
100713 TTGTTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 4 0.12
9 8 0.25
10 3 0.09
11 14 0.44
12 3 0.09
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATTATTC
Found at i:100692 original size:22 final size:22
Alignment explanation
Indices: 100667--100708 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
100657 TCTCTTTCTT
*
100667 TTTATTATTCTTGTATTATTAC
1 TTTATTATTCTTATATTATTAC
*
100689 TTTATTATTTTTATATTATT
1 TTTATTATTCTTATATTATT
100709 TATTTTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTATTATTCTTATATTATTAC
Found at i:100722 original size:19 final size:21
Alignment explanation
Indices: 100667--100723 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
100657 TCTCTTTCTT
* *
100667 TTTATTATTCTTGTATTATTAC
1 TTTATTATTGTTATA-TATTAC
100689 TTTATTATT-TT-TATATTA-
1 TTTATTATTGTTATATATTAC
100707 TTTATT-TTGTTATATAT
1 TTTATTATTGTTATATAT
100724 ATATATATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 10 0.30
20 2 0.06
21 2 0.06
22 9 0.27
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTATTATTGTTATATATTAC
Found at i:105917 original size:17 final size:17
Alignment explanation
Indices: 105890--105956 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
105880 AGAGTTATTC
*
105890 TAATAAATGAACTAGTT
1 TAATGAATGAACTAGTT
*
105907 TGATGAATGAACTAGTT
1 TAATGAATGAACTAGTT
* *
105924 TAATTAATGAACTAACTT
1 TAATGAATGAACT-AGTT
* *
105942 TATTCAATGAACTAG
1 TAATGAATGAACTAG
105957 ATGCATGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 27 0.66
18 14 0.34
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
TAATGAATGAACTAGTT
Found at i:106100 original size:18 final size:19
Alignment explanation
Indices: 106072--106115 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
106062 ACACTTATAA
*
106072 AATTCAATGAATCTCATGC
1 AATTCAATGAAACTCATGC
*
106091 AATT-AATGAAACTTATGC
1 AATTCAATGAAACTCATGC
106109 AAATTCA
1 -AATTCA
106116 TGCAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 12 0.57
19 8 0.38
20 1 0.05
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (19 bp):
AATTCAATGAAACTCATGC
Found at i:106645 original size:15 final size:16
Alignment explanation
Indices: 106619--106648 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106609 TTAAAGAACA
106619 TTTCTCTTCACTTTCT
1 TTTCTCTTCACTTTCT
106635 TTTCT-TTCACTTTC
1 TTTCTCTTCACTTTC
106649 ATGCTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCTCTTCACTTTCT
Found at i:109145 original size:17 final size:17
Alignment explanation
Indices: 109118--109197 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
109108 AGAGTTATTC
*
109118 TAATAAATGAACTAGTT
1 TAATGAATGAACTAGTT
*
109135 TGATGAATGAACTAGTT
1 TAATGAATGAACTAGTT
* *
109152 TAATTAATGAACTAACTT
1 TAATGAATGAACT-AGTT
* * *
109170 TATTTAATGAACTAGATG
1 TAATGAATGAACTAG-TT
109188 T-ATGAATGAA
1 TAATGAATGAA
109198 ATAGCTTACT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
17 34 0.67
18 17 0.33
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (17 bp):
TAATGAATGAACTAGTT
Found at i:114587 original size:14 final size:14
Alignment explanation
Indices: 114570--114597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
114560 TGGGCGTGAT
114570 TGGTGATGGAAATA
1 TGGTGATGGAAATA
114584 TGGTGATGGAAATA
1 TGGTGATGGAAATA
114598 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
TGGTGATGGAAATA
Found at i:117822 original size:27 final size:27
Alignment explanation
Indices: 117792--117863 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
117782 TTTAAAGTTT
*
117792 TCGAGTTCGAGTTGAGCTCAGTAGTAC
1 TCGAGTTCGAGTTCAGCTCAGTAGTAC
117819 TCGAGTTCGAGTTCAGCTCAGTAGTAC
1 TCGAGTTCGAGTTCAGCTCAGTAGTAC
*
117846 TCGAGTTCGA-CTCAGCTC
1 TCGAGTTCGAGTTCAGCTC
117864 GTTTAACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
26 7 0.16
27 36 0.84
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (27 bp):
TCGAGTTCGAGTTCAGCTCAGTAGTAC
Found at i:117956 original size:30 final size:30
Alignment explanation
Indices: 117920--117993 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
117910 AGAGAATTGG
*
117920 CGGTTCACACCGGTTTTGCTGGGTT-TCAAC
1 CGGTTCACACCGGTTTTGC-CGGTTCTCAAC
117950 CGGTTCAC-CCTGGTTTTGCCGGTTCTCAAC
1 CGGTTCACACC-GGTTTTGCCGGTTCTCAAC
*
117980 CGGTTC-TACCGGTT
1 CGGTTCACACCGGTT
117994 CTGTTCTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 10 0.26
30 29 0.74
ACGTcount: A:0.11, C:0.30, G:0.26, T:0.34
Consensus pattern (30 bp):
CGGTTCACACCGGTTTTGCCGGTTCTCAAC
Found at i:118466 original size:21 final size:21
Alignment explanation
Indices: 118437--118481 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
118427 ATTCTGACTA
118437 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
118458 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
118479 TCG
1 TCG
118482 TAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:118511 original size:20 final size:20
Alignment explanation
Indices: 118483--118625 Score: 171
Period size: 20 Copynumber: 7.1 Consensus size: 20
118473 CCTAATTCGT
118483 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* ** *
118503 AACGCGAATTTGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
*
118524 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
118544 AATGAGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
118564 AATGCGATTACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* * *
118584 AATGCGAATATGTAAATTGT
1 AATGCGAATACGTAAATCGC
118604 AATGCGAAT-CTGTAAATCGC
1 AATGCGAATAC-GTAAATCGC
118624 AA
1 AA
118626 CAAGATTCTG
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 86 0.85
21 15 0.15
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:119538 original size:24 final size:24
Alignment explanation
Indices: 119487--119540 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
119477 GTATTCGAAA
* *
119487 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGCCAATACCCAGAC
* *
119511 TTTGATCTTGGCCAATACTCAGAT
1 TTTGATCTTGGCCAATACCCAGAC
119535 TTTGAT
1 TTTGAT
119541 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGCCAATACCCAGAC
Found at i:121942 original size:20 final size:19
Alignment explanation
Indices: 121917--122009 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 19
121907 GACATTCATT
121917 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAA-A
121937 TGACTATCGCAGCACG-GAAA
1 TGACTATCGCA--ACGCGAAA
*
121957 TGACTATCGCAATGC-ATAA
1 TGACTATCGCAACGCGA-AA
*
121976 TTACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC-GAAA
121996 TGACTATCGCAACG
1 TGACTATCGCAACG
122010 AGAGAATCGC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 15 0.24
20 38 0.60
21 4 0.06
22 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:121994 original size:39 final size:40
Alignment explanation
Indices: 121917--122009 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 40
121907 GACATTCATT
*
121917 TGACTATCGCAACGCGAATATGACTATCGCAGCACGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
* * *
121957 TGACTATCGCAATGC--ATAATTACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGAAT-ATGACTATCGCAACACGGAAA
121996 TGACTATCGCAACG
1 TGACTATCGCAACG
122010 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 2 0.04
39 31 0.66
40 14 0.30
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
Found at i:122038 original size:19 final size:19
Alignment explanation
Indices: 122014--122059 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
122004 GCAACGAGAG
122014 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
122033 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
122052 AATCGCAA
1 AATCGCAA
122060 CGAGTGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:122148 original size:33 final size:34
Alignment explanation
Indices: 122096--122161 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
122086 TTCACATTGC
122096 GATTTTCATTTTCGCATTGCGATTCACTCGTTGT
1 GATTTTCATTTTCGCATTGCGATTCACTCGTTGT
* *
122130 GATTTTCA-TTTCGTATTGCGATTCTCTCGTTG
1 GATTTTCATTTTCGCATTGCGATTCACTCGTTG
122162 CGATAGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (34 bp):
GATTTTCATTTTCGCATTGCGATTCACTCGTTGT
Found at i:122306 original size:14 final size:14
Alignment explanation
Indices: 122287--122323 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
122277 CATCAATTAA
122287 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
122301 ACAAATCATCTTTT
1 ACAAATCAACATTT
122315 ACAAATCAA
1 ACAAATCAA
122324 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:123784 original size:42 final size:42
Alignment explanation
Indices: 123677--123784 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
123667 TCTAGAATGT
* * * *
123677 TGGGAG-GGACCTCTTCAACGATGAAAGTGGTCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
* * ** *
123719 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
123761 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
123785 CAGGTGAGTC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 47 0.90
43 5 0.10
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGAAAGGGGCCTCTTGAACGA
Found at i:124299 original size:20 final size:20
Alignment explanation
Indices: 124276--124354 Score: 104
Period size: 20 Copynumber: 4.0 Consensus size: 20
124266 AAATCGCAAC
124276 GCGAAAATGACTATCACAAT
1 GCGAAAATGACTATCACAAT
*
124296 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCACAAT
* * *
124316 ACAAAAATGACTATCGCAAT
1 GCGAAAATGACTATCACAAT
**
124336 GCGAATTTGACTATCACAA
1 GCGAAAATGACTATCACAA
124355 CGAGAGAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (20 bp):
GCGAAAATGACTATCACAAT
Found at i:124420 original size:20 final size:20
Alignment explanation
Indices: 124395--124463 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
124385 CAACAACAAA
**
124395 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
*
124415 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
124435 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
124455 ATCGCAACG
1 ATCGCAACG
124464 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:124548 original size:20 final size:20
Alignment explanation
Indices: 124508--124617 Score: 168
Period size: 20 Copynumber: 5.5 Consensus size: 20
124498 GATTCTTTCG
*
124508 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
* *
124528 TTGAGATAGACATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
124548 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
124568 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
124588 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
124608 TTGCGATAGT
1 TTGCGATAGT
124618 AAATTATTCT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
19 4 0.05
20 78 0.95
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:124575 original size:60 final size:56
Alignment explanation
Indices: 124487--124617 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 56
124477 GCGATTTTCA
124487 TTTCGCATTGCGAT--TCTTTCGTTGCGATAGTCAAATTTGCATTGAGATAGACAT
1 TTTCGCATTGCGATAGTCTTTCGTTGCGATAGTCAAATTTGCATTGAGATAGACAT
** * *
124541 TTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTC--TTTCG--TTGCGATAGTCAAATTTGCATTGAGATAGACAT
124601 TTTCGCATTGCGATAGT
1 TTTCGCATTGCGATAGT
124618 AAATTATTCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
54 14 0.21
56 2 0.03
58 5 0.07
60 46 0.69
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (56 bp):
TTTCGCATTGCGATAGTCTTTCGTTGCGATAGTCAAATTTGCATTGAGATAGACAT
Found at i:124617 original size:40 final size:40
Alignment explanation
Indices: 124470--124617 Score: 168
Period size: 40 Copynumber: 3.9 Consensus size: 40
124460 AACGAGAGAA
* **
124470 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* * *
124505 TCG--TTGCGATAGTCAAATTT-GCATTGAGATAGACATTT
1 TCGCATTGCGATAGTC-ATTTTCGCATTGCGATAGTCATTT
124543 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
124583 TTGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
124618 AAATTATTCT
Statistics
Matches: 95, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
33 8 0.08
34 10 0.11
35 6 0.06
36 1 0.01
38 5 0.05
39 4 0.04
40 61 0.64
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:126977 original size:22 final size:22
Alignment explanation
Indices: 126916--126977 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
126906 TGACCGTGAA
* *
126916 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
126938 T-ATTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
126956 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
126978 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 12 0.38
19 4 0.12
21 4 0.12
22 12 0.38
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:127195 original size:20 final size:20
Alignment explanation
Indices: 127172--127265 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
127162 CGATAGTCAG
127172 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
127192 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
127212 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* ** *
127233 ATCCGTGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
127253 ATTCGCATTGCGA
1 ATTCGCATTGCGA
127266 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 45 0.79
21 12 0.21
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:128836 original size:25 final size:25
Alignment explanation
Indices: 128808--128860 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
128798 AATGTGCGAC
128808 TATAATTATAAACTTAACACATAAT
1 TATAATTATAAACTTAACACATAAT
128833 TATAATTATAAACTTAACACATAAT
1 TATAATTATAAACTTAACACATAAT
128858 TAT
1 TAT
128861 GATATTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (25 bp):
TATAATTATAAACTTAACACATAAT
Found at i:135481 original size:17 final size:17
Alignment explanation
Indices: 135461--135498 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
135451 TAATATGACA
135461 AATAAAAT-AAATTAATT
1 AATAAAATGAAA-TAATT
*
135478 AATAAAATGACATAATT
1 AATAAAATGAAATAATT
135495 AATA
1 AATA
135499 TTTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
AATAAAATGAAATAATT
Found at i:137009 original size:23 final size:23
Alignment explanation
Indices: 136945--137051 Score: 150
Period size: 22 Copynumber: 4.8 Consensus size: 23
136935 CAAAAATACA
* *
136945 AATGGGTACCGATACCCC-TATG
1 AATGGGTATCAATACCCCTTATG
136967 AAT-GGTATCAAT-CCCCTTATG
1 AATGGGTATCAATACCCCTTATG
136988 AATGGGTATCAATACCCCTTATG
1 AATGGGTATCAATACCCCTTATG
137011 AATGGGTATCAATA-CCCTTATG
1 AATGGGTATCAATACCCCTTATG
* *
137033 AATGGGTACCGATACCCCT
1 AATGGGTATCAATACCCCT
137052 ATGGGTATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
20 4 0.05
21 14 0.18
22 32 0.42
23 27 0.35
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (23 bp):
AATGGGTATCAATACCCCTTATG
Found at i:137031 original size:45 final size:44
Alignment explanation
Indices: 136945--137068 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 44
136935 CAAAAATACA
*
136945 AATGGGTACCGATACCCC-TATGAATGGTATCAATCCCCTTATG
1 AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCTTATG
* *
136988 AATGGGTATCAATACCCCTTATGAATGGGTATCAATACCCTTATG
1 AATGGGTACCGATACCCCTTATGAAT-GGTATCAATACCCTTATG
137033 AATGGGTACCGATACCCC-TATG---GGTATCAATACCCT
1 AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCT
137069 AGGTATTGAT
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
40 14 0.19
43 16 0.22
44 11 0.15
45 33 0.45
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCTTATG
Found at i:137989 original size:24 final size:24
Alignment explanation
Indices: 137962--138007 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
137952 ATGCTGATTG
* *
137962 CCTTGTGC-CTTTGAAGCTTCTTCT
1 CCTTGAGCTCTTTCAAG-TTCTTCT
137986 CCTTGAGCTCTTTCAAGTTCTT
1 CCTTGAGCTCTTTCAAGTTCTT
138008 GTGAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.11, C:0.28, G:0.15, T:0.46
Consensus pattern (24 bp):
CCTTGAGCTCTTTCAAGTTCTTCT
Found at i:138263 original size:22 final size:21
Alignment explanation
Indices: 138238--138279 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
138228 CAATTCATTT
138238 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTT-TTTTA
138260 ATCTTATTTTTATCTTTTTT
1 ATCTTATTTTTATCTTTTTT
138280 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (21 bp):
ATCTTATTTTTATCTTTTTTA
Found at i:139611 original size:11 final size:11
Alignment explanation
Indices: 139587--139631 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
139577 TTGGTGCTGG
139587 AAACAAGATAA
1 AAACAAGATAA
* *
139598 AAATAAGATTA
1 AAACAAGATAA
139609 AAACAAGATAA
1 AAACAAGATAA
139620 AGAA-AAGATAA
1 A-AACAAGATAA
139631 A
1 A
139632 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:139615 original size:22 final size:22
Alignment explanation
Indices: 139587--139628 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
139577 TTGGTGCTGG
139587 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
139609 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
139629 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:145988 original size:11 final size:11
Alignment explanation
Indices: 145964--146008 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
145954 TTGGTGCTGG
145964 AAACAAGATAA
1 AAACAAGATAA
* *
145975 AAATAAGATTA
1 AAACAAGATAA
145986 AAACAAGATAA
1 AAACAAGATAA
145997 AGAA-AAGATAA
1 A-AACAAGATAA
146008 A
1 A
146009 TGAATTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:145992 original size:22 final size:22
Alignment explanation
Indices: 145964--146005 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
145954 TTGGTGCTGG
145964 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
145986 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
146006 AAATGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:149621 original size:14 final size:15
Alignment explanation
Indices: 149581--149622 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
149571 ACCTTAATGA
149581 TTATT-AAAAATTTG
1 TTATTAAAAAATTTG
*
149595 TTACTAAATAAATTT-
1 TTATTAAA-AAATTTG
149610 TTATTAAAAAATT
1 TTATTAAAAAATT
149623 CAAAGAGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TTATTAAAAAATTTG
Found at i:150064 original size:15 final size:14
Alignment explanation
Indices: 150044--150074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
150034 TATTTAAGAC
150044 CTAGTCAATTTAGAG
1 CTAGTCAATTTA-AG
150059 CTAGTCAATTTAAG
1 CTAGTCAATTTAAG
150073 CT
1 CT
150075 CGGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (14 bp):
CTAGTCAATTTAAG
Found at i:152635 original size:32 final size:32
Alignment explanation
Indices: 152579--152654 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
152569 CAATAGCTTC
* *
152579 ATCAAAATATTATAAATTATTAATTACAATTT
1 ATCAAATTATTATAAATTAATAATTACAATTT
** *
152611 ATTGAATTATTATAGAA-TAATAATTACATTTT
1 ATCAAATTATTATA-AATTAATAATTACAATTT
152643 ATCAAATTATTA
1 ATCAAATTATTA
152655 CAAAATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (32 bp):
ATCAAATTATTATAAATTAATAATTACAATTT
Found at i:152744 original size:15 final size:14
Alignment explanation
Indices: 152708--152746 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
152698 ACCATAATGA
152708 TTATTAAAAATTTG
1 TTATTAAAAATTTG
* *
152722 TTACTAAATAATTTT
1 TTATTAAA-AATTTG
152737 TTATTAAAAA
1 TTATTAAAAA
152747 ATTCAATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATTAAAAATTTG
Found at i:154711 original size:23 final size:23
Alignment explanation
Indices: 154643--154704 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
154633 GAATGGGTAT
154643 CCCTTATAAATGGGTATCAATAC
1 CCCTTATAAATGGGTATCAATAC
154666 CCCTTATAAATGGGTATCAATAC
1 CCCTTATAAATGGGTATCAATAC
*
154689 CCCTTATGAATGGGTA
1 CCCTTATAAATGGGTA
154705 CCGATACTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (23 bp):
CCCTTATAAATGGGTATCAATAC
Found at i:157347 original size:18 final size:18
Alignment explanation
Indices: 157324--157381 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
157314 CAACAATTGG
*
157324 TAACAATGGGTATCTTTT
1 TAACAATTGGTATCTTTT
157342 TAACAATTGGTATCCTTTT
1 TAACAATTGGTAT-CTTTT
157361 GTAAACAATTGGTATCTTTT
1 -T-AACAATTGGTATCTTTT
157381 T
1 T
157382 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 6 0.17
21 12 0.33
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:157606 original size:22 final size:21
Alignment explanation
Indices: 157581--157647 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
157571 CAAAAATAAA
157581 AATGAGTACCGATACCCCTATG
1 AATG-GTACCGATACCCCTATG
* *
157603 AATGGTATCAATACCCCTTATG
1 AATGGTACCGATACCCC-TATG
*
157625 AATGGGTACCGATACCCTTATG
1 AAT-GGTACCGATACCCCTATG
157647 A
1 A
157648 GTATCAATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 11 0.29
22 16 0.42
23 11 0.29
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
AATGGTACCGATACCCCTATG
Found at i:161268 original size:11 final size:11
Alignment explanation
Indices: 161254--161296 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
161244 ATTCGAGCTC
161254 AAAACTCGATT
1 AAAACTCGATT
161265 AAAACTCGATTT
1 AAAACTCGA-TT
** *
161277 TGAGCTCGATT
1 AAAACTCGATT
161288 AAAACTCGA
1 AAAACTCGA
161297 GACAGGACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (11 bp):
AAAACTCGATT
Found at i:161374 original size:21 final size:21
Alignment explanation
Indices: 161350--161393 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
161340 TATACACTCT
161350 ACCCTACCCCCTTATTCTCCA
1 ACCCTACCCCCTTATTCTCCA
161371 ACCCTACCCCCTTATTCTCCA
1 ACCCTACCCCCTTATTCTCCA
161392 AC
1 AC
161394 ACCCACCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.52, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCCTACCCCCTTATTCTCCA
Found at i:162635 original size:7 final size:7
Alignment explanation
Indices: 162625--162707 Score: 80
Period size: 7 Copynumber: 11.7 Consensus size: 7
162615 AGGGCTTAGA
162625 GTTTATG
1 GTTTATG
162632 GTTTATG
1 GTTTATG
162639 GTTTATG
1 GTTTATG
162646 GTTTATG
1 GTTTATG
*
162653 GTTTAAG
1 GTTTATG
*
162660 ATTT-TAG
1 GTTTAT-G
162667 GTTT-TAG
1 GTTTAT-G
162674 AGTTTATG
1 -GTTTATG
*
162682 GTTTATA
1 GTTTATG
*
162689 GTTTAAG
1 GTTTATG
*
162696 GTTTAAG
1 GTTTATG
162703 GTTTA
1 GTTTA
162708 CGTCTAGGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
7 60 0.91
8 5 0.08
9 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (7 bp):
GTTTATG
Found at i:162678 original size:29 final size:28
Alignment explanation
Indices: 162625--162707 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
162615 AGGGCTTAGA
* * *
162625 GTTTATGGTTTATGGTTTATGGTTTATG
1 GTTTATAGTTTAAGGTTTAAGGTTTATG
* *
162653 GTTTA-AGATTTTAGGTTTTAGAGTTTATG
1 GTTTATAG-TTTAAGGTTTAAG-GTTTATG
162682 GTTTATAGTTTAAGGTTTAAGGTTTA
1 GTTTATAGTTTAAGGTTTAAGGTTTA
162708 CGTCTAGGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 19 0.42
29 23 0.51
30 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (28 bp):
GTTTATAGTTTAAGGTTTAAGGTTTATG
Found at i:174231 original size:163 final size:162
Alignment explanation
Indices: 174045--174361 Score: 483
Period size: 163 Copynumber: 2.0 Consensus size: 162
174035 ATCCAAATTA
* * ***
174045 AAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
* *
174110 AACCGGTAAAGCGCTACCGGATACATTTAAAGTGTC-AGTACTTTAATATAAGGATCGACACTTC
66 AACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGA-TACTTT-ATATAAGGATCGACACTTC
174174 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
129 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
* * *
174208 AAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCTGTAACAAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
* * *
174273 AACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTGT
66 AACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
*
174338 GAATTTAAAAGAGAAGTAGTTTTA
131 GAATTTAAAAGAGAAGCAGTTTTA
174362 GCGCCTATAA
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 43 0.31
163 95 0.68
164 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (162 bp):
AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
AACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
Found at i:174261 original size:20 final size:19
Alignment explanation
Indices: 174237--174283 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
174227 CGATATACCA
174237 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
174257 TGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
174277 GGTAAAA
1 GGTAAAA
174284 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:176159 original size:21 final size:21
Alignment explanation
Indices: 176133--176197 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
176123 AAGACAATCA
*
176133 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
176154 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
176175 AGAGTCAAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
176196 AG
1 AG
176198 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:176294 original size:32 final size:32
Alignment explanation
Indices: 176231--176290 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
176221 AAATAGATGG
*
176231 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
*
176263 AGTGGTGAAAGAAGTTG-GGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
176291 GTGATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:176899 original size:6 final size:6
Alignment explanation
Indices: 176888--176999 Score: 98
Period size: 6 Copynumber: 18.7 Consensus size: 6
176878 CAAGCGATCA
* * * * *
176888 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * *
176936 ATGACG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGATG ACGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
176984 ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGA
177000 TGATCCAAAC
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:177003 original size:12 final size:12
Alignment explanation
Indices: 176888--176999 Score: 143
Period size: 12 Copynumber: 9.3 Consensus size: 12
176878 CAAGCGATCA
*
176888 ATGAAGATGAAG
1 ATGACGATGAAG
*
176900 CTGACGATGAAG
1 ATGACGATGAAG
176912 ATGACGATGAAG
1 ATGACGATGAAG
*
176924 ATGACGATGATG
1 ATGACGATGAAG
176936 ATGACGATGAAG
1 ATGACGATGAAG
*
176948 CTGACGATGAAG
1 ATGACGATGAAG
176960 ATGACGATGAAG
1 ATGACGATGAAG
* * *
176972 ATGATGACGATG
1 ATGACGATGAAG
* *
176984 ATGATGATGATG
1 ATGACGATGAAG
176996 ATGA
1 ATGA
177000 TGATCCAAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 89 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:178446 original size:183 final size:183
Alignment explanation
Indices: 178208--178964 Score: 1319
Period size: 183 Copynumber: 4.2 Consensus size: 183
178198 CAAAGTTTTC
* * *
178208 ACAC-TTTTAATA-TGTGTCTGTAC-TTATGTCCAGAATGGAA-AAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGAGTCGATACCTTGT
178269 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
178334 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
178387 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGAGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGAGTCGATACCTTGT
*
178452 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAAATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * *
178517 AACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
* * *
178570 ACAATTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAGAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGAGTCGATACCTTGT
*
178635 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
178700 AACCGGTATAAATATACC-AGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGA-TTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
178753 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAAT-ATGTCGATACCTTG
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGA-GTCGATACCTTG
*
178817 TCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATA
65 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
178882 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
178936 ACACTTTTTAATATTGTGTCGGTACTTTA
1 ACACTTTTTAATATTGTGTCGGTACTTTA
178965 CAATAGGAGT
Statistics
Matches: 548, Mismatches: 23, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
179 4 0.01
180 8 0.01
181 10 0.02
182 16 0.03
183 510 0.93
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGAGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:181376 original size:25 final size:25
Alignment explanation
Indices: 181348--181412 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
181338 TTATCATTAA
*
181348 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAAATACAT
181373 ATTTAGGTATGTACAATAAATACAT
1 ATTTAGGTATGTACAATAAATACAT
181398 ATTTAGGTATGTACA
1 ATTTAGGTATGTACA
181413 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAAATACAT
Found at i:181792 original size:21 final size:21
Alignment explanation
Indices: 181747--181817 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
181737 GTAAAATATG
181747 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCG-TT-TATA
181770 ATGTAATAGGTAGCGTTTATA
1 ATGTAATAGGTAGCGTTTATA
*
181791 ATGTAATAGGTAGTGTTTATA
1 ATGTAATAGGTAGCGTTTATA
*
181812 TTGTAA
1 ATGTAA
181818 AGTATCTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 29 0.63
22 2 0.04
23 15 0.33
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (21 bp):
ATGTAATAGGTAGCGTTTATA
Found at i:182244 original size:23 final size:23
Alignment explanation
Indices: 182174--182244 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
182164 ATAGGTAAAA
* *
182174 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
182197 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
182220 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
182243 AT
1 AT
182245 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:182291 original size:432 final size:423
Alignment explanation
Indices: 181496--182347 Score: 1455
Period size: 432 Copynumber: 2.0 Consensus size: 423
181486 TATTATTAAA
181496 AAAAACAATAACATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCT
1 AAAAACAATAACATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCT
181561 AATATTATTTATAAAATATAAAAACAATAAAATAATTTTTGTGCAAATGAAATTATTAAATTAAT
66 AATATTATTTATAAAATATAAAAACAATAAAATAATTTTTGTGCAAATGAAATTATTAAATTAAT
*
181626 ATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAGTTACATAACTTTAAAAAA
131 ATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAA
*
181691 AGTATCGATCCTTTTTATAAAAGTATGGACACTTTCAATATAATAGGTAAAATATGATGTAATAG
196 AGTATCGATCCTTTTTATAAAAGTATAGACACTTTCAATATAATAGGTAAAATATGATGTAATAG
* *
181756 GTAGCGCTTATATAATGTAATAGGTAGCGTTTATAATGTAATAGGTAGTGTTTATATTGTAAAGT
261 GTAGCACTTATATAATGTAATAGGTAGCGTTTATAATGTAATAGGTAGTGTCTATATTGTAAAGT
*
181821 ATCTATCCTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCT
326 ATCTATCCTTTTATAAAAGTGTCCATACTTTATTCACTGTGGAAAACATTAATTTAAGGTTATCT
181886 TTTGAGTGAGTTTTAAGATAT-AATTTAGTAAATT
391 TTTGAGTGA-TTTT-AGATATCAATTTAGTAAATT
*
181920 AAAAACAATAAACATATATTACATATTTATTATTATCTTTGGTTAATATTGTTACATTTAAATTC
1 AAAAACAAT-AACATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTC
*
181985 TAAATATTATTTTATAAAATATCAAAACAA-ACAAATAATTTTTTGTGCAAATGAAATTATTAAA
65 T-AATATTA-TTTATAAAATATAAAAACAATA-AAATAA-TTTTTGTGCAAATGAAATTATTAAA
182049 TTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT-ACTT
126 TTAATA-TGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTT
182113 TAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATAGACACTTTCAATATAATAGGTAAAAATAT
189 T-AAAAAAAGTATCGATCCTTTTTAT-AAAAGTATAGACACTTTCAATATAATAGGT-AAAATAT
182178 GATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTG-CT
251 GATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCG-TT-TATAATGTAATAGGTAGTGTCT
*
182242 -TATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATAC-TTATTCACTGTGGAAAACATTAA
314 ATATTGTAAAGTATCTATC-CTTTTATAAAAGTGTCCATACTTTATTCACTGTGGAAAACATTAA
182305 TTTAAGGTTATCTTTTGAGTGATTTTAGATATCAATTTAGTAA
378 TTTAAGGTTATCTTTTGAGTGATTTTAGATATCAATTTAGTAA
182348 TTATATGTAT
Statistics
Matches: 406, Mismatches: 8, Indels: 21
0.93 0.02 0.05
Matches are distributed among these distances:
424 9 0.02
425 55 0.14
426 8 0.02
427 25 0.06
428 31 0.08
429 32 0.08
430 54 0.13
431 43 0.11
432 107 0.26
433 23 0.06
434 19 0.05
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (423 bp):
AAAAACAATAACATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCT
AATATTATTTATAAAATATAAAAACAATAAAATAATTTTTGTGCAAATGAAATTATTAAATTAAT
ATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAA
AGTATCGATCCTTTTTATAAAAGTATAGACACTTTCAATATAATAGGTAAAATATGATGTAATAG
GTAGCACTTATATAATGTAATAGGTAGCGTTTATAATGTAATAGGTAGTGTCTATATTGTAAAGT
ATCTATCCTTTTATAAAAGTGTCCATACTTTATTCACTGTGGAAAACATTAATTTAAGGTTATCT
TTTGAGTGATTTTAGATATCAATTTAGTAAATT
Found at i:182888 original size:14 final size:14
Alignment explanation
Indices: 182869--182896 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
182859 AGCGCCGCAC
182869 CGCATAACTACCCA
1 CGCATAACTACCCA
182883 CGCATAACTACCCA
1 CGCATAACTACCCA
182897 TTAAATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.07, T:0.14
Consensus pattern (14 bp):
CGCATAACTACCCA
Done.