Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 164 of 253
Found at i:53104624 original size:43 final size:42
Alignment explanation
Indices: 53104533--53104639 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
53104523 ATGATTTAGG
* * *
53104533 TGTAAGACCATGTCTAGGACGTTGACATCGTATTTGGTTTCG
1 TGTAAGACCATGTCTAGGACGTTGACATCGTATTTGATTACA
* * *
53104575 TGTAAGACCCTTTCTAGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTAGGAC-GTTGACATCG-TATTTGATTACA
* *
53104618 TGTAAGACCACGTCTGGGACGT
1 TGTAAGACCATGTCTAGGACGT
53104640 CGGTATTATA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTAGGACGTTGACATCGTATTTGATTACA
Found at i:53120810 original size:17 final size:17
Alignment explanation
Indices: 53120788--53120822 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
53120778 TAATTAGACC
53120788 ATTAAAGAAAAGTATGT
1 ATTAAAGAAAAGTATGT
*
53120805 ATTAAATAAAAGTATGT
1 ATTAAAGAAAAGTATGT
53120822 A
1 A
53120823 GACTTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
ATTAAAGAAAAGTATGT
Found at i:53123169 original size:22 final size:21
Alignment explanation
Indices: 53123129--53123170 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53123119 CTGTAGCACG
**
53123129 GGAGTGTCCTAGGGTCACACT
1 GGAGTGTCCTAGGACCACACT
53123150 GGAGTGTCCCTAGGACCACAC
1 GGAGTGT-CCTAGGACCACAC
53123171 GGGCATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (21 bp):
GGAGTGTCCTAGGACCACACT
Found at i:53135867 original size:40 final size:40
Alignment explanation
Indices: 53135812--53135946 Score: 220
Period size: 40 Copynumber: 3.4 Consensus size: 40
53135802 GATGATAACT
53135812 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC
1 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC
*
53135852 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTGTATCC
1 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC
* *
53135892 GGGCTAGGACCCGAAGGCATTTGTGCGAGTTGTTATATCC
1 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC
53135932 -GGCTAA-ATCCCGAAG
1 GGGCTAAGA-CCCGAAG
53135947 ATACTTGGGT
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 76 0.85
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.24
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC
Found at i:53136215 original size:22 final size:22
Alignment explanation
Indices: 53136173--53136216 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53136163 AAAATGTGCA
* *
53136173 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
53136195 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
53136217 CGAAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:53143990 original size:40 final size:40
Alignment explanation
Indices: 53143935--53144110 Score: 257
Period size: 40 Copynumber: 4.4 Consensus size: 40
53143925 GGATGATAAC
53143935 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
*
53143975 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
* * *
53144015 CGGGCTAAAACCCCAAGGCATTTGTGCGAGTTGCTGTATT
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
* * *
53144055 CGGGCTAGGACCCGATGGCATTTGTGCGAGTTGTTATA-T
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
*
53144094 CCGGCTAA-ATCCCGAAG
1 CGGGCTAAGA-CCCGAAG
53144111 ATACTTGGGT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 107 0.88
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATT
Found at i:53144379 original size:22 final size:22
Alignment explanation
Indices: 53144337--53144380 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53144327 AAAATGTGCA
* *
53144337 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
53144359 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
53144381 CGAAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:53155726 original size:51 final size:51
Alignment explanation
Indices: 53155650--53155750 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
53155640 CACCCTTTAC
53155650 CCATGTCCGATGCCGGAACAGGGTACGAGACATTACCGAACTTAAACATAT
1 CCATGTCCGATGCCGGAACAGGGTACGAGACATTACCGAACTTAAACATAT
*
53155701 CCATGTCCGATGCTGGAACAGGGTACGAGACATTACCGAACTTAAACATA
1 CCATGTCCGATGCCGGAACAGGGTACGAGACATTACCGAACTTAAACATA
53155751 CACATTCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (51 bp):
CCATGTCCGATGCCGGAACAGGGTACGAGACATTACCGAACTTAAACATAT
Found at i:53158589 original size:20 final size:18
Alignment explanation
Indices: 53158555--53158592 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
53158545 GGAAAAAAAT
53158555 GGAGAGAAAAATGAGAGA
1 GGAGAGAAAAATGAGAGA
53158573 GGAGAAGAAAGAATGAGAGA
1 GGAG-AGAAA-AATGAGAGA
53158593 ATGTTGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.05
Consensus pattern (18 bp):
GGAGAGAAAAATGAGAGA
Found at i:53165859 original size:87 final size:87
Alignment explanation
Indices: 53165762--53165935 Score: 303
Period size: 87 Copynumber: 2.0 Consensus size: 87
53165752 ATCCTTAATT
*
53165762 AAGATCAAGAAAAGAGGAATTCAGACTTAGACCAAGGGAAATCGAAGATTGTAGAATAAACAGTG
1 AAGATCAAGAAAAGAGGAATTCAGACTTAGACCAAGGGAAATCGAAGATTGTAGAATAAACAGTC
*
53165827 CAAGTCGACAAATTCTGAGTAC
66 CAAGTCGAAAAATTCTGAGTAC
* *
53165849 AAGATCAAGAAAAGAGGAATTCAGACTTAGATCGAGGGAAATCGAAGATTGTAGAATAAACAGTC
1 AAGATCAAGAAAAGAGGAATTCAGACTTAGACCAAGGGAAATCGAAGATTGTAGAATAAACAGTC
*
53165914 CGAGTCGAAAAATTCTGAGTAC
66 CAAGTCGAAAAATTCTGAGTAC
53165936 GAGGTAAGTT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (87 bp):
AAGATCAAGAAAAGAGGAATTCAGACTTAGACCAAGGGAAATCGAAGATTGTAGAATAAACAGTC
CAAGTCGAAAAATTCTGAGTAC
Found at i:53178034 original size:47 final size:48
Alignment explanation
Indices: 53177925--53178052 Score: 179
Period size: 46 Copynumber: 2.7 Consensus size: 48
53177915 CATAGGGTAT
* *
53177925 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTC
* * * * *
53177973 GAGGCCGATG-CATGTCCGAGACAT-GTCTTACACTAGCTCCCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTC
53178019 AATGCCGATGCCATGTCCCAGACATGGTCTTACA
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACA
53178053 TTGGCTCTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 26 0.38
47 26 0.38
48 16 0.24
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTC
Found at i:53178081 original size:47 final size:47
Alignment explanation
Indices: 53177928--53178103 Score: 161
Period size: 47 Copynumber: 3.7 Consensus size: 47
53177918 AGGGTATAAT
* *
53177928 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACAT-CTCGAG
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCT-CATAAT-GTG
* *
53177976 GCCGATG-CATGTCCGAGACATGTCTTACACTAGCTCCCGTC-TCAA--T-
1 GCCGATGCCATGTCCCAGACATGTCTTACACTGGCT--C-TCAT-AATGTG
*
53178022 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGTG
* *
53178070 GCCGATG-CATGTCCCAAACATATCTTACACTGGC
1 GCCGATGCCATGTCCCAGACATGTCTTACACTGGC
53178104 ACACAAATAA
Statistics
Matches: 106, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
45 4 0.04
46 33 0.31
47 40 0.38
48 27 0.25
49 1 0.01
50 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTG
Found at i:53178096 original size:94 final size:94
Alignment explanation
Indices: 53177925--53178100 Score: 266
Period size: 94 Copynumber: 1.9 Consensus size: 94
53177915 CATAGGGTAT
*
53177925 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCC
* * *
53177990 GAGACATGTCTTACACTAGCTCCCGTCTC
66 CAAACATATCTTACACTAGCTCCCGTCTC
* *
53178019 AATGCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCT-CATAAT-GTGGCCGATGCATGT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACAT-ATCGAGGCCGATGCATGT
53178082 CCCAAACATATCTTACACT
64 CCCAAACATATCTTACACT
53178101 GGCACACAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 72 0.97
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (94 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCC
CAAACATATCTTACACTAGCTCCCGTCTC
Found at i:53182753 original size:50 final size:51
Alignment explanation
Indices: 53182557--53182799 Score: 210
Period size: 50 Copynumber: 4.8 Consensus size: 51
53182547 GTAACCGAAG
* *
53182557 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC--AA
1 CTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAA
* * * * * * * *
53182606 CAATCCGGTACACGTAGTAACCTGCACTTAGTACTACACA-CCTGA-TTGAA
1 CTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGC-GACCTAAA
* * * * *
53182656 GT-TGTCGGTACGCATAGTAGCCTGCACTTGGTACTACACATGCGACCT-AA
1 CTATCT-GATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAA
** * *
53182706 CTATCTGATACACGCAGTAGCCTGCACTTAGTACTACACAAGTGACCTAAAA
1 CTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCT-AAA
* * * *
53182758 CCATCTTAAACACATAGTAGCCTGCACATAGTACTACACATG
1 CTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATG
53182800 TGTTCTCACA
Statistics
Matches: 152, Mismatches: 33, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 72 0.47
51 4 0.03
52 37 0.24
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CTATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAA
Found at i:53188312 original size:20 final size:22
Alignment explanation
Indices: 53188294--53188336 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
53188284 TCACCAATAT
*
53188294 CGCAGCATAGCTGCTAATAGTAA
1 CGCAGCAAAGCTGCTAATAGT-A
53188317 CGCAGCAAAGCTGCTAATAG
1 CGCAGCAAAGCTGCTAATAG
53188337 CGATAAACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (22 bp):
CGCAGCAAAGCTGCTAATAGTA
Found at i:53194275 original size:17 final size:17
Alignment explanation
Indices: 53194253--53194289 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
53194243 ATGATGCTCA
53194253 TTAAAACTTTATTTTAT
1 TTAAAACTTTATTTTAT
53194270 TTAAAACTTTATTTTAT
1 TTAAAACTTTATTTTAT
53194287 TTA
1 TTA
53194290 TGCTTCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAAACTTTATTTTAT
Found at i:53201198 original size:9 final size:8
Alignment explanation
Indices: 53201182--53201206 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53201172 ATTATCATAT
53201182 ATAAAAAA
1 ATAAAAAA
53201190 ATAAAAAA
1 ATAAAAAA
53201198 ATAAAAAA
1 ATAAAAAA
53201206 A
1 A
53201207 GAGAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:53201219 original size:12 final size:12
Alignment explanation
Indices: 53201202--53201239 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53201192 AAAAAAATAA
*
53201202 AAAAAGAGAGAG
1 AAAAAGAGAAAG
*
53201214 AAAAAGAAAAAG
1 AAAAAGAGAAAG
53201226 AAAAA-AGAAAG
1 AAAAAGAGAAAG
53201237 AAA
1 AAA
53201240 CGATTCTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:53201253 original size:6 final size:6
Alignment explanation
Indices: 53201242--53201285 Score: 79
Period size: 6 Copynumber: 7.2 Consensus size: 6
53201232 GAAAGAAACG
53201242 ATTCTA ATTCTA ATTCTA ATTCTA ATTCTA ATTCTA ATTTCTA A
1 ATTCTA ATTCTA ATTCTA ATTCTA ATTCTA ATTCTA A-TTCTA A
53201286 AGGTAAAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCTA
Found at i:53201714 original size:31 final size:31
Alignment explanation
Indices: 53201654--53201714 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
53201644 ATATAACATG
*
53201654 TGAAATTCTAATTATGATTCAAATGTATATT
1 TGAAATTCTAATTATGATTCAAATATATATT
* * * *
53201685 TGAAATTTTAATTTTGATTTAATTATATAT
1 TGAAATTCTAATTATGATTCAAATATATAT
53201715 ATTTAAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (31 bp):
TGAAATTCTAATTATGATTCAAATATATATT
Found at i:53201884 original size:29 final size:30
Alignment explanation
Indices: 53201841--53201899 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
53201831 TAATTGGATC
* *
53201841 AAATCTAAATTTCATGTATAA-AATTGCACA
1 AAATCTAAAGTTCATATA-AACAATTGCACA
53201871 AAATC-AAAGTTCATATAAACAATTGCACA
1 AAATCTAAAGTTCATATAAACAATTGCACA
53201900 TTAAACCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 19 0.73
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCTAAAGTTCATATAAACAATTGCACA
Found at i:53202372 original size:12 final size:12
Alignment explanation
Indices: 53202339--53202375 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
53202329 AAAATGTATT
53202339 TTTTTTCTAATAA
1 TTTTTT-TAATAA
53202352 TTTTATTTAATAA
1 TTTT-TTTAATAA
53202365 TTTTTTTAATA
1 TTTTTTTAATA
53202376 TCTAATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 14 0.61
14 2 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTTTTAATAA
Found at i:53203072 original size:18 final size:18
Alignment explanation
Indices: 53203029--53203072 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
53203019 CAACCGATTT
* *
53203029 GATTAATTTGATTGGTTC
1 GATTAATTTGACTGGTAC
* *
53203047 AATCAATTTGACTGGTAC
1 GATTAATTTGACTGGTAC
53203065 GATTAATT
1 GATTAATT
53203073 CTACCAATCC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (18 bp):
GATTAATTTGACTGGTAC
Found at i:53205951 original size:37 final size:37
Alignment explanation
Indices: 53205892--53206030 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
53205882 AGCTCAGACG
* *
53205892 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53205929 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGGCA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53205966 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
53206003 TACTCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
53206031 TAGAGCTCGG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:53206227 original size:47 final size:47
Alignment explanation
Indices: 53206149--53206514 Score: 590
Period size: 47 Copynumber: 7.7 Consensus size: 47
53206139 CCCTTCGGGA
* * * *
53206149 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* * *
53206196 CCTGTCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53206243 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53206290 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53206337 CTTATCACATATATATACACTTTCATATTCATCACATCGACTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53206386 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53206433 CTTATCACATATATACACTTTCACGTTCATCAAATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53206480 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
53206515 AGAATCCTAA
Statistics
Matches: 296, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
46 2 0.01
47 250 0.84
49 44 0.15
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53206405 original size:143 final size:141
Alignment explanation
Indices: 53206149--53206514 Score: 592
Period size: 143 Copynumber: 2.6 Consensus size: 141
53206139 CCCTTCGGGA
* * * * * *
53206149 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGCCCTGTCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATATACA
53206213 CTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
53206278 CGGCCATTAGGC
130 CGGCCATTAGGC
53206290 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
53206355 ACTTTCATATTCATCACATC-GACTATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
64 ACTTTCACATTCATCACATCAG-CCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
53206419 ATCGGCCATTAGGC
128 ATCGGCCATTAGGC
* *
53206433 CTTATCACATATATACACTTTCACGTTCATCAAATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
53206498 TTTCACATTCATCACAT
66 TTTCACATTCATCACAT
53206515 AGAATCCTAA
Statistics
Matches: 210, Mismatches: 11, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
140 2 0.01
141 72 0.34
142 1 0.00
143 135 0.64
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:53208439 original size:56 final size:56
Alignment explanation
Indices: 53208372--53208491 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
53208362 TATTAGTTTA
53208372 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
53208428 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
53208484 TTGCCCAT
1 TTGCCCAT
53208492 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:53212051 original size:802 final size:802
Alignment explanation
Indices: 53210502--53212110 Score: 3182
Period size: 802 Copynumber: 2.0 Consensus size: 802
53210492 AAAAAAAATC
*
53210502 TACATTTAATTAAAACAAACAATTTACTTACTCATCTCTACACTTAATTCACTAAAAAACTTTAA
1 TACACTTAATTAAAACAAACAATTTACTTACTCATCTCTACACTTAATTCACTAAAAAACTTTAA
53210567 ACAATAATCATATATCGAGACTTTGTCGGGTGGGCTATTACAACTCTTACCCACTTAGAAAATTC
66 ACAATAATCATATATCGAGACTTTGTCGGGTGGGCTATTACAACTCTTACCCACTTAGAAAATTC
53210632 CGTCCTCGAAATTCATACATGAAAATAACTGAGGATATGGCTCTTCCTGTAACATCCCAAAATTT
131 CGTCCTCGAAATTCATACATGAAAATAACTGAGGATATGGCTCTTCCTGTAACATCCCAAAATTT
53210697 GGCTTAATGAGAAAGTAGAATTATAAATAAAAAAATGTTAGCTAAGTGGTTATTTCTAAATGTAA
196 GGCTTAATGAGAAAGTAGAATTATAAATAAAAAAATGTTAGCTAAGTGGTTATTTCTAAATGTAA
*
53210762 CACCCCTAACTTGTATTCGTCACCGGAACAGGGTTTTAGAGTATTATCGAAATATTCAGAACATT
261 CACCCCTAACCTGTATTCGTCACCGGAACAGGGTTTTAGAGTATTATCGAAATATTCAGAACATT
53210827 TTTCAAATAATTCCTGTAAATTACCATTCATTTACCAAGATCATTCAAAAAAATCCTTTAATTGG
326 TTTCAAATAATTCCTGTAAATTACCATTCATTTACCAAGATCATTCAAAAAAATCCTTTAATTGG
53210892 ACCCTCGAGGCCCAATACGAGCATTAGAATCGAGTCGGGACTTAATCAAAAACTCATAAAAATTT
391 ACCCTCGAGGCCCAATACGAGCATTAGAATCGAGTCGGGACTTAATCAAAAACTCATAAAAATTT
53210957 TCGCAAAATTTTAAAAATTTTCTAAGGTTGCAGGGCTCACACGCCCGTATGGTCTAGGGACACAC
456 TCGCAAAATTTTAAAAATTTTCTAAGGTTGCAGGGCTCACACGCCCGTATGGTCTAGGGACACAC
53211022 CCCTGTGCTCAAGCCGTGTGACTACACAAGCCCGTGTTCCTAACCCGTGTAACTCTCTAACTTAT
521 CCCTGTGCTCAAGCCGTGTGACTACACAAGCCCGTGTTCCTAACCCGTGTAACTCTCTAACTTAT
53211087 AAGGCATGAAGAAATTGAAGTCACACGGCCAAGTCACACGCCCGTGTGCTAGGCTCGTGGCGATT
586 AAGGCATGAAGAAATTGAAGTCACACGGCCAAGTCACACGCCCGTGTGCTAGGCTCGTGGCGATT
53211152 TTATTTTCGAAATTTAGGTGTAGTTTTCACACAGCCATGTAACATGCCCGTGTTCAAGTCCGTGT
651 TTATTTTCGAAATTTAGGTGTAGTTTTCACACAGCCATGTAACATGCCCGTGTTCAAGTCCGTGT
53211217 CAACCACACGGTTGAGACACACGCATGTGTCTCTTCCCGTATCCCCAATTTTGAGCATTCTATTT
716 CAACCACACGGTTGAGACACACGCATGTGTCTCTTCCCGTATCCCCAATTTTGAGCATTCTATTT
53211282 CTCATTTTAAAGATACAGGGGA
781 CTCATTTTAAAGATACAGGGGA
53211304 TACACTTAATTAAAACAAACAATTTACTTACTCATCTCTACACTTAATTCACTAAAAAACTTTAA
1 TACACTTAATTAAAACAAACAATTTACTTACTCATCTCTACACTTAATTCACTAAAAAACTTTAA
53211369 ACAATAATCATATATCGAGACTTTGTCGGGTGGGCTATTACAACTCTTACCCACTTAGAAAATTC
66 ACAATAATCATATATCGAGACTTTGTCGGGTGGGCTATTACAACTCTTACCCACTTAGAAAATTC
53211434 CGTCCTCGAAATTCATACATGAAAATAACTGAGGATATGGCTCTTCCTGTAACATCCCAAAATTT
131 CGTCCTCGAAATTCATACATGAAAATAACTGAGGATATGGCTCTTCCTGTAACATCCCAAAATTT
53211499 GGCTTAATGAGAAAGTAGAATTATAAATAAAAAAATGTTAGCTAAGTGGTTATTTCTAAATGTAA
196 GGCTTAATGAGAAAGTAGAATTATAAATAAAAAAATGTTAGCTAAGTGGTTATTTCTAAATGTAA
*
53211564 CACCCCTAACCTGTATTCGTCACTGGAACAGGGTTTTAGAGTATTATCGAAATATTCAGAACATT
261 CACCCCTAACCTGTATTCGTCACCGGAACAGGGTTTTAGAGTATTATCGAAATATTCAGAACATT
53211629 TTTCAAATAATTCCTGTAAATTACCATTCATTTACCAAGATCATTCAAAAAAATCCTTTAATTGG
326 TTTCAAATAATTCCTGTAAATTACCATTCATTTACCAAGATCATTCAAAAAAATCCTTTAATTGG
53211694 ACCCTCGAGGCCCAATACGAGCATTAGAATCGAGTCGGGACTTAATCAAAAACTCATAAAAATTT
391 ACCCTCGAGGCCCAATACGAGCATTAGAATCGAGTCGGGACTTAATCAAAAACTCATAAAAATTT
53211759 TCGCAAAATTTTAAAAATTTTCTAAGGTTGCAGGGCTCACACGCCCGTATGGTCTAGGGACACAC
456 TCGCAAAATTTTAAAAATTTTCTAAGGTTGCAGGGCTCACACGCCCGTATGGTCTAGGGACACAC
53211824 CCCTGTGCTCAAGCCGTGTGACTACACAAGCCCGTGTTCCTAACCCGTGTAACTCTCTAACTTAT
521 CCCTGTGCTCAAGCCGTGTGACTACACAAGCCCGTGTTCCTAACCCGTGTAACTCTCTAACTTAT
53211889 AAGGCATGAAGAAATTGAAGTCACACGGCCAAGTCACACGCCCGTGTGCTAGGCTCGTGGCGATT
586 AAGGCATGAAGAAATTGAAGTCACACGGCCAAGTCACACGCCCGTGTGCTAGGCTCGTGGCGATT
53211954 TTATTTTCGAAATTTAGGTGTAGTTTTCACACAGCCATGTAACATGCCCGTGTTCAAGTCCGTGT
651 TTATTTTCGAAATTTAGGTGTAGTTTTCACACAGCCATGTAACATGCCCGTGTTCAAGTCCGTGT
*
53212019 CAACCACACGGTTGAGACACACGCATGTGTCTCTTCCCGTATGCCCAATTTTGAGCATTCTATTT
716 CAACCACACGGTTGAGACACACGCATGTGTCTCTTCCCGTATCCCCAATTTTGAGCATTCTATTT
53212084 CTCATTTTAAAGATACAGGGGA
781 CTCATTTTAAAGATACAGGGGA
53212106 TACAC
1 TACAC
53212111 GGCCGGACCA
Statistics
Matches: 803, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
802 803 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (802 bp):
TACACTTAATTAAAACAAACAATTTACTTACTCATCTCTACACTTAATTCACTAAAAAACTTTAA
ACAATAATCATATATCGAGACTTTGTCGGGTGGGCTATTACAACTCTTACCCACTTAGAAAATTC
CGTCCTCGAAATTCATACATGAAAATAACTGAGGATATGGCTCTTCCTGTAACATCCCAAAATTT
GGCTTAATGAGAAAGTAGAATTATAAATAAAAAAATGTTAGCTAAGTGGTTATTTCTAAATGTAA
CACCCCTAACCTGTATTCGTCACCGGAACAGGGTTTTAGAGTATTATCGAAATATTCAGAACATT
TTTCAAATAATTCCTGTAAATTACCATTCATTTACCAAGATCATTCAAAAAAATCCTTTAATTGG
ACCCTCGAGGCCCAATACGAGCATTAGAATCGAGTCGGGACTTAATCAAAAACTCATAAAAATTT
TCGCAAAATTTTAAAAATTTTCTAAGGTTGCAGGGCTCACACGCCCGTATGGTCTAGGGACACAC
CCCTGTGCTCAAGCCGTGTGACTACACAAGCCCGTGTTCCTAACCCGTGTAACTCTCTAACTTAT
AAGGCATGAAGAAATTGAAGTCACACGGCCAAGTCACACGCCCGTGTGCTAGGCTCGTGGCGATT
TTATTTTCGAAATTTAGGTGTAGTTTTCACACAGCCATGTAACATGCCCGTGTTCAAGTCCGTGT
CAACCACACGGTTGAGACACACGCATGTGTCTCTTCCCGTATCCCCAATTTTGAGCATTCTATTT
CTCATTTTAAAGATACAGGGGA
Found at i:53221905 original size:20 final size:20
Alignment explanation
Indices: 53221863--53221905 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
53221853 TTATCTATGA
*
53221863 ATAAATTTTAATTTTCTACC
1 ATAAATTTTAATTTTCTAAC
53221883 ATAAATTTCTAATTTT-TAAC
1 ATAAATTT-TAATTTTCTAAC
53221903 ATA
1 ATA
53221906 TTAATTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATTTTAATTTTCTAAC
Found at i:53246947 original size:19 final size:19
Alignment explanation
Indices: 53246923--53246962 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53246913 TTTTTCCAGA
53246923 TTCCACTCAAGTACTGCTT
1 TTCCACTCAAGTACTGCTT
53246942 TTCCACTCAAGTACTGCTT
1 TTCCACTCAAGTACTGCTT
53246961 TT
1 TT
53246963 ACCTAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (19 bp):
TTCCACTCAAGTACTGCTT
Found at i:53250699 original size:43 final size:41
Alignment explanation
Indices: 53250652--53250789 Score: 118
Period size: 43 Copynumber: 3.2 Consensus size: 41
53250642 TCTTACATGT
* *
53250652 AATCAAATATCGATGCCACTATCTTAGACAGGGTTTTACACAA
1 AATCAAATAT-GATGCCAATATCCTAGACAGGG-TTTACACAA
* * *
53250695 AATCATATATGATGCCAATGTCCTAGACATGGTTTACACGTAA
1 AATCAAATATGATGCCAATATCCTAGACAGGGTTTACAC--AA
* * *
53250738 ATCTCAAAT-TGATGCCAACATCCTAGAC-GTGGTCTTACACGA
1 A-ATCAAATATGATGCCAATATCCTAGACAG-GGT-TTACACAA
*
53250780 AATCACATAT
1 AATCAAATAT
53250790 CTGAATCCTG
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
41 12 0.16
42 21 0.28
43 32 0.42
44 11 0.14
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (41 bp):
AATCAAATATGATGCCAATATCCTAGACAGGGTTTACACAA
Found at i:53253502 original size:20 final size:19
Alignment explanation
Indices: 53253479--53253579 Score: 89
Period size: 20 Copynumber: 5.1 Consensus size: 19
53253469 TGAAGTGTAG
53253479 ACAGAGGCACAAATGTGCAA
1 ACAGAGGCACAAA-GTGCAA
* **
53253499 ACAGGGGCACCGTAGTGCAA
1 ACAGAGGCA-CAAAGTGCAA
*
53253519 ACA-AGGACACCAAAGTGCAT
1 ACAGAGG-CA-CAAAGTGCAA
53253539 ACA-AGGGCACCAAAGTGCAA
1 ACAGA-GGCA-CAAAGTGCAA
53253559 ACAGAGGCACTAAAGTGCAA
1 ACAGAGGCAC-AAAGTGCAA
53253579 A
1 A
53253580 TCTCGTACAA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.04
20 60 0.88
21 5 0.07
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.09
Consensus pattern (19 bp):
ACAGAGGCACAAAGTGCAA
Found at i:53253505 original size:40 final size:39
Alignment explanation
Indices: 53253453--53253579 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
53253443 GCATCATTGA
* * *
53253453 TGCATAACAGGGGCACTGAAGTGTAGACAGAGGCACAAATG
1 TGCA-AACAGGGGCACCGAAGTGCAAACAGAGGCACAAA-G
*
53253494 TGCAAACAGGGGCACCGTAGTGCAAACA-AGGACACCAAAG
1 TGCAAACAGGGGCACCGAAGTGCAAACAGAGG-CA-CAAAG
* * *
53253534 TGCATACAAGGGCACCAAAGTGCAAACAGAGGCACTAAAG
1 TGCAAACAGGGGCACCGAAGTGCAAACAGAGGCAC-AAAG
53253574 TGCAAA
1 TGCAAA
53253580 TCTCGTACAA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.05
40 58 0.79
41 11 0.15
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.11
Consensus pattern (39 bp):
TGCAAACAGGGGCACCGAAGTGCAAACAGAGGCACAAAG
Found at i:53258988 original size:37 final size:38
Alignment explanation
Indices: 53258860--53259047 Score: 177
Period size: 38 Copynumber: 5.0 Consensus size: 38
53258850 AAAATTGAAT
** *
53258860 ACTGATTATACCAAATGTTGCTCAAAGGAGCAATATCA
1 ACTGATTATACTGAATGTTGCTCAAACGAGCAATATCA
* * *
53258898 ACTGATTATACGGAATGTTGCTCAAACAAGTAATATCA
1 ACTGATTATACTGAATGTTGCTCAAACGAGCAATATCA
* * * *
53258936 ACTAATTATATTGAATG-TGCTCCAAA-GAGCAATGTCT
1 ACTGATTATACTGAATGTTGCT-CAAACGAGCAATATCA
*
53258973 ACTGATTAAACTGAATG-TGCTCAAACGAGCAATAATC-
1 ACTGATTATACTGAATGTTGCTCAAACGAGCAAT-ATCA
** * * *
53259010 ACAAATTATTCTAAATGTTTGCTCAAACGAGCATTATC
1 ACTGATTATACTGAATG-TTGCTCAAACGAGCAATATC
53259048 CACTAATCAT
Statistics
Matches: 123, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
36 4 0.03
37 48 0.39
38 56 0.46
39 15 0.12
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (38 bp):
ACTGATTATACTGAATGTTGCTCAAACGAGCAATATCA
Found at i:53260547 original size:39 final size:39
Alignment explanation
Indices: 53260475--53260744 Score: 215
Period size: 39 Copynumber: 6.9 Consensus size: 39
53260465 TAGCAGATAA
* * * *
53260475 CTGTTGTACTTCGGTAACACTGA-TCGCAGTTATGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACT-GCACTTACGTGCCC
* *** * *
53260514 CTATTGTACTTCGGTATTGCTGACTGCACTTATGTGCCG
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * *
53260553 CTGTTGTACTTTGGTACTCCTCACTGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * *
53260592 CTGTTGTACTTTGGTACCCCTGACAGCACTTACGTGCCT
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* ** * *
53260631 TTGTAATACTTCGATACCCCTGA-TCGCACTTATGTTG-CC
1 CTGTTGTACTTCGGTACCCCTGACT-GCACTTACG-TGCCC
* * * *
53260670 CTGTTGTACTTCAGTATCCCTGACCGCACTTGCGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * * *
53260709 CTATTGTACTTCGATACTCCTGA-TAGCACTTTCGTG
1 CTGTTGTACTTCGGTACCCCTGACT-GCACTTACGTG
53260745 TCGTGGTTAC
Statistics
Matches: 184, Mismatches: 41, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.01
39 179 0.97
40 3 0.02
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (39 bp):
CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
Found at i:53263050 original size:42 final size:42
Alignment explanation
Indices: 53262929--53263081 Score: 121
Period size: 42 Copynumber: 3.5 Consensus size: 42
53262919 CATAGGATTA
* ** * *
53262929 CGATATGTGATTTCGTGTAAGACCACATCTGGGA-TGTTGGCAT
1 CGATA-GTGATTACGTGTAAGACCATGTCTAGGACAG-TGGCAT
* * * * *
53262972 CGATTTGAGATTTATGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TAGTGA-TTACGTGTAAGACCATGTCTAGGACAGTGGCAT
* *
53263016 CGTATA-TGATTTCGTGTAAGACCCTGTCTAGGACAGTGGCAT
1 CG-ATAGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCAT
*
53263058 CGATAGTTGATTACATGTAAGACC
1 CGATAG-TGATTACGTGTAAGACC
53263082 TCATCTGGGA
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 3 0.03
42 30 0.34
43 23 0.26
44 30 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (42 bp):
CGATAGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCAT
Found at i:53268199 original size:42 final size:41
Alignment explanation
Indices: 53268097--53268216 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 41
53268087 ATCTGAGACA
* *
53268097 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATT
1 TCGTGTAAGACCATGTCTGGGACAC-GGCATCGATTGAGATT
*
53268139 TACGTATAAGACCATGTCTGGGACATCGGCATCGTATCT-A-ATT
1 T-CGTGTAAGACCATGTCTGGGACA-CGGCATCG-AT-TGAGATT
* *
53268182 TCGTGTAAGACCCTGTCTGGGACAGAGGCATCGAT
1 TCGTGTAAGACCATGTCTGGGACA-CGGCATCGAT
53268217 ATTGAATTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
41 2 0.03
42 29 0.43
43 31 0.46
44 4 0.06
45 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTGGGACACGGCATCGATTGAGATT
Found at i:53280258 original size:40 final size:40
Alignment explanation
Indices: 53280191--53280367 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
53280181 ACCCAAGTAT
*
53280191 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
53280230 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
53280270 CTTCGGGTTTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
53280310 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
53280350 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
53280368 TTATCATCCG
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 102 0.86
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:53280324 original size:80 final size:79
Alignment explanation
Indices: 53280191--53280355 Score: 251
Period size: 80 Copynumber: 2.1 Consensus size: 79
53280181 ACCCAAGTAT
* * *
53280191 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCA
1 CTTCGGGATTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
53280256 ACTCGCACAAATGC
66 ACTCGCACAAATGC
* *
53280270 CTTCGGGTTTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAG
1 CTTCGGGATTTAG-CCGGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAG
*
53280334 CAACTCGCACGAATGC
64 CAACTCGCACAAATGC
53280350 CTTCGG
1 CTTCGG
53280356 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
79 12 0.15
80 65 0.83
81 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
CTTCGGGATTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:53288250 original size:40 final size:40
Alignment explanation
Indices: 53288183--53288359 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
53288173 ACCCAAGTAT
*
53288183 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
53288222 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
53288262 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
53288302 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
53288342 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
53288360 TTATCATCCG
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 104 0.87
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:53293677 original size:40 final size:40
Alignment explanation
Indices: 53293626--53293781 Score: 172
Period size: 40 Copynumber: 3.9 Consensus size: 40
53293616 GATTTAGCCG
*
53293626 GATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCT
1 GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCT
* * *
53293666 TATATAGCAACTCGCACAAATGCCTTCGGGTTTTAGCCCG
1 GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCT
* * * * * *
53293706 GATATAATC-ACTAGCATAAATGCCTTCAGGACATAG-CCT
1 GATAT-AGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCT
* *
53293745 GGATATAGCAACTCGCACGAATGCCTTCGGATCTTAG
1 -GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAG
53293782 TCCGGTTATC
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
39 4 0.04
40 86 0.93
41 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (40 bp):
GATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCT
Found at i:53293756 original size:80 final size:79
Alignment explanation
Indices: 53293618--53293774 Score: 210
Period size: 80 Copynumber: 2.0 Consensus size: 79
53293608 ATCTTCAGGA
* * * * *
53293618 TTTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCTTATATAGCAACTCGCAC
1 TTTAGCCGGATATAACAACTAGCACAAATGCCTTCAGGACATAGCCCTGATATAGCAACTCGCAC
53293683 AAATGCCTTCGGGT
66 AAATGCCTTCGGGT
*
53293697 TTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCAGGACATAG-CCTGGATATAGCAACTCG
1 TTTAG-CCGGATATAA-CAACTAGCACAAATGCCTTCAGGACATAGCCCT-GATATAGCAACTCG
*
53293760 CACGAATGCCTTCGG
63 CACAAATGCCTTCGG
53293775 ATCTTAGTCC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 8 0.12
80 59 0.87
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (79 bp):
TTTAGCCGGATATAACAACTAGCACAAATGCCTTCAGGACATAGCCCTGATATAGCAACTCGCAC
AAATGCCTTCGGGT
Found at i:53300093 original size:44 final size:42
Alignment explanation
Indices: 53300039--53300141 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 42
53300029 TTACGATATG
*
53300039 TGATTTCGTGTAAGACCACGTCTGGGACATTAGCATCG-ATT
1 TGATTTCGTGTAAGACCACGTCTGGGACATTAGCATCGTATA
* *
53300080 TGAGATTTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
1 T--GATTT-CGTGTAAGACCACGTCTGGGACATTAGCATCGTATA
53300125 TGATTTCGTGTAAGACC
1 TGATTTCGTGTAAGACC
53300142 CTATTTGGGA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
41 1 0.02
42 11 0.20
43 10 0.18
44 30 0.55
45 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCACGTCTGGGACATTAGCATCGTATA
Found at i:53302278 original size:46 final size:46
Alignment explanation
Indices: 53302228--53302402 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
53302218 TGGTTGAGCA
*
53302228 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53302274 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
53302319 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53302367 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
53302403 AGCGGGTTAC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53302337 original size:93 final size:93
Alignment explanation
Indices: 53302225--53302396 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
53302215 GGATGGTTGA
* * *
53302225 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53302290 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53302318 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53302383 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53302397 CTTATGAGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53305217 original size:14 final size:14
Alignment explanation
Indices: 53305198--53305227 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53305188 AACACTTACT
53305198 CCATATCAATCTTA
1 CCATATCAATCTTA
53305212 CCATATCAATCTTA
1 CCATATCAATCTTA
53305226 CC
1 CC
53305228 CAAGCTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (14 bp):
CCATATCAATCTTA
Found at i:53305471 original size:50 final size:50
Alignment explanation
Indices: 53305417--53305957 Score: 593
Period size: 50 Copynumber: 10.7 Consensus size: 50
53305407 CTGGTATGCA
* *
53305417 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * *
53305467 TAGTAGCCTGCACTTAGTACTACACACATGACCTAACCATCTGATTCACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * * * ** *
53305517 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGCTATCAGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGGTACACG
* *
53305568 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * *** *
53305618 TAGTAGCCTGCACTTAGTACTACACATGTAACCTAA-AACCGTCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA---TCTGGTACACG
* * * * *
53305670 TAGTAGCCTGTACATAGTACTACACACATGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * * * *
53305720 AAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCTGGTACACG
* * * *
53305771 TAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAATCTGCTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
* * * *
53305821 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGCTATCGGGTACGCG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CAATCTGGTACACG
* * *
53305872 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCAT-GTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC-TGGTACACG
53305922 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
53305958 AACCGTCTTA
Statistics
Matches: 403, Mismatches: 78, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
49 4 0.01
50 241 0.60
51 118 0.29
52 39 0.10
53 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGGTACACG
Found at i:53305592 original size:101 final size:101
Alignment explanation
Indices: 53305417--53305952 Score: 671
Period size: 101 Copynumber: 5.3 Consensus size: 101
53305407 CTGGTATGCA
* * * * * * *
53305417 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CAATCTGGTACACGTAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
*** * *
53305481 TAGTACTACACACATGACCTAACCATCTGATTCACG
66 TAGTACTACACATGCGACCTAACAATCTGATACACG
* * **
53305517 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGCTATCAGGTATGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
*
53305582 TAGTACTACACATGCGACCTAACAATCTGGTACACG
66 TAGTACTACACATGCGACCTAACAATCTGATACACG
* * * * * ** **** *
53305618 TAGTAGCCTGCACTTAGTACTACACATGTAACCTAAAACCGTCTTAAACACATAGTAGCCTGTAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGATC-GAAGCTATCGGGTACACATAGTAGCCTGCAC
* *** *
53305683 ATAGTACTACACACATGACCTAACCATCTGATACACG
65 TTAGTACTACACATGCGACCTAACAATCTGATACACG
*
53305720 AAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
* *
53305785 TAGTACTACACATGCGACTTAACAATCTGCTACACG
66 TAGTACTACACATGCGACCTAACAATCTGATACACG
* * * *
53305821 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGCTATCGGGTACGCGTAGTAGCCTACACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
53305886 TAGTACTACACATGCGACCTAACAATCATG-TACACG
66 TAGTACTACACATGCGACCTAACAATC-TGATACACG
53305922 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
53305953 CCTAAAACCG
Statistics
Matches: 370, Mismatches: 63, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
100 31 0.08
101 257 0.69
102 82 0.22
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACT
TAGTACTACACATGCGACCTAACAATCTGATACACG
Found at i:53305753 original size:203 final size:201
Alignment explanation
Indices: 53305417--53305952 Score: 754
Period size: 203 Copynumber: 2.7 Consensus size: 201
53305407 CTGGTATGCA
*
53305417 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAA-TCTGGTACACGTAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-AACTCTGGTACACGTAGTAGCCTGCACT
* *
53305481 TAGTACTACACACATGACCTAACCATCTGATTCACGTAGTAGCCTACACTTAGTACTACACACGT
65 TAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGT
**
53305546 GATCGAAGCTATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTG
130 GATCGAAGCTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTG
*
53305611 GTACACG
195 CTACACG
* *** * *
53305618 TAGTAGCCTGCACTTAGTACTACACATGTAACCTAAAACCGTCTTAAACACATAGTAGCCTGTAC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAAAA-C-TCTGGTACACGTAGTAGCCTGCAC
* *
53305683 ATAGTACTACACACATGACCTAACCATCTGATACACGAAGTAGCCTGCACTTAGTACTACACACG
64 TTAGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACG
* *
53305748 TGATCGAAGCTATCGGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAATCT
129 TGATCGAAGCTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCT
53305813 GCTACACG
194 GCTACACG
* * * * * * *
53305821 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGCTATCGGGTACGCGTAGTAGCCTACAC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAAAAC--TCTGGTACACGTAGTAGCCTGCAC
*** *
53305885 TTAGTACTACACATGCGACCTAACAATCATG-TACACGTAGTAGCCTGCACTTAGTACTACACAC
64 TTAGTACTACACACATGACCTAACCATC-TGATACACGTAGTAGCCTGCACTTAGTACTACACAC
53305949 GTGA
128 GTGA
53305953 CCTAAAACCG
Statistics
Matches: 294, Mismatches: 36, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
200 2 0.01
201 35 0.12
202 78 0.27
203 179 0.61
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (201 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAAAACTCTGGTACACGTAGTAGCCTGCACTT
AGTACTACACACATGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
ATCGAAGCTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGC
TACACG
Found at i:53305921 original size:304 final size:303
Alignment explanation
Indices: 53305418--53305978 Score: 899
Period size: 304 Copynumber: 1.8 Consensus size: 303
53305408 TGGTATGCAT
* * * *
53305418 AGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTA
1 AGTAGCCTGCACTTAGTACTACACACGCGACCGAACAATCGGGTACACATAGTAGCCTGCACTTA
* * *
53305483 GTACTACACACATGACCTAACCATCTGATTCACGTAGTAGCCTACACTTAGTACTACACACGTGA
66 GTACTACACACACGACCTAACAATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGA
* *
53305548 TCGAAGCTATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGT
131 TCGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGT
*
53305613 ACACGTAGTAGCCTGCACTTAGTACTACACATGTAACCTAAAACCGTCTTAAACACATAGTAGCC
196 ACACGTAGTAGCCTGCACTTAGTACTACACACGTAACCTAAAACCGTCTTAAACACATAGTAGCC
53305678 TGTACATAGTACTACACACATGACCTAACCATCTGATACACGA
261 TGTACATAGTACTACACACATGACCTAACCATCTGATACACGA
* * *
53305721 AGTAGCCTGCACTTAGTACTACACACGTGATCGAAGCTATCGGGTACACATAGTAGCCTGCACTT
1 AGTAGCCTGCACTTAGTACTACACACGCGACCGAA-CAATCGGGTACACATAGTAGCCTGCACTT
** * * *
53305786 AGTACTACACATGCGACTTAACAATCTGCTACACGTAGTAGCCTGCACTTAGTACTACACACGTG
65 AGTACTACACACACGACCTAACAATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTG
* * *
53305851 ATTGAAGCTATCGGGTACGCGTAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCAT-
130 ATCGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATC-TG
*
53305915 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCGTCTTAAACACATAGTA
194 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTAACCTAAAACCGTCTTAAACACATAGTA
53305979 CTACTCATTA
Statistics
Matches: 234, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
303 31 0.13
304 202 0.86
305 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (303 bp):
AGTAGCCTGCACTTAGTACTACACACGCGACCGAACAATCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACACGACCTAACAATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGA
TCGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGT
ACACGTAGTAGCCTGCACTTAGTACTACACACGTAACCTAAAACCGTCTTAAACACATAGTAGCC
TGTACATAGTACTACACACATGACCTAACCATCTGATACACGA
Found at i:53310772 original size:22 final size:22
Alignment explanation
Indices: 53310746--53310803 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
53310736 GAAACAGGGT
*
53310746 CACACGCCCGTGTGGACACAGG
1 CACACGCCCATGTGGACACAGG
53310768 CACACGCCCATGTGGACACAGG
1 CACACGCCCATGTGGACACAGG
53310790 CACACGCCCATGTG
1 CACACGCCCATGTG
53310804 TCTCCAACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.24, C:0.38, G:0.28, T:0.10
Consensus pattern (22 bp):
CACACGCCCATGTGGACACAGG
Found at i:53312691 original size:50 final size:50
Alignment explanation
Indices: 53312559--53312733 Score: 217
Period size: 50 Copynumber: 3.5 Consensus size: 50
53312549 TTGGTAAGCA
*
53312559 TAGTAGCCTGCACTTAGTACTACACATACGACC-AACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
* *
53312608 TAGTAGCCTGCACTTAGTACTACAAATGCGACCTAACTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
* * * * *** *
53312658 TAGTAGACTGCACTTAGTACTACACACGGGACCTAAAACCATCTTAAACACT
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCT--AACAATCTGGTACACG
*
53312710 TAGTAGCCTGCACATAGTACTACA
1 TAGTAGCCTGCACTTAGTACTACA
53312734 TATGTGTTCT
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
49 31 0.28
50 45 0.41
52 33 0.30
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
Found at i:53315880 original size:68 final size:64
Alignment explanation
Indices: 53315794--53316015 Score: 214
Period size: 67 Copynumber: 3.4 Consensus size: 64
53315784 TAATACGGGA
* * *
53315794 TGTATACCATGTGTACAAGAGAGCAACGAGACATTATGAGGTAGCTAGGTCGCATGGGTGATACA
1 TGTACACCATGTGTACAAGAGAGCTACGAG--A-TA-GAAGTAGCTAGGTCGCATGGGTGATACA
53315859 ATG
62 ATG
* * * * * *
53315862 TGTACACCATGTAG-ACAAGAGAGCTACGAGATAGATGTAGCTAGGTTGCATGTGTGGTTCCAGG
1 TGTACACCATGT-GTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCGCATGGGT-GATACA-A
53315926 TG
63 TG
* * ** * * *
53315928 AAGGACACCATGTAAACAAGAGAGCTACGAGATA-AAGTGGCTAGGTCACATGGGTGATACTATG
1 -TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCGCATGGGTGATACAATG
53315992 TGTACACCATGTGTACAAGAGAGC
1 TGTACACCATGTGTACAAGAGAGC
53316016 CAAAATTATG
Statistics
Matches: 125, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
63 20 0.16
64 21 0.17
65 9 0.07
66 19 0.15
67 29 0.23
68 26 0.21
69 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (64 bp):
TGTACACCATGTGTACAAGAGAGCTACGAGATAGAAGTAGCTAGGTCGCATGGGTGATACAATG
Found at i:53320113 original size:42 final size:42
Alignment explanation
Indices: 53320003--53320157 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
53319993 TACCACACCA
* * * * ** *
53320003 ATGTCAGATCCCAAATATGGTCTTATATGGGATCTCATTTCG
1 ATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
53320045 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGTC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
53320088 ATGTCATATCCCAGATATGGTCTTACACGAAATCTCATAAT-G
1 ATGTCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
* *
53320130 ATGACGTATCCCAGATATGGTCTTACAC
1 ATGTCATATCCCAGATATGGTCTTACAC
53320158 AATCTTGGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 62 0.65
43 34 0.35
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:53327444 original size:51 final size:51
Alignment explanation
Indices: 53327284--53327441 Score: 271
Period size: 51 Copynumber: 3.1 Consensus size: 51
53327274 ACTTCTGATC
* * * *
53327284 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGCGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
53327335 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
53327386 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
53327437 AGTGA
1 AGTGA
53327442 TAAATGTGAT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 102 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:53328735 original size:42 final size:41
Alignment explanation
Indices: 53328625--53328779 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 41
53328615 TATCACACCA
* * ** * *
53328625 ATGCCATATCCCAGATATGGTCTTATATGGGATCTCGTTTTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTC-ATATG
* * *
53328667 ATGCTAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGC-CATATCCCAGATATGGTCTTACACGAAATCTCATAT-G
* * *
53328710 ATGCTATATCCCAGATATGGTCTTACACAAAATCTTATAATG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATG
*
53328752 ATGCCGTATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
53328780 ATAGTCTCGG
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 62 0.66
43 32 0.34
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATG
Found at i:53330104 original size:17 final size:17
Alignment explanation
Indices: 53330082--53330173 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
53330072 ATTTTAATAT
53330082 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
53330099 TTTAATACTT--ATCTTAA
1 TTTAATA-TTAAAT-TTAA
** *
53330116 --TAATATTTTA-TTCA
1 TTTAATATTAAATTTAA
*
53330130 CTTAATATTAAAGTGATT-A
1 TTTAATATTAAA-T--TTAA
53330149 TCTTAATATTAAATTTAA
1 T-TTAATATTAAATTTAA
53330167 TTTAATA
1 TTTAATA
53330174 GCCCTTAGGT
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
14 5 0.08
15 5 0.08
16 11 0.19
17 19 0.32
18 4 0.07
19 2 0.03
20 13 0.22
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:53331192 original size:27 final size:27
Alignment explanation
Indices: 53331148--53331200 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53331138 GAACTATCCC
* **
53331148 GTGTTTAACGTCTTGTCGGACTATCTT
1 GTGTTTAACATCCCGTCGGACTATCTT
*
53331175 GTGTTTAACATCCCGTCGGGCTATCT
1 GTGTTTAACATCCCGTCGGACTATCT
53331201 ACGATGTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (27 bp):
GTGTTTAACATCCCGTCGGACTATCTT
Found at i:53331799 original size:50 final size:50
Alignment explanation
Indices: 53331729--53331829 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
53331719 TCATCCTATT
53331729 TCCCTTTCCTACCTTCCTCTAACCCTTTTTTAATCCCCTTTAAATTTTCC
1 TCCCTTTCCTACCTTCCTCTAACCCTTTTTTAATCCCCTTTAAATTTTCC
53331779 TCCCTTTCCTACCTTCCTCTAACCCTTTTTTAATCCCCTTTAAATTTTCC
1 TCCCTTTCCTACCTTCCTCTAACCCTTTTTTAATCCCCTTTAAATTTTCC
53331829 T
1 T
53331830 TTCTATCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.47
Consensus pattern (50 bp):
TCCCTTTCCTACCTTCCTCTAACCCTTTTTTAATCCCCTTTAAATTTTCC
Found at i:53332151 original size:20 final size:20
Alignment explanation
Indices: 53332126--53332168 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
53332116 CTTAGAACCT
53332126 TACCAGTTTACTGGTTTCTC
1 TACCAGTTTACTGGTTTCTC
53332146 TACCAGTTTACTGGTTTCTC
1 TACCAGTTTACTGGTTTCTC
53332166 TAC
1 TAC
53332169 TTTTCCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.26, G:0.14, T:0.44
Consensus pattern (20 bp):
TACCAGTTTACTGGTTTCTC
Found at i:53335342 original size:61 final size:58
Alignment explanation
Indices: 53335233--53335346 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 58
53335223 ACTTTAATAA
** * *
53335233 TAAATTAATATTATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAGTCTAT
1 TAAATTAATAGAATATTTATTAAGATAAATATTAAATTAAATTAAATATTAAGTCTAT
53335291 TAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTAAATATTAAG
1 TAAATTAATAGAATATTTAT-T--AAGATAAATATTAAATTAAATTAAATATTAAG
53335347 ATAATCACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 18 0.37
59 1 0.02
61 30 0.61
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (58 bp):
TAAATTAATAGAATATTTATTAAGATAAATATTAAATTAAATTAAATATTAAGTCTAT
Found at i:53335370 original size:61 final size:58
Alignment explanation
Indices: 53335229--53335370 Score: 153
Period size: 61 Copynumber: 2.4 Consensus size: 58
53335219 AATCACTTTA
* * *
53335229 ATAATAAATTAATATTATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAGT
1 ATAATAAATTAATATTAAATTTATTAAGATAAATATTAAATTAAATTAAATATTAAGT
* * *
53335287 CTATTAAATTAATA-GAATATTTATCTACAAGATAAATATTAAATTAAATTAAATATTAAG-
1 ATAATAAATTAATATTAA-ATTTAT-T--AAGATAAATATTAAATTAAATTAAATATTAAGT
* *
53335347 ATAATCACTTAAATATTAAATTTA
1 ATAATAAATT-AATATTAAATTTA
53335371 ATTTAATATT
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 18 0.27
59 1 0.01
60 6 0.09
61 39 0.58
62 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (58 bp):
ATAATAAATTAATATTAAATTTATTAAGATAAATATTAAATTAAATTAAATATTAAGT
Found at i:53335395 original size:17 final size:17
Alignment explanation
Indices: 53335319--53335392 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
53335309 ATCTACAAGA
*
53335319 TAAATATTAAATTAAAT
1 TAAATATTAAATTTAAT
* *
53335336 TAAATATTAAGATAATCACT
1 TAAATATTAA-AT--TTAAT
53335356 TAAATATTAAATTTAAT
1 TAAATATTAAATTTAAT
*
53335373 TTAATATTAAATTT-AT
1 TAAATATTAAATTTAAT
53335389 TAAA
1 TAAA
53335393 ATAATATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
16 5 0.10
17 26 0.54
18 2 0.04
19 2 0.04
20 13 0.27
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATATTAAATTTAAT
Found at i:53336500 original size:22 final size:22
Alignment explanation
Indices: 53336475--53336553 Score: 158
Period size: 22 Copynumber: 3.6 Consensus size: 22
53336465 TGTAGGGCTC
53336475 ACACACCCGTGTGGTCCAAGGG
1 ACACACCCGTGTGGTCCAAGGG
53336497 ACACACCCGTGTGGTCCAAGGG
1 ACACACCCGTGTGGTCCAAGGG
53336519 ACACACCCGTGTGGTCCAAGGG
1 ACACACCCGTGTGGTCCAAGGG
53336541 ACACACCCGTGTG
1 ACACACCCGTGTG
53336554 ACCCTAGGAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (22 bp):
ACACACCCGTGTGGTCCAAGGG
Found at i:53341942 original size:23 final size:23
Alignment explanation
Indices: 53341915--53341970 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
53341905 GTCACAAGTA
53341915 AATTAATTCACAAACAAAATCAG
1 AATTAATTCACAAACAAAATCAG
* *
53341938 AATTAATTCACTAACGAAATCAG
1 AATTAATTCACAAACAAAATCAG
53341961 AATTAATTCA
1 AATTAATTCA
53341971 ACTTGGGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (23 bp):
AATTAATTCACAAACAAAATCAG
Found at i:53345269 original size:23 final size:23
Alignment explanation
Indices: 53345236--53345286 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
53345226 TTGTGGGCAT
53345236 GTTATACGTGCCATATGAAAGCG
1 GTTATACGTGCCATATGAAAGCG
*
53345259 GTTATATGTGCCATATGAAAGCG
1 GTTATACGTGCCATATGAAAGCG
53345282 GTTAT
1 GTTAT
53345287 GTCGTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (23 bp):
GTTATACGTGCCATATGAAAGCG
Found at i:53347578 original size:18 final size:19
Alignment explanation
Indices: 53347541--53347578 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53347531 TGAGTACACG
*
53347541 ATAATGTTGAATTATGAAC
1 ATAATGTTGAATCATGAAC
*
53347560 ATAATG-TGAATCATTAAC
1 ATAATGTTGAATCATGAAC
53347578 A
1 A
53347579 AATCATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (19 bp):
ATAATGTTGAATCATGAAC
Found at i:53348464 original size:25 final size:24
Alignment explanation
Indices: 53348413--53348464 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
53348403 TTAGTTATAT
* * *
53348413 TAACATATTTTAATATTTATAGCA
1 TAACATATTTAAATATTTAAAGAA
*
53348437 TAACATATATTAAATATTTAAATAA
1 TAACATAT-TTAAATATTTAAAGAA
53348462 TAA
1 TAA
53348465 TACCTATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (24 bp):
TAACATATTTAAATATTTAAAGAA
Found at i:53348813 original size:26 final size:25
Alignment explanation
Indices: 53348767--53348815 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
53348757 TTTAATTGGA
53348767 TATTTAATAATATTTATTATTATTT
1 TATTTAATAATATTTATTATTATTT
*
53348792 TATTTAAATATATGTTTA-TATTAT
1 TATTT-AATA-ATATTTATTATTAT
53348816 AAAAAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 10 0.48
27 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTTAATAATATTTATTATTATTT
Found at i:53369721 original size:35 final size:35
Alignment explanation
Indices: 53369675--53369745 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
53369665 TAATTCGAAT
53369675 TAAATAAATTAACCACAAGGCCTAGCACACGGGCG
1 TAAATAAATTAACCACAAGGCCTAGCACACGGGCG
53369710 TAAATAAATTAACCACAAGGCCTAGCACACGGGCG
1 TAAATAAATTAACCACAAGGCCTAGCACACGGGCG
53369745 T
1 T
53369746 GTGGCATGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.15
Consensus pattern (35 bp):
TAAATAAATTAACCACAAGGCCTAGCACACGGGCG
Found at i:53371349 original size:17 final size:16
Alignment explanation
Indices: 53371323--53371366 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
53371313 ATTAACTTTT
* *
53371323 AATAAATTTATTATTA
1 AATAAATTTAATAATA
53371339 AATATAATTTAATAATA
1 AATA-AATTTAATAATA
53371356 AAT-AATTTAAT
1 AATAAATTTAAT
53371367 CATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATTTAATAATA
Found at i:53374288 original size:15 final size:16
Alignment explanation
Indices: 53374252--53374287 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53374242 ATTTTGTTGC
*
53374252 AAAAGTTATAATTTAA
1 AAAAATTATAATTTAA
*
53374268 AAAAATTATAATTGAA
1 AAAAATTATAATTTAA
53374284 AAAA
1 AAAA
53374288 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAATTATAATTTAA
Found at i:53384784 original size:40 final size:41
Alignment explanation
Indices: 53384705--53384802 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 41
53384695 AACGGGCCTA
* *
53384705 CTCACACAAACTGTCAATCGAGACGTAGCTACACGGTGCTG
1 CTCACACAAGCTGTCAATCGAGACGTAGCTACACAGTGCTG
* ***
53384746 CTCACAC-AGCTGTCAGTCGAGACGTAGCTATGTAGTGCTG
1 CTCACACAAGCTGTCAATCGAGACGTAGCTACACAGTGCTG
*
53384786 CTCATACAAGCTGTCAA
1 CTCACACAAGCTGTCAA
53384803 GTAACCGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.69
41 15 0.31
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (41 bp):
CTCACACAAGCTGTCAATCGAGACGTAGCTACACAGTGCTG
Found at i:53390762 original size:99 final size:96
Alignment explanation
Indices: 53390587--53390767 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 96
53390577 GGGTATAATA
* * * * *
53390587 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTCCCAGG
1 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCCATGTCCCAGA
*
53390652 CATGGTCTTACATTGACTATCAAAATTGAGG
66 CATGGTCTTACACTGACTATCAAAATTGAGG
* * *
53390683 CCGACGCCATGTCCCAAATATGGTCTTACACTAGCTC-TCACATATCTATGCCGATGCCATGTCT
1 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATC-C--ATC-AAGCCGATGCCATGTCC
53390747 CAGACATGGTCTTACACTGAC
62 CAGACATGGTCTTACACTGAC
53390768 ACATCTCGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
95 2 0.03
96 34 0.47
98 3 0.04
99 33 0.46
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (96 bp):
CCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGACTATCAAAATTGAGG
Found at i:53390817 original size:46 final size:47
Alignment explanation
Indices: 53390587--53390948 Score: 221
Period size: 46 Copynumber: 7.6 Consensus size: 47
53390577 GGGTATAATA
* *
53390587 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT--CATC-CATCAAG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCGT-ATG
* * * * * *
53390634 TCGATGCCATGTCCCAGGCATGGTCTTACATTGACTATCAAAAT-T-G-AGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGC--TC-ACATCTCGTATG
* * * * *
53390683 CCGACGCCATGTCCCAAATATGGTCTTACACTAGCTCTCACATATC-TATG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACT-G-GCTCACATCTCGTATG
* *
53390733 CCGATGCCATGTCTCAGACATGGTCTTACACT-G-ACACATCTCGTA-G
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCGTATG
* *
53390779 CCGATGCATGTCCCAGACATGTCTTATACTGGCTCACATCTCG-AGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGTATG
* * * * *
53390825 CCGATGCATGTCCTAGACAAGTCTTACACTAGCTCTCATCTC-AATG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGTATG
* * * * *
53390871 CCGATGCCATGTCCCAAACTTGGTCTTACACTGGCTCTCATAAT-GT-GG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACAT-CTCGTATG
*
53390919 CCGATGCATGTCCTAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
53390949 AGCACACAAA
Statistics
Matches: 252, Mismatches: 43, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
44 9 0.04
45 15 0.06
46 79 0.31
47 54 0.21
48 28 0.11
49 33 0.13
50 31 0.12
51 1 0.00
52 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCGTATG
Found at i:53390923 original size:94 final size:94
Alignment explanation
Indices: 53390682--53390956 Score: 278
Period size: 94 Copynumber: 2.9 Consensus size: 94
53390672 CAAAATTGAG
* * * * *
53390682 GCCGACGCCATGTCCCAAA-TATGGTCTTACACTAGCTCTCACATATCTATGCCGATGCCATGT-
1 GCCGATGCCATGTCCCAAACT-TGGTCTTACACTGGCTCTCATA-ATGT-GGCCGATG-CATGTC
* *
53390745 CTCAGACATGGTCTTACACT-G-ACACATCTCGTA
62 CT-AGACA-AGTCTTACACTAGCACACATCTCATA
* * * * * *
53390778 GCCGATG-CATGTCCCAGACAT-GTCTTATACTGGCTCACAT-CTCGAGGCCGATGCATGTCCTA
1 GCCGATGCCATGTCCCAAACTTGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCTA
* *
53390840 GACAAGTCTTACACTAGCTCTCATCTCA-A
65 GACAAGTCTTACACTAGCACACATCTCATA
53390869 TGCCGATGCCATGTCCCAAACTTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCTA
1 -GCCGATGCCATGTCCCAAACTTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCTA
*
53390934 GACATGTCTTACACTAGCACACA
65 GACAAGTCTTACACTAGCACACA
53390957 AATAACCCGA
Statistics
Matches: 146, Mismatches: 24, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
90 10 0.07
91 12 0.08
92 24 0.16
93 12 0.08
94 70 0.48
95 12 0.08
96 6 0.04
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAAACTTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCTAG
ACAAGTCTTACACTAGCACACATCTCATA
Found at i:53399643 original size:40 final size:40
Alignment explanation
Indices: 53399599--53399868 Score: 301
Period size: 40 Copynumber: 6.8 Consensus size: 40
53399589 TATTTATCGA
* *
53399599 TGATTGCATATACGTGCCCCTGTTTGTACTTCGATACCTC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
* * *
53399639 TGATTGCACATATGTGCCCCTGTTTGTGCTT-TAGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGA-TACCCC
* * *
53399679 TGATTGCACATACGTGCCCTTATTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
* * * *
53399719 TGATTTCACATATGTTCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
* * * *
53399759 TAATTGCACATATGTGCCCCTG-TTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
* * *
53399798 TGATTGCACATTCGTGCCCATGTTTGTACTTCTATACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
* * * * *
53399838 TGAATGCACTTACATGCCCCTATTTATACTT
1 TGATTGCACATACGTGCCCCTGTTTGTACTT
53399869 TGGTAACCCT
Statistics
Matches: 193, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
39 35 0.18
40 158 0.82
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
Found at i:53399686 original size:80 final size:80
Alignment explanation
Indices: 53399599--53399878 Score: 332
Period size: 80 Copynumber: 3.5 Consensus size: 80
53399589 TATTTATCGA
* * * *
53399599 TGATTGCATATACGTGCCCCTGTTTGTACTTCGATACCTCTGATTGCACATATGTGCCCCTGTTT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTGTTT
*
53399664 GTGCTTTAGTACCCC
66 GTACTTTAGTACCCC
* * *
53399679 TGATTGCACATACGTGCCCTTATTTGTACTTCGGTACCCCTGATTTCACATATGTTCCCCTGTTT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTGTTT
**
53399744 GTACTTCGGTACCCC
66 GTACTTTAGTACCCC
* * * * *
53399759 TAATTGCACATATGTGCCCCT-GTTGTACTTTGGTACCCCTGATTGCACAT-TCGTGCCCATGTT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATAT-GTGCCCCTGTT
53399822 TGTACTTCTA-TACCCC
65 TGTACTT-TAGTACCCC
* * * * * *
53399838 TGAATGCACTTACATGCCCCTATTTATACTTTGGTAACCCT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
53399879 AAATCAAATA
Statistics
Matches: 169, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
78 1 0.01
79 64 0.38
80 104 0.62
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (80 bp):
TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTGTTT
GTACTTTAGTACCCC
Found at i:53399758 original size:20 final size:20
Alignment explanation
Indices: 53399615--53399839 Score: 71
Period size: 20 Copynumber: 11.3 Consensus size: 20
53399605 CATATACGTG
*
53399615 CCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTCGGTA
* * * * ** *
53399635 CCTCTGATTGCACATATGTG
1 CCCCTGTTTGTACTTCGGTA
* **
53399655 CCCCTGTTTGTGCTTTAGTA
1 CCCCTGTTTGTACTTCGGTA
* * * *
53399675 CCCCTGATTGCACATAC-GTG
1 CCCCTGTTTGTAC-TTCGGTA
* *
53399695 CCCTTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * ** *
53399715 CCCCTGATTT-CACATATGTT
1 CCCCTG-TTTGTACTTCGGTA
53399735 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * ** *
53399755 CCCCTAATTGCACATATGTG
1 CCCCTGTTTGTACTTCGGTA
*
53399775 CCCCTG-TTGTACTTTGGTA
1 CCCCTGTTTGTACTTCGGTA
* * *
53399794 CCCCTGATTGCACATTC-GTG
1 CCCCTGTTTGTAC-TTCGGTA
* **
53399814 CCCATGTTTGTACTTCTATA
1 CCCCTGTTTGTACTTCGGTA
53399834 CCCCTG
1 CCCCTG
53399840 AATGCACTTA
Statistics
Matches: 136, Mismatches: 62, Indels: 14
0.64 0.29 0.07
Matches are distributed among these distances:
19 22 0.16
20 108 0.79
21 6 0.04
ACGTcount: A:0.16, C:0.30, G:0.17, T:0.37
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:53403287 original size:40 final size:40
Alignment explanation
Indices: 53403243--53403322 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
53403233 GGCTAAGAAC
** *
53403243 GGCACTTAGTGTGCGGTTTGAAATAGTTTCGGCTAAATGT
1 GGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTAAATGT
* * *
53403283 GGCACTTCGTGTGCAATTTGAGATAGCTTCGGCTATATGT
1 GGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTAAATGT
53403323 ATATGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (40 bp):
GGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTAAATGT
Found at i:53403402 original size:28 final size:28
Alignment explanation
Indices: 53403332--53403402 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
53403322 TATATGTGGC
* *
53403332 ACTTAGTGTGCGAAATATTGAGAATGAC
1 ACTTAGTGTGCGAGATATTGAGAATGAA
* * *
53403360 ACTTGGTGTGTGAGATATTGAGTATGAA
1 ACTTAGTGTGCGAGATATTGAGAATGAA
53403388 ACTTAGTGTGCGAGA
1 ACTTAGTGTGCGAGA
53403403 CATCGAAGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.31
Consensus pattern (28 bp):
ACTTAGTGTGCGAGATATTGAGAATGAA
Found at i:53418126 original size:46 final size:47
Alignment explanation
Indices: 53418035--53418260 Score: 187
Period size: 47 Copynumber: 4.8 Consensus size: 47
53418025 ATTTGTTTGT
* *
53418035 GAGCCAGTGTAAGACCATGTCTGGGACATGACATCGGCATTGAGACA-A
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCATCGAGACATA
* * *
53418083 GAGCTAGTGTAAGACATGTTTAGGACATGCATCGGCCTCGAGACATA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACATA
* * *
53418130 -AGCTAGTGCAAGACTTGTCTGGGACATGCATCGGC-TACGAGATGATA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGA-CATA
* * * * * * * *
53418177 G-TC-AGTTTTAGACCTTGTCTGGGACATGGCTTCGAC-TTGAGATAT-
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACATA
53418222 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
53418261 CCTTACCCAT
Statistics
Matches: 145, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
45 2 0.01
46 59 0.41
47 64 0.44
48 20 0.14
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACATA
Found at i:53421727 original size:39 final size:40
Alignment explanation
Indices: 53421680--53421811 Score: 171
Period size: 40 Copynumber: 3.3 Consensus size: 40
53421670 GGACTAAGAT
* *
53421680 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTC
* * *
53421719 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTC
*
53421759 CCGAAGGCATTTGTGCGAGTTACTATAA-CC-GGTCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCAGG-CTAAGTC
53421799 CCGAAGGCATTTG
1 CCGAAGGCATTTG
53421812 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
39 35 0.43
40 45 0.55
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTC
Found at i:53421818 original size:40 final size:39
Alignment explanation
Indices: 53421680--53421844 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 39
53421670 GGACTAAGAT
* * *
53421680 CCGAAGGCATTTGTGCGAGATACTA-ATTCCAGGCTAAG-C
1 CCGAAGGCATTTGTGCGAGTTACTATA-ACC-GGTTAAGTC
*
53421719 CCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAA-CC-GGTTAAGTC
*
53421759 CCGAAGGCATTTGTGCGAGTTACTATAACCGGTCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGT-TAAGTC
** * * *
53421799 CCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATT
1 CCGAAGGCATTTGTGCGAGTTA-CTATAACCGGTTAAGTC
53421838 CCGAAGG
1 CCGAAGG
53421845 TACGTGATTC
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 47 0.44
40 59 0.55
41 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTACTATAACCGGTTAAGTC
Found at i:53421833 original size:79 final size:79
Alignment explanation
Indices: 53421680--53421844 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
53421670 GGACTAAGAT
* **
53421680 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
53421745 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
53421759 CCGAAGGCATTTGTGCGAGTTACT-ATAACC-GGTCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCAGG-CTAAG-CCCGAAGGCATTGGAACGAGTTA-
* *
53421821 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
53421838 CCGAAGG
1 CCGAAGG
53421845 TACGTGATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.05
79 45 0.62
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:53431369 original size:16 final size:16
Alignment explanation
Indices: 53431348--53431382 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53431338 CCTTCCTCTA
*
53431348 TATGATGAATTCCTGG
1 TATGATGAATGCCTGG
53431364 TATGATGAATGCCTGG
1 TATGATGAATGCCTGG
53431380 TAT
1 TAT
53431383 ACGGAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (16 bp):
TATGATGAATGCCTGG
Found at i:53459280 original size:17 final size:17
Alignment explanation
Indices: 53459258--53459290 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53459248 CTAAGTACAC
53459258 ATTGTCATTGCATTTTT
1 ATTGTCATTGCATTTTT
53459275 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
53459291 CATGTTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:53460311 original size:177 final size:177
Alignment explanation
Indices: 53460015--53460369 Score: 665
Period size: 177 Copynumber: 2.0 Consensus size: 177
53460005 TTCATTCATT
*
53460015 GAGATTTTAGGTGATTCAAGTTGCTAGAATGCTTATTCGCCTTAGTGAATTTTTGTAGCCTTGCT
1 GAGATTTTAGGTGATTCAAGTTGCTAGAATGCTCATTCGCCTTAGTGAATTTTTGTAGCCTTGCT
53460080 AGTTTCTGTTTTACTTGAGGACAAGTAAAAACTCAAGTTTGGAGGTGTGATAGTACTAGAAAAAA
66 AGTTTCTGTTTTACTTGAGGACAAGTAAAAACTCAAGTTTGGAGGTGTGATAGTACTAGAAAAAA
** *
53460145 CATTTGTTCCCATTTAGTTATGGTTAGCACATATTTTAGCATTTTCA
131 CATTTGTTCCCATTTAGTTAAAGTTACCACATATTTTAGCATTTTCA
*
53460192 GAGATTTTAGGTGATTCAAGTTGCTAGAATGCTCATTTGCCTTAGTGAATTTTTGTAGCCTTGCT
1 GAGATTTTAGGTGATTCAAGTTGCTAGAATGCTCATTCGCCTTAGTGAATTTTTGTAGCCTTGCT
53460257 AGTTTCTGTTTTACTTGAGGACAAGTAAAAACTCAAGTTTGGAGGTGTGATAGTACTAGAAAAAA
66 AGTTTCTGTTTTACTTGAGGACAAGTAAAAACTCAAGTTTGGAGGTGTGATAGTACTAGAAAAAA
53460322 CATTTGTTCCCATTTAGTTAAAGTTACCACATATTTTAGCATTTTCA
131 CATTTGTTCCCATTTAGTTAAAGTTACCACATATTTTAGCATTTTCA
53460369 G
1 G
53460370 TTTAGTAAAT
Statistics
Matches: 173, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 173 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (177 bp):
GAGATTTTAGGTGATTCAAGTTGCTAGAATGCTCATTCGCCTTAGTGAATTTTTGTAGCCTTGCT
AGTTTCTGTTTTACTTGAGGACAAGTAAAAACTCAAGTTTGGAGGTGTGATAGTACTAGAAAAAA
CATTTGTTCCCATTTAGTTAAAGTTACCACATATTTTAGCATTTTCA
Found at i:53466415 original size:38 final size:38
Alignment explanation
Indices: 53466321--53466432 Score: 104
Period size: 38 Copynumber: 2.9 Consensus size: 38
53466311 AATCCTTCTA
* *
53466321 GGCACAAAGCTTGATT-GACACATAGCCCAAATAA-AACT
1 GGCACAAAGCTTG-TTAGGCACATAG-CCGAATAACAACT
* ** *
53466359 GGCACAAAGCCTACTAGGCACATAGTCCGAATAACATC-
1 GGCACAAAGCTTGTTAGGCACATAG-CCGAATAACAACT
*
53466397 GGCACAAAGCTTGTTAGGCATATAGCCTGAATAACA
1 GGCACAAAGCTTGTTAGGCACATAGCC-GAATAACA
53466433 CCGTTTCTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 3 0.05
38 55 0.92
39 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (38 bp):
GGCACAAAGCTTGTTAGGCACATAGCCGAATAACAACT
Found at i:53470200 original size:20 final size:20
Alignment explanation
Indices: 53470175--53470240 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
53470165 TACTTTGGTA
53470175 CCCCTGATTACACATACGTG
1 CCCCTGATTACACATACGTG
* * * *
53470195 CCCCTGTTTATAC-TCCGGTA
1 CCCCTGATTACACATAC-GTG
* *
53470215 CCCCTAATTACACATATGTG
1 CCCCTGATTACACATACGTG
53470235 CCCCTG
1 CCCCTG
53470241 TTTGTACTTT
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.91
21 1 0.03
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (20 bp):
CCCCTGATTACACATACGTG
Found at i:53470215 original size:40 final size:40
Alignment explanation
Indices: 53470139--53470419 Score: 355
Period size: 40 Copynumber: 7.0 Consensus size: 40
53470129 TATTTATCGA
* * *
53470139 TGATTGCACATATGTGCTCCTATTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * **
53470179 TGATTACACATACGTGCCCCTGTTTATACTCCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
53470219 TAATTACACATATGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
53470259 TGATTGCACATGCGTGCCCTTATTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
**
53470299 TGATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * * *
53470339 TGATTGTACATATGTGCCCCTATTAGTACTTTGGTACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
53470379 TGATTGCACATTCGTGCCCATGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
53470419 T
1 T
53470420 AAATGAACTT
Statistics
Matches: 203, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 203 1.00
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
Found at i:53470258 original size:20 final size:20
Alignment explanation
Indices: 53470235--53470419 Score: 95
Period size: 20 Copynumber: 9.2 Consensus size: 20
53470225 CACATATGTG
53470235 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* * * *
53470255 CCCCTGATTGCAC-ATGCGTG
1 CCCCTGTTTGTACTTTG-GTA
* *
53470275 CCCTTATTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* * * ** *
53470295 CCCCTGATTGCACATACGTG
1 CCCCTGTTTGTACTTTGGTA
**
53470315 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTTGGTA
* * *
53470335 CCCCTGATTGTACATAT-GTG
1 CCCCTGTTTGTAC-TTTGGTA
* *
53470355 CCCCTATTAGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* * * * * *
53470375 CCCTTGATTGCACATTCGTG
1 CCCCTGTTTGTACTTTGGTA
* *
53470395 CCCATGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTTGGTA
53470415 CCCCT
1 CCCCT
53470420 AAATGAACTT
Statistics
Matches: 112, Mismatches: 49, Indels: 8
0.66 0.29 0.05
Matches are distributed among these distances:
19 4 0.04
20 105 0.94
21 3 0.03
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (20 bp):
CCCCTGTTTGTACTTTGGTA
Found at i:53470336 original size:120 final size:119
Alignment explanation
Indices: 53470139--53470419 Score: 400
Period size: 120 Copynumber: 2.3 Consensus size: 119
53470129 TATTTATCGA
*
53470139 TGATTGCACATATGTGCTCCTATTTGTACTTTGGTACCCCTGATTACACATACGTGCCCCTGTTT
1 TGATTGCACATACGTGC-CCTATTTGTACTTTGGTACCCCTGATTACACATACGTGCCCCTGTTT
* * *
53470204 ATACTCCGGTACCCCTAATTACACATATGTGCCCCTGTTTGTACTTTGGTACCCC
65 ATACTCCAGTACCCCTAATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
* *
53470259 TGATTGCACATGCGTGCCCTTATTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTT
1 TGATTGCACATACGTGCCC-TATTTGTACTTTGGTACCCCTGATTACACATACGTGCCCCTGTTT
* * * ** *
53470324 GTACTTCAGTACCCCTGATTGTACATATGTGCCCCTATTAGTACTTTGGTACCCT
65 ATACTCCAGTACCCCTAATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
* * *
53470379 TGATTGCACATTCGTGCCCATGTTTGTACTTCGGTACCCCT
1 TGATTGCACATACGTGCCC-TATTTGTACTTTGGTACCCCT
53470420 AAATGAACTT
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
119 2 0.01
120 142 0.99
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (119 bp):
TGATTGCACATACGTGCCCTATTTGTACTTTGGTACCCCTGATTACACATACGTGCCCCTGTTTA
TACTCCAGTACCCCTAATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
Found at i:53470437 original size:40 final size:40
Alignment explanation
Indices: 53470139--53470454 Score: 312
Period size: 40 Copynumber: 7.9 Consensus size: 40
53470129 TATTTATCGA
* * * *
53470139 TGATTGCACATATGTGCTCCTATTTGTACTTTGGTACCCC
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* **
53470179 TGATT-ACACATACGTGCCCCTGTTTATACTCCGGTACCCC
1 TGATTGA-ACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* *
53470219 TAATT-ACACATATGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGA-ACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * *
53470259 TGATTGCACATGCGTGCCCTTATTTGTACTTTGGTACCCC
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* **
53470299 TGATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCC
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * * *
53470339 TGATTGTACATATGTGCCCCTATTAGTACTTTGGTACCCT
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * *
53470379 TGATTGCACATTCGTGCCCATGTTTGTACTTCGGTACCCC
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * * * * *
53470419 TAAATGAACTTACATGCCCCTGGTTATACTCTGGTA
1 TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTA
53470455 ATCCTGAATC
Statistics
Matches: 225, Mismatches: 49, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
40 225 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (40 bp):
TGATTGAACATACGTGCCCCTGTTTGTACTTTGGTACCCC
Found at i:53470461 original size:120 final size:118
Alignment explanation
Indices: 53470139--53470454 Score: 375
Period size: 120 Copynumber: 2.6 Consensus size: 118
53470129 TATTTATCGA
* *
53470139 TGATTGCACATAT-GTGCTCCTATTTGTACTTTGGTACCCCTGATTACACATACGTGCCCCTGTT
1 TGATTGCACAT-TCGTGC-CCTATTTGTACTTTGGTACCCCTAATGA-ACATACGTGCCCCTGTT
* * * *
53470203 TATACTCCGGTACCCCTAATTACACATATGTGCCCCTGTTTGTACTTTGGTACCCC
63 TATACTCTGGTACCCCTGATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
* * *
53470259 TGATTGCACATGCGTGCCCTTATTTGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTT
1 TGATTGCACATTCGTGCCC-TATTTGTACTTTGGTACCCCT-AATGAACATACGTGCCCCTGTTT
* * ** *
53470324 GTACT-TCAGTACCCCTGATTGTACATATGTGCCCCTATTAGTACTTTGGTACCCT
64 ATACTCT-GGTACCCCTGATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
* * * * *
53470379 TGATTGCACATTCGTGCCCATGTTTGTACTTCGGTACCCCTAAATGAACTTACATGCCCCTGGTT
1 TGATTGCACATTCGTGCCC-TATTTGTACTTTGGTACCCCT-AATGAACATACGTGCCCCTGTTT
53470444 ATACTCTGGTA
64 ATACTCTGGTA
53470455 ATCCTGAATC
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
119 2 0.01
120 161 0.98
121 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (118 bp):
TGATTGCACATTCGTGCCCTATTTGTACTTTGGTACCCCTAATGAACATACGTGCCCCTGTTTAT
ACTCTGGTACCCCTGATTACACATATGTGCCCCTATTAGTACTTTGGTACCCC
Found at i:53487011 original size:16 final size:17
Alignment explanation
Indices: 53486975--53487012 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53486965 AAAAAAAGCA
53486975 AAAATAGAAAATGAATT
1 AAAATAGAAAATGAATT
* *
53486992 AAAATATAAAAT-ATTT
1 AAAATAGAAAATGAATT
53487008 AAAAT
1 AAAAT
53487013 TTATTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
AAAATAGAAAATGAATT
Found at i:53487675 original size:19 final size:18
Alignment explanation
Indices: 53487626--53487667 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
53487616 CGATCCAATC
53487626 TCTTTCCTTTAAATGTTT
1 TCTTTCCTTTAAATGTTT
53487644 TCTTTCCTTTAAATGTTT
1 TCTTTCCTTTAAATGTTT
53487662 TCTTTC
1 TCTTTC
53487668 TTTTTAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.62
Consensus pattern (18 bp):
TCTTTCCTTTAAATGTTT
Found at i:53493025 original size:19 final size:19
Alignment explanation
Indices: 53493001--53493038 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53492991 GATAGTTTAA
53493001 TGAGTTAGCAAATACGAAG
1 TGAGTTAGCAAATACGAAG
53493020 TGAGTTAGCAAATACGAAG
1 TGAGTTAGCAAATACGAAG
53493039 CTCTGATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (19 bp):
TGAGTTAGCAAATACGAAG
Found at i:53493821 original size:12 final size:12
Alignment explanation
Indices: 53493804--53493829 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53493794 CGGTTATGCA
53493804 GTAAGATTTGTG
1 GTAAGATTTGTG
53493816 GTAAGATTTGTG
1 GTAAGATTTGTG
53493828 GT
1 GT
53493830 GAATTTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (12 bp):
GTAAGATTTGTG
Found at i:53503801 original size:7 final size:7
Alignment explanation
Indices: 53503789--53503843 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
53503779 TGACCATCCT
53503789 TAAACCC
1 TAAACCC
53503796 TAAACCC
1 TAAACCC
53503803 TAATA-CC
1 TAA-ACCC
53503810 TAAACCC
1 TAAACCC
53503817 TAATA-CC
1 TAA-ACCC
*
53503824 TAAACTC
1 TAAACCC
*
53503831 TAAACCT
1 TAAACCC
53503838 TAAACC
1 TAAACC
53503844 TTAACCCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 2 0.05
7 37 0.90
8 2 0.05
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:53503813 original size:14 final size:14
Alignment explanation
Indices: 53503794--53503843 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
53503784 ATCCTTAAAC
53503794 CCTAAACCCTAATA
1 CCTAAACCCTAATA
53503808 CCTAAACCCTAATA
1 CCTAAACCCTAATA
*
53503822 CCTAAACTCTAA-A
1 CCTAAACCCTAATA
53503835 CCTTAAACC
1 CC-TAAACC
53503844 TTAACCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 3 0.09
14 30 0.91
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAACCCTAATA
Found at i:53503815 original size:21 final size:21
Alignment explanation
Indices: 53503789--53503843 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
53503779 TGACCATCCT
53503789 TAAACCCTAAACCCTAATAC-C
1 TAAACCCTAAACCCTAA-ACTC
53503810 TAAACCCTAATA-CCTAAACTC
1 TAAACCCTAA-ACCCTAAACTC
*
53503831 TAAACCTTAAACC
1 TAAACCCTAAACC
53503844 TTAACCCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.10
21 26 0.87
22 1 0.03
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACTC
Found at i:53503844 original size:7 final size:7
Alignment explanation
Indices: 53503786--53503854 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 7
53503776 TTTTGACCAT
53503786 CCTTAAA
1 CCTTAAA
*
53503793 CCCTAAA
1 CCTTAAA
*
53503800 CCCTAATA
1 CCTTAA-A
53503808 CC-TAAA
1 CCTTAAA
*
53503814 CCCTAATA
1 CCTTAA-A
53503822 CC-TAAA
1 CCTTAAA
53503828 -CTCTAAA
1 CCT-TAAA
53503835 CCTTAAA
1 CCTTAAA
*
53503842 CCTTAAC
1 CCTTAAA
53503849 CCTTAA
1 CCTTAA
53503855 CACTTTAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
5 1 0.02
6 4 0.07
7 41 0.76
8 8 0.15
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.25
Consensus pattern (7 bp):
CCTTAAA
Found at i:53503928 original size:21 final size:21
Alignment explanation
Indices: 53503904--53503946 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53503894 TCTATAGTCG
*
53503904 TAAATCATAAACTA-TAAACCT
1 TAAACCATAAA-TATTAAACCT
*
53503925 TAAACCCTAAATATTAAACCT
1 TAAACCATAAATATTAAACCT
53503946 T
1 T
53503947 GGATCCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCATAAATATTAAACCT
Found at i:53505327 original size:6 final size:6
Alignment explanation
Indices: 53505316--53505356 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
53505306 CCTAACTCAA
* *
53505316 TCTGCG TCTGCG TCTGCG TCTGCG TCTGCA TTTGCG TCTGC
1 TCTGCG TCTGCG TCTGCG TCTGCG TCTGCG TCTGCG TCTGC
53505357 CTCTTCTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.02, C:0.32, G:0.29, T:0.37
Consensus pattern (6 bp):
TCTGCG
Found at i:53508166 original size:37 final size:37
Alignment explanation
Indices: 53508105--53508183 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53508095 TTATTACGAA
* * *
53508105 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
53508142 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
53508179 GTCTT
1 GTCTT
53508184 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:53508389 original size:47 final size:47
Alignment explanation
Indices: 53508302--53508602 Score: 449
Period size: 47 Copynumber: 6.4 Consensus size: 47
53508292 CCTTTCGGGA
* * * * * * * *
53508302 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53508349 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53508396 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53508443 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53508490 CTTATTAGATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53508537 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53508584 CTTATCACACATATACACT
1 CTTATCACATATATACACT
53508603 CTCTTGGCTG
Statistics
Matches: 234, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 234 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53511826 original size:29 final size:27
Alignment explanation
Indices: 53511808--53511877 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
53511798 ATATTAAGTC
53511808 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
53511835 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
53511863 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
53511878 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:53511871 original size:28 final size:28
Alignment explanation
Indices: 53511808--53511905 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
53511798 ATATTAAGTC
*
53511808 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53511835 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53511863 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53511892 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53511906 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53520152 original size:28 final size:28
Alignment explanation
Indices: 53520094--53520189 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
53520084 TATTTAAGTC
*
53520094 CGCACACTCAGTGCTATAT--TC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53520119 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53520147 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53520176 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53520190 CAATCTCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
25 18 0.29
27 2 0.03
28 23 0.37
29 19 0.31
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53538256 original size:21 final size:21
Alignment explanation
Indices: 53538230--53538275 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
53538220 AACTTAGAGT
*
53538230 GGAGGCAACAGCGCGGGAGGC
1 GGAGGCAACAGCGAGGGAGGC
53538251 GGAGGCAACAGCGAGGGAGGC
1 GGAGGCAACAGCGAGGGAGGC
53538272 GGAG
1 GGAG
53538276 CAGACTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.54, T:0.00
Consensus pattern (21 bp):
GGAGGCAACAGCGAGGGAGGC
Found at i:53543077 original size:19 final size:19
Alignment explanation
Indices: 53543041--53543079 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53543031 TTTTCACCAT
* *
53543041 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
53543060 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
53543079 A
1 A
53543080 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:53543583 original size:55 final size:56
Alignment explanation
Indices: 53543518--53543632 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
53543508 AGCATGGCTG
* * *
53543518 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
53543574 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
53543629 CCAG
1 CCAG
53543633 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:53543629 original size:28 final size:27
Alignment explanation
Indices: 53543543--53543632 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
53543533 GTGACAGAGT
*
53543543 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
53543572 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
53543599 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
53543627 CACCAG
1 CACCAG
53543633 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:53543785 original size:28 final size:28
Alignment explanation
Indices: 53543738--53543801 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
53543728 AAATTAACCC
*
53543738 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
53543766 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
53543794 TAGGGGTA
1 TAGGGGTA
53543802 CTCTAGTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:53548721 original size:9 final size:9
Alignment explanation
Indices: 53548709--53548735 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53548699 AGCGATGAGA
53548709 TGGATGATG
1 TGGATGATG
53548718 TGGATGATG
1 TGGATGATG
53548727 TGGATGATG
1 TGGATGATG
53548736 ATTAGAACTT
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:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (9 bp):
TGGATGATG
Found at i:53551004 original size:19 final size:19
Alignment explanation
Indices: 53550980--53551020 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
53550970 CACCAATTAC
53550980 TTAGTTTATAATCTATTTT
1 TTAGTTTATAATCTATTTT
*
53550999 TTAGTTTATAATCTCTTTT
1 TTAGTTTATAATCTATTTT
53551018 TTA
1 TTA
53551021 ATTTTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (19 bp):
TTAGTTTATAATCTATTTT
Found at i:53556132 original size:22 final size:24
Alignment explanation
Indices: 53556104--53556147 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
53556094 ATTTTGTTCA
53556104 ACTTTAA-CTTTTAT-TCAAAAAT
1 ACTTTAATCTTTTATATCAAAAAT
*
53556126 ACTTTAATTTTTTATATCAAAA
1 ACTTTAATCTTTTATATCAAAA
53556148 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (24 bp):
ACTTTAATCTTTTATATCAAAAAT
Found at i:53565619 original size:6 final size:6
Alignment explanation
Indices: 53565614--53565697 Score: 123
Period size: 6 Copynumber: 13.7 Consensus size: 6
53565604 AAACTTAAAC
* * *
53565614 GAAAAC GAAAAC GAAAAT GAAAAC GAAAAT GAAAAT GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
53565662 GAAAAT GAAAAT GAAAAT GAAAAT AGAGAAAT GAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT -GA-AAAT GAAA
53565698 CCATTTGGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
6 65 0.89
7 4 0.05
8 4 0.05
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.12
Consensus pattern (6 bp):
GAAAAT
Found at i:53567092 original size:17 final size:19
Alignment explanation
Indices: 53567039--53567092 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 19
53567029 TTATTTAGAA
* *
53567039 ATTTTTTATCATACTAAA-
1 ATTTTTTATAATAATAAAT
*
53567057 A-TTTTTATAATAATTAAT
1 ATTTTTTATAATAATAAAT
53567075 ATTTTTTA-AAT-ATAAAT
1 ATTTTTTATAATAATAAAT
53567092 A
1 A
53567093 AAGTAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 19 0.63
18 5 0.17
19 6 0.20
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTATAATAATAAAT
Done.