Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 157 of 297
Found at i:53467083 original size:29 final size:29
Alignment explanation
Indices: 53467023--53467084 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
53467013 TTTAATATGT
* *
53467023 AATTGTATACATGAACTTTGAATTTGTGC
1 AATTGTATACATGAACTTTGAATTTATCC
* *
53467052 AATTTTATACATGAGATTTTG-ATTTATCC
1 AATTGTATACATGA-ACTTTGAATTTATCC
53467081 AATT
1 AATT
53467085 CTTGTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (29 bp):
AATTGTATACATGAACTTTGAATTTATCC
Found at i:53474764 original size:20 final size:20
Alignment explanation
Indices: 53474739--53474837 Score: 58
Period size: 20 Copynumber: 5.0 Consensus size: 20
53474729 AATGCGTAAT
53474739 AGAGGCACTGAAGTGCAAAC
1 AGAGGCACTGAAGTGCAAAC
* * * *
53474759 AGAGGCACCGTAGTGCGAAT
1 AGAGGCACTGAAGTGCAAAC
* * *
53474779 AGAGACAGC-GAACTGCATAC
1 AGAGGCA-CTGAAGTGCAAAC
* *
53474799 AGAGGCA-TCAAAGTGCAAAT
1 AGAGGCACT-GAAGTGCAAAC
* * *
53474819 GGAGGCACTAAAGTACAAA
1 AGAGGCACTGAAGTGCAAA
53474838 TCCTGTATAA
Statistics
Matches: 58, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.12
Consensus pattern (20 bp):
AGAGGCACTGAAGTGCAAAC
Found at i:53479900 original size:25 final size:25
Alignment explanation
Indices: 53479872--53479931 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 25
53479862 TAATTTTACT
53479872 TAAAAATTTGGACCATATACTATTA
1 TAAAAATTTGGACCATATACTATTA
53479897 TAAAAAATTAATTTGGACCATATACTATTA
1 T---AAA--AATTTGGACCATATACTATTA
53479927 TAAAA
1 TAAAA
53479932 CTACAAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
25 2 0.07
27 3 0.10
28 3 0.10
30 22 0.73
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (25 bp):
TAAAAATTTGGACCATATACTATTA
Found at i:53483712 original size:2 final size:2
Alignment explanation
Indices: 53483707--53483741 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53483697 TGTGGTTTTT
53483707 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
53483742 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:53489516 original size:18 final size:17
Alignment explanation
Indices: 53489492--53489532 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
53489482 CAAAAATATG
*
53489492 GGCCCACATGCCCGTGT
1 GGCCCACATGCACGTGT
*
53489509 GAGCCCACGTGCACGTGT
1 G-GCCCACATGCACGTGT
53489527 GGCCCA
1 GGCCCA
53489533 TACGCCCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.15, C:0.39, G:0.32, T:0.15
Consensus pattern (17 bp):
GGCCCACATGCACGTGT
Found at i:53493714 original size:36 final size:36
Alignment explanation
Indices: 53493668--53493739 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
53493658 GGATACAAGT
*
53493668 GTCACGACATTAAGGGAATGAGATCCCATGTAAGAC
1 GTCACGACATTAAGGGAATGAGATCCCATATAAGAC
*
53493704 GTCATGACATTAAGGGAATGAGATCCCATATAAGAC
1 GTCACGACATTAAGGGAATGAGATCCCATATAAGAC
53493740 CATGTCTGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (36 bp):
GTCACGACATTAAGGGAATGAGATCCCATATAAGAC
Found at i:53494197 original size:20 final size:20
Alignment explanation
Indices: 53494172--53494220 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
53494162 TGAGTTATTT
53494172 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
53494192 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
53494212 AAG-AAGCAA
1 AAGTAAGCAA
53494221 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:53502831 original size:6 final size:6
Alignment explanation
Indices: 53502821--53502859 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
53502811 TGATCATTGA
* * *
53502821 TTTTAA TTTTAT TTTTAT TTTTAT TTTTAC CTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
53502860 CATTGGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:53504198 original size:5 final size:6
Alignment explanation
Indices: 53504143--53504204 Score: 55
Period size: 5 Copynumber: 11.3 Consensus size: 6
53504133 TTATCTTGTA
* * *
53504143 AATATT AAT-TT AAT-TT AAT-TT AATAGT AA-CTT AATATT TATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
53504187 -ATATT AAT-TT AATATT AA
1 AATATT AATATT AATATT AA
53504205 AGTGATTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
5 28 0.60
6 19 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AATATT
Found at i:53504201 original size:11 final size:11
Alignment explanation
Indices: 53504143--53504204 Score: 74
Period size: 11 Copynumber: 5.7 Consensus size: 11
53504133 TTATCTTGTA
53504143 AATATTAATTT
1 AATATTAATTT
53504154 AAT-TTAATTT
1 AATATTAATTT
* *
53504164 AATAGTAACTT
1 AATATTAATTT
*
53504175 AATATTTATATT
1 AATATTAAT-TT
53504187 -ATATTAATTT
1 AATATTAATTT
53504197 AATATTAA
1 AATATTAA
53504205 AGTGATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 12 0.29
11 28 0.67
12 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATATTAATTT
Found at i:53506682 original size:81 final size:81
Alignment explanation
Indices: 53506547--53506709 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
53506537 AATAAATAAA
53506547 TAAATATTCGTCTAAATTTCATGTTTTATTATTATTTTATTTAGTATATAAGAAAAGAAATATGA
1 TAAATATTCGTCTAAATTTCATGTTTTATTATTATTTTATTTAGTATATAAGAAAAGAAATATGA
53506612 AGAATTCTCTTCATCT
66 AGAATTCTCTTCATCT
53506628 TAAATATTCGTCTAAATTTCATGTTTTATTATTATTTTATTTAGTATATAAGAAAAGAAATATGA
1 TAAATATTCGTCTAAATTTCATGTTTTATTATTATTTTATTTAGTATATAAGAAAAGAAATATGA
53506693 AGAATTCTCTTCATCT
66 AGAATTCTCTTCATCT
53506709 T
1 T
53506710 TCCATGCTAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (81 bp):
TAAATATTCGTCTAAATTTCATGTTTTATTATTATTTTATTTAGTATATAAGAAAAGAAATATGA
AGAATTCTCTTCATCT
Found at i:53511146 original size:37 final size:37
Alignment explanation
Indices: 53511096--53511172 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
53511086 GAATAATGCA
* *
53511096 TCTCCTCTAACAATGCTATCAAGACGCAGACAATGTG
1 TCTCCTCTAACAATACTATCAAGACGCAGACAACGTG
*
53511133 TCTCCTCTTACAATACTATCAAGACGCAGACAACGTG
1 TCTCCTCTAACAATACTATCAAGACGCAGACAACGTG
53511170 TCT
1 TCT
53511173 ATACAAACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (37 bp):
TCTCCTCTAACAATACTATCAAGACGCAGACAACGTG
Found at i:53511934 original size:6 final size:6
Alignment explanation
Indices: 53511923--53511953 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
53511913 TTAACCCAAT
53511923 TCAGTA TCAGTA TCAGTA TCAGTA TCAGTA T
1 TCAGTA TCAGTA TCAGTA TCAGTA TCAGTA T
53511954 GCACAAGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (6 bp):
TCAGTA
Found at i:53514481 original size:81 final size:81
Alignment explanation
Indices: 53514346--53514508 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
53514336 TATCTATATA
53514346 TTCAATGAATTGCATCATATAAATGCTCTTTTCAGTATTTCATATAAGAAAAATTAAATATTGAA
1 TTCAATGAATTGCATCATATAAATGCTCTTTTCAGTATTTCATATAAGAAAAATTAAATATTGAA
53514411 ATAATTTACATCCAGC
66 ATAATTTACATCCAGC
53514427 TTCAATGAATTGCATCATATAAATGCTCTTTTCAGTATTTCATATAAGAAAAATTAAATATTGAA
1 TTCAATGAATTGCATCATATAAATGCTCTTTTCAGTATTTCATATAAGAAAAATTAAATATTGAA
* *
53514492 TTAATTTACTTCCAGC
66 ATAATTTACATCCAGC
53514508 T
1 T
53514509 GGAATTTACT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (81 bp):
TTCAATGAATTGCATCATATAAATGCTCTTTTCAGTATTTCATATAAGAAAAATTAAATATTGAA
ATAATTTACATCCAGC
Found at i:53519962 original size:19 final size:19
Alignment explanation
Indices: 53519918--53519963 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 19
53519908 GAAAACCGAA
53519918 GCAAAATCTCTTCAGATCT
1 GCAAAATCTCTTCAGATCT
53519937 G---AATCTCTTCAGATCT
1 GCAAAATCTCTTCAGATCT
53519953 GCAAAATCTCT
1 GCAAAATCTCT
53519964 GACTTGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 16 0.67
19 8 0.33
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (19 bp):
GCAAAATCTCTTCAGATCT
Found at i:53525037 original size:43 final size:43
Alignment explanation
Indices: 53524970--53525203 Score: 225
Period size: 43 Copynumber: 5.7 Consensus size: 43
53524960 ATCTTTAGCG
* * * *
53524970 TTTAGCGGCGCTTTTCTCAAAAACGCCGCTATAGACCATGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
* *
53525013 TTTAGCAGCACTTTTCCCACAAACGCCGCTATGGACCACGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
*
53525056 TTTAGCGG------T-CCACAAACGCCGCTATAGACCACAACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
* * * * *
53525092 TTTAGCGGCGCTTTTCCCACAAACGCTGCTCTAAAACACGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
* ** *
53525135 TTTAGCGGCACTTTTACCACAAACG--TATATAGACTACGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
* * * *
53525176 TTTAGTGACGCTTTTCCCACAAATGCCG
1 TTTAGCGGCACTTTTCCCACAAACGCCG
53525204 TGAAAAATCA
Statistics
Matches: 154, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
36 33 0.21
37 1 0.01
41 30 0.19
42 1 0.01
43 89 0.58
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (43 bp):
TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGACCACGACC
Found at i:53525076 original size:36 final size:36
Alignment explanation
Indices: 53525029--53525099 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
53525019 AGCACTTTTC
* *
53525029 CCACAAACGCCGCTATGGACCACGACCTTTAGCGGT
1 CCACAAACGCCGCTATAGACCACAACCTTTAGCGGT
53525065 CCACAAACGCCGCTATAGACCACAACCTTTAGCGG
1 CCACAAACGCCGCTATAGACCACAACCTTTAGCGG
53525100 CGCTTTTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.37, G:0.20, T:0.15
Consensus pattern (36 bp):
CCACAAACGCCGCTATAGACCACAACCTTTAGCGGT
Found at i:53525132 original size:79 final size:79
Alignment explanation
Indices: 53524990--53525142 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
53524980 CTTTTCTCAA
** ** *
53524990 AAACGCCGCTATAGACCATGACCTTTAGCAGCACTTTTCCCACAAACGCCGCTATGGACCACGAC
1 AAACGCCGCTATAGACCACAACCTTTAGCAGCACTTTTCCCACAAACGCCGCTATAAAACACGAC
53525055 CTTTAGCGGTCCAC
66 CTTTAGCGGTCCAC
* * * *
53525069 AAACGCCGCTATAGACCACAACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTCTAAAACACGAC
1 AAACGCCGCTATAGACCACAACCTTTAGCAGCACTTTTCCCACAAACGCCGCTATAAAACACGAC
53525134 CTTTAGCGG
66 CTTTAGCGG
53525143 CACTTTTACC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (79 bp):
AAACGCCGCTATAGACCACAACCTTTAGCAGCACTTTTCCCACAAACGCCGCTATAAAACACGAC
CTTTAGCGGTCCAC
Found at i:53525219 original size:84 final size:84
Alignment explanation
Indices: 53525078--53525243 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 84
53525068 CAAACGCCGC
* * * * *
53525078 TATAGACCACAACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTCTAAAACACGACCTTTAGCGG
1 TATAGACCACAACCTTTAGCGACGCTTTTCCCACAAACGCCGCTCAAAAACACGACCTTCAGCGA
53525143 CACTTTTACCACAAACGTA
66 CACTTTTACCACAAACGTA
* * * * * *
53525162 TATAGACTACGACCTTTAGTGACGCTTTTCCCACAAATGCCG-TGAAAAATCATGACCTTCAGCG
1 TATAGACCACAACCTTTAGCGACGCTTTTCCCACAAACGCCGCTCAAAAA-CACGACCTTCAGCG
* *
53525226 ACGCTTTTATCACAAACG
65 ACACTTTTACCACAAACG
53525244 CCGCTAAAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 5 0.07
84 63 0.93
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (84 bp):
TATAGACCACAACCTTTAGCGACGCTTTTCCCACAAACGCCGCTCAAAAACACGACCTTCAGCGA
CACTTTTACCACAAACGTA
Found at i:53525276 original size:47 final size:47
Alignment explanation
Indices: 53525222--53525311 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
53525212 CATGACCTTC
* * *
53525222 AGCGACGCTT-TTATCACAAACGCCGCTAAAGAACA-AACCTTTAGCTT
1 AGCGACGCTTCTCA-CAAAAACACCGCTAAA-AACATAACCTTTAGCTT
53525269 AGCGACGCTTCTCACAAAAACACCGCTAAAAACATAACCTTTA
1 AGCGACGCTTCTCACAAAAACACCGCTAAAAACATAACCTTTA
53525312 AAAAAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 4 0.11
47 32 0.84
48 2 0.05
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (47 bp):
AGCGACGCTTCTCACAAAAACACCGCTAAAAACATAACCTTTAGCTT
Found at i:53533241 original size:13 final size:13
Alignment explanation
Indices: 53533223--53533247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53533213 TATTTTAATA
53533223 TTATTTTGTGTGT
1 TTATTTTGTGTGT
53533236 TTATTTTGTGTG
1 TTATTTTGTGTG
53533248 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:53534876 original size:41 final size:41
Alignment explanation
Indices: 53534831--53534932 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
53534821 GCTTAGCGCT
*
53534831 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
* * *
53534872 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
53534913 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
53534933 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
Found at i:53535966 original size:13 final size:13
Alignment explanation
Indices: 53535948--53535973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53535938 GCTGGAGCTT
53535948 TGTAAAATGTAAA
1 TGTAAAATGTAAA
53535961 TGTAAAATGTAAA
1 TGTAAAATGTAAA
53535974 AATTTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTAAAATGTAAA
Found at i:53538289 original size:14 final size:14
Alignment explanation
Indices: 53538246--53538302 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
53538236 ATCCTAAATT
**
53538246 AACCATATACCCTA
1 AACCATATACTATA
53538260 AACCATATACTATA
1 AACCATATACTATA
53538274 AACCATATA-TATTA
1 AACCATATACTA-TA
* *
53538288 AACCCTAAACTATA
1 AACCATATACTATA
53538302 A
1 A
53538303 TAATAATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCATATACTATA
Found at i:53538583 original size:20 final size:20
Alignment explanation
Indices: 53538546--53538584 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53538536 TCAATTAAAA
*
53538546 TAAATAAACAAATTAAATAG
1 TAAATAAACAAATAAAATAG
* *
53538566 TAAATAGACAGATAAAATA
1 TAAATAAACAAATAAAATA
53538585 TTTTTGCGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAATAAACAAATAAAATAG
Found at i:53538638 original size:41 final size:41
Alignment explanation
Indices: 53538590--53538821 Score: 297
Period size: 41 Copynumber: 5.7 Consensus size: 41
53538580 AAATATTTTT
* *
53538590 GCGGCGCTTTTTTAAAAATGCCGCTAAATCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
* *
53538631 GCAGCGCTTTTCTAAAAACGCCGCTAAAAGCT-TGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCT-AAAGCTCTGAGCATTA
* *
53538672 GCGGCTCTTTTTTAAAATCGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
* ** * **
53538713 GCGACATTTTTTTTAAAACGCCAATAAAAGCT-TGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCT-AAAGCTCTGAGCATTA
*
53538754 GCGGCGCTTTTTTAAAAACGCTGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
* *
53538795 GTGGCGCTTTTTCAAAAACGCCGCTAA
1 GCGGCGCTTTTTTAAAAACGCCGCTAA
53538822 TGTCCCAAAA
Statistics
Matches: 162, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
40 12 0.07
41 139 0.86
42 11 0.07
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:53548106 original size:21 final size:21
Alignment explanation
Indices: 53548071--53548304 Score: 107
Period size: 21 Copynumber: 11.1 Consensus size: 21
53548061 TTTACTTTTC
* *
53548071 GTTTAGCTCTCATGAGCTTCT
1 GTTTAACTCTTATGAGCTTCT
* * *
53548092 GTTTAACTCATATGAGTTTCC
1 GTTTAACTCTTATGAGCTTCT
* * *
53548113 GTTTAGCTTTTTTGAGCTTCT
1 GTTTAACTCTTATGAGCTTCT
* * *
53548134 GTTTAACCCTTATG-GGTTTT
1 GTTTAACTCTTATGAGCTTCT
* *
53548154 CGTTTAGCTCTTTTGAGCTTCT
1 -GTTTAACTCTTATGAGCTTCT
* * *
53548176 GTTTAACCCTTATG-GGTTTT
1 GTTTAACTCTTATGAGCTTCT
* * * * *
53548196 CGTTCAGCTCTTTTGAACTTTT
1 -GTTTAACTCTTATGAGCTTCT
* * *
53548218 GTTTAA-TCCTTTTG-GGTTTT
1 GTTTAACT-CTTATGAGCTTCT
* * *
53548238 CGTTTAGCTCTTATAAGCTTCC
1 -GTTTAACTCTTATGAGCTTCT
* * *
53548260 GTTTAACCCTTATGGGTTTCT
1 GTTTAACTCTTATGAGCTTCT
* * *
53548281 GTTTAGCACTTATGTGCTTCT
1 GTTTAACTCTTATGAGCTTCT
53548302 GTT
1 GTT
53548305 CAACCTTCTA
Statistics
Matches: 152, Mismatches: 53, Indels: 16
0.69 0.24 0.07
Matches are distributed among these distances:
20 13 0.09
21 127 0.84
22 12 0.08
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (21 bp):
GTTTAACTCTTATGAGCTTCT
Found at i:53548129 original size:42 final size:42
Alignment explanation
Indices: 53548066--53548309 Score: 301
Period size: 42 Copynumber: 5.8 Consensus size: 42
53548056 TTTTGTTTAC
** * * *
53548066 TTTTCGTTTAGCTCTCATGAGCTTCTGTTTAACTCATATGAG
1 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
* *
53548108 TTTCCGTTTAGCTTTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
53548150 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
* * * * *
53548192 TTTTCGTTCAGCTCTTTTGAACTTTTGTTTAATCCTTTTGGG
1 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
* * *
53548234 TTTTCGTTTAGCTCTTATAAGCTTCCGTTTAACCCTTATGGG
1 TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
* * * *
53548276 -TTTCTGTTTAGCACTTATGTGCTTCTGTTCAACC
1 TTTTC-GTTTAGCTCTTTTGAGCTTCTGTTTAACC
53548310 TTCTAGCTTT
Statistics
Matches: 174, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 4 0.02
42 170 0.98
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (42 bp):
TTTTCGTTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
Found at i:53556535 original size:29 final size:29
Alignment explanation
Indices: 53556510--53556573 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
53556500 ATGCATAGTT
53556510 TCATGTACTATGAAGAGTTCACCATACAA
1 TCATGTACTATGAAGAGTTCACCATACAA
*
53556539 TCATGTACTTTGAAGAGTTCACCATACAA
1 TCATGTACTATGAAGAGTTCACCATACAA
53556568 TC-TGTA
1 TCATGTA
53556574 ATATCCCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (29 bp):
TCATGTACTATGAAGAGTTCACCATACAA
Found at i:53562866 original size:16 final size:16
Alignment explanation
Indices: 53562845--53562899 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
53562835 CACCATATCT
53562845 CACTCTTGACAATCCA
1 CACTCTTGACAATCCA
** *
53562861 CACTCTTGACCCTCTCT
1 CACTCTTGACAATC-CA
* *
53562878 CACTCTCGACAATACA
1 CACTCTTGACAATCCA
53562894 CACTCT
1 CACTCT
53562900 CGACCCTCTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.27
Consensus pattern (16 bp):
CACTCTTGACAATCCA
Found at i:53562889 original size:33 final size:33
Alignment explanation
Indices: 53562842--53562909 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
53562832 CTACACCATA
* * *
53562842 TCTCACTCTTGACAATCCACACTCTTGACCCTC
1 TCTCACTCTCGACAATACACACTCTCGACCCTC
53562875 TCTCACTCTCGACAATACACACTCTCGACCCTC
1 TCTCACTCTCGACAATACACACTCTCGACCCTC
53562908 TC
1 TC
53562910 GTCAACCACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.44, G:0.06, T:0.28
Consensus pattern (33 bp):
TCTCACTCTCGACAATACACACTCTCGACCCTC
Found at i:53568917 original size:57 final size:57
Alignment explanation
Indices: 53568849--53568956 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
53568839 TACACTAACA
53568849 ACAATATCATTATCAATCAAGCCAACACTCAATCGACAAAACACTCGTATACTAGCT
1 ACAATATCATTATCAATCAAGCCAACACTCAATCGACAAAACACTCGTATACTAGCT
* * *
53568906 ACAATATCATTATCATTCAAGCTAACACTCAATCGACAAAATACTCGTATA
1 ACAATATCATTATCAATCAAGCCAACACTCAATCGACAAAACACTCGTATA
53568957 AAACTACCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (57 bp):
ACAATATCATTATCAATCAAGCCAACACTCAATCGACAAAACACTCGTATACTAGCT
Found at i:53582457 original size:73 final size:71
Alignment explanation
Indices: 53582317--53582459 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 71
53582307 CAGGGTTGTT
*
53582317 CTAAACCCGCTAGTTGGGTTAACTAACTTAACAACACTTCATCCCATCCCATGGTTCTACTCGTA
1 CTAAACCCGCTAGTTGGGTTAACTAACTTAACAACACTGCATCCCATCCCATGGTTCTACTCGTA
53582382 TCTTCNC
66 TCTTC-C
*
53582389 CTAAACCCGCTAGTTGGGTTAACTAACTTAACCAACACTGCATCCCATCCCATGGTTCTACTCTT
1 CTAAACCCGCTAGTTGGGTTAACTAACTTAA-CAACACTGCATCCCATCCCATGGTTCTACTCGT
53582454 ATCTTC
65 ATCTTC
53582460 GGATCTAAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 31 0.46
73 37 0.54
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.31
Consensus pattern (71 bp):
CTAAACCCGCTAGTTGGGTTAACTAACTTAACAACACTGCATCCCATCCCATGGTTCTACTCGTA
TCTTCC
Found at i:53584884 original size:33 final size:33
Alignment explanation
Indices: 53584847--53584916 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
53584837 AAAAGTGCTT
* * *
53584847 CTTCCTCATCCTCTTCTTC-CCCTTCCCCTTCTC
1 CTTCCCCATCATCTTATTCTCCC-TCCCCTTCTC
* *
53584880 CTTCCCCTTCATCTTATTCTCCCTCTCCTTCTC
1 CTTCCCCATCATCTTATTCTCCCTCCCCTTCTC
53584913 CTTC
1 CTTC
53584917 TCCTTCTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.04, C:0.51, G:0.00, T:0.44
Consensus pattern (33 bp):
CTTCCCCATCATCTTATTCTCCCTCCCCTTCTC
Found at i:53584906 original size:6 final size:6
Alignment explanation
Indices: 53584862--53584928 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
53584852 TCATCCTCTT
* * * * *
53584862 CTTCCC CTTCCC CTTCTC CTTCCC CTTCATC TTATTCTC CCTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTC-TC --CTTCTC CTTCTC CTTCTC
*
53584913 CTTCTC CTTCTA CTTC
1 CTTCTC CTTCTC CTTC
53584929 ATACCTCTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
6 44 0.88
7 1 0.02
8 2 0.04
9 3 0.06
ACGTcount: A:0.04, C:0.51, G:0.00, T:0.45
Consensus pattern (6 bp):
CTTCTC
Found at i:53590464 original size:14 final size:15
Alignment explanation
Indices: 53590432--53590465 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
53590422 ATATACAAAT
53590432 AAAAGAATTATTAGA
1 AAAAGAATTATTAGA
53590447 AAAAGAATTATTAGA
1 AAAAGAATTATTAGA
53590462 AAAA
1 AAAA
53590466 CTTAATAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
AAAAGAATTATTAGA
Found at i:53591387 original size:18 final size:18
Alignment explanation
Indices: 53591364--53591400 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53591354 ATGTTAATTA
53591364 AAGCTTCCACAAATTCAT
1 AAGCTTCCACAAATTCAT
53591382 AAGCTTCCACAAATTCAT
1 AAGCTTCCACAAATTCAT
53591400 A
1 A
53591401 CACAAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (18 bp):
AAGCTTCCACAAATTCAT
Found at i:53592730 original size:45 final size:45
Alignment explanation
Indices: 53592669--53592860 Score: 167
Period size: 45 Copynumber: 4.2 Consensus size: 45
53592659 TCAAACTTAA
** *
53592669 TATTATTTTAGTTTTATTATTAATATTGTTT-AATTTATTGTATAT
1 TATTATTTTAAATTTATCATTAATATT-TTTAAATTTATTGTATAT
* * * * * **
53592714 TATTATCTTAGATTTATCATGCATTATTATTTGTAATTTA-TCAATAT
1 TATTATTTTAAATTTATCAT-TAATATT-TTT-AAATTTATTGTATAT
* *
53592761 TATTATTTTAAATTCATCATTAACATTATTTAAATTTATCATGTATA-
1 TATTATTTTAAATTTATCATTAATATT-TTTAAATTTAT--TGTATAT
**
53592808 T-TTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATAT
1 TATTATTTTAAATTTATCATTAATATTTTTAAATTTATTGTATAT
53592852 TATTATTTT
1 TATTATTTT
53592861 GGATGTATTA
Statistics
Matches: 118, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
43 4 0.03
44 1 0.01
45 41 0.35
46 39 0.33
47 23 0.19
48 10 0.08
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (45 bp):
TATTATTTTAAATTTATCATTAATATTTTTAAATTTATTGTATAT
Found at i:53592818 original size:24 final size:25
Alignment explanation
Indices: 53592668--53592937 Score: 140
Period size: 24 Copynumber: 11.7 Consensus size: 25
53592658 TTCAAACTTA
** *
53592668 ATATTATTTTAGTTTTATTAT-TA-
1 ATATTATTTTAAATTTATCATGTAT
*
53592691 ATATT-GTTT-AATTTAT--TGTAT
1 ATATTATTTTAAATTTATCATGTAT
* * *
53592712 ATTATTATCTTAGATTTATCATGCAT
1 A-TATTATTTTAAATTTATCATGTAT
*
53592738 -TATTATTTGT-AATTTATCA-ATAT
1 ATATTATTT-TAAATTTATCATGTAT
*
53592761 -TATTATTTTAAATTCATCAT-TA-
1 ATATTATTTTAAATTTATCATGTAT
*
53592783 ACATTA-TTTAAATTTATCATGTAT
1 ATATTATTTTAAATTTATCATGTAT
53592807 AT-TTATTTTAAATTTATCAT-TA-
1 ATATTATTTTAAATTTATCATGTAT
*
53592829 ATA-T-TTTTAAATTTATCATATAT
1 ATATTATTTTAAATTTATCATGTAT
** * * *
53592852 -TATTATTTTGGATGTATTACGTA-
1 ATATTATTTTAAATTTATCATGTAT
* * *
53592875 CTATTATTTTAAAATTATCAT-CA-
1 ATATTATTTTAAATTTATCATGTAT
* *
53592898 A-AAT-TTTTAAATTTATTATGTAT
1 ATATTATTTTAAATTTATCATGTAT
**
53592921 -TATTATTTCGAATTTAT
1 ATATTATTTTAAATTTAT
53592938 TCTATATTGT
Statistics
Matches: 187, Mismatches: 36, Indels: 47
0.69 0.13 0.17
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 34 0.18
22 31 0.17
23 42 0.22
24 72 0.39
25 1 0.01
26 4 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (25 bp):
ATATTATTTTAAATTTATCATGTAT
Found at i:53592845 original size:114 final size:114
Alignment explanation
Indices: 53592725--53592937 Score: 254
Period size: 114 Copynumber: 1.9 Consensus size: 114
53592715 ATTATCTTAG
* * * * *
53592725 ATTTATCATGCATTATTA-TTTGTAATTTATCA-ATATTATTATTTT-AAATTCATCATTAACAT
1 ATTTATCATACATTATTATTTTG-AATGTATCACATACTATTATTTTAAAATT-ATCATCAAAAT
*
53592787 TATTTAAATTTATCATGTA-TATTTATTTTAAATTTATCATTAATATTTTTAA
64 T-TTTAAATTTATCATGTATTA-TTATTTCAAATTTATCATTAATATTTTTAA
* * * *
53592839 ATTTATCATATATTATTATTTTGGATGTATTACGTACTATTATTTTAAAATTATCATCAAAATTT
1 ATTTATCATACATTATTATTTTGAATGTATCACATACTATTATTTTAAAATTATCATCAAAATTT
* *
53592904 TTAAATTTATTATGTATTATTATTTCGAATTTAT
66 TTAAATTTATCATGTATTATTATTTCAAATTTAT
53592938 TCTATATTGT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
114 51 0.61
115 27 0.33
116 5 0.06
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (114 bp):
ATTTATCATACATTATTATTTTGAATGTATCACATACTATTATTTTAAAATTATCATCAAAATTT
TTAAATTTATCATGTATTATTATTTCAAATTTATCATTAATATTTTTAA
Found at i:53592882 original size:69 final size:68
Alignment explanation
Indices: 53592668--53592928 Score: 233
Period size: 69 Copynumber: 3.8 Consensus size: 68
53592658 TTCAAACTTA
** * ** *
53592668 ATATTATTTTAGTTTTATTATTAATATTGTTT-AATTTATTGTATATTATTATCTTAGATTTATC
1 ATATTATTTTAAATTTATCATTAATATT-TTTAAATTTATCATATATTATTATTTTAGATTTATC
*
53592732 ATGC
65 ATGT
* * * ** *
53592736 ATTATTATTTGT-AATTTATCAATATTATTATTTTAAATTCATCAT-TAACATTA-TTTAAATTT
1 A-TATTATTT-TAAATTTATCATTAATA-T-TTTTAAATTTATCATATATTATTATTTTAGATTT
53592798 ATCATGT
62 ATCATGT
* * *
53592805 ATATTTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATATTATTATTTTGGATGTATT
1 ATA-TTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATATTATTATTTTAGATTTATC
*
53592870 ACGT
65 ATGT
* * * * *
53592874 ACTATTATTTTAAAATTATCATCAAAATTTTTAAATTTATTATGTATTATTATTT
1 A-TATTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATATTATTATTT
53592929 CGAATTTATT
Statistics
Matches: 155, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
67 14 0.09
68 11 0.07
69 109 0.70
70 13 0.08
71 8 0.05
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (68 bp):
ATATTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATATTATTATTTTAGATTTATCA
TGT
Found at i:53592959 original size:69 final size:70
Alignment explanation
Indices: 53592808--53592959 Score: 159
Period size: 69 Copynumber: 2.2 Consensus size: 70
53592798 ATCATGTATA
* * * *
53592808 TTTATTTTAAATTTATCATTAATATTTTTAAATTTATCATATATTATTATTTTGGATGTATTACG
1 TTTA-TTTAAA-TTATCATCAAAATTTTTAAATTTATCATATATTATTATTTCGAATGTATTACG
53592873 TACTATT
64 TACTATT
* * * * *
53592880 ATT-TTAAAATTATCATCAAAATTTTTAAATTTATTATGTATTATTATTTCGAATTTATT-C-TA
1 TTTATTTAAATTATCATCAAAATTTTTAAATTTATCATATATTATTATTTCGAATGTATTACGTA
53592942 -TATT
66 CTATT
53592946 GTTTATTGTAAATT
1 -TTTATT-TAAATT
53592960 GCTCTATTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
66 4 0.06
67 4 0.06
68 3 0.05
69 48 0.73
70 5 0.08
72 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (70 bp):
TTTATTTAAATTATCATCAAAATTTTTAAATTTATCATATATTATTATTTCGAATGTATTACGTA
CTATT
Found at i:53593233 original size:13 final size:13
Alignment explanation
Indices: 53593215--53593246 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53593205 TTACATGTAA
53593215 TTTTAAAAGATTT
1 TTTTAAAAGATTT
53593228 TTTTAAAAGATTT
1 TTTTAAAAGATTT
53593241 TTTTAA
1 TTTTAA
53593247 TTCGTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
TTTTAAAAGATTT
Found at i:53602385 original size:14 final size:14
Alignment explanation
Indices: 53602366--53602397 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53602356 TAGAAGCCGC
53602366 TGGTGGATTTTCTT
1 TGGTGGATTTTCTT
53602380 TGGTGGATTTTCTT
1 TGGTGGATTTTCTT
53602394 TGGT
1 TGGT
53602398 TAAGGCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.56
Consensus pattern (14 bp):
TGGTGGATTTTCTT
Found at i:53611074 original size:14 final size:14
Alignment explanation
Indices: 53611055--53611086 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53611045 TAGAAGCCGC
53611055 TGGTGGATTTTCTT
1 TGGTGGATTTTCTT
53611069 TGGTGGATTTTCTT
1 TGGTGGATTTTCTT
53611083 TGGT
1 TGGT
53611087 TAAGGCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.56
Consensus pattern (14 bp):
TGGTGGATTTTCTT
Found at i:53619177 original size:25 final size:25
Alignment explanation
Indices: 53619143--53619211 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
53619133 TATTTTAAGT
*
53619143 GTTTTCAGTATAGT-CTATCTATAGTA
1 GTTTT-AGTATA-TACTATCTATAGCA
53619169 GTTTTAGTATATACTATCTATAGCA
1 GTTTTAGTATATACTATCTATAGCA
*
53619194 GTTTTAGGATATACTATC
1 GTTTTAGTATATACTATC
53619212 AAAGATAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.03
25 34 0.85
26 5 0.12
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (25 bp):
GTTTTAGTATATACTATCTATAGCA
Found at i:53619221 original size:25 final size:25
Alignment explanation
Indices: 53619157--53619222 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
53619147 TCAGTATAGT
* *
53619157 CTATCTATAGTAGTTTTAGTATATA
1 CTATCTAAAGTAGTTTTAGGATATA
* *
53619182 CTATCTATAGCAGTTTTAGGATATA
1 CTATCTAAAGTAGTTTTAGGATATA
53619207 CTATC-AAAGATAGTTT
1 CTATCTAAAG-TAGTTT
53619223 CAGTTTTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 3 0.08
25 33 0.92
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (25 bp):
CTATCTAAAGTAGTTTTAGGATATA
Found at i:53620943 original size:22 final size:23
Alignment explanation
Indices: 53620865--53620966 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 23
53620855 AAGTTTACAT
*
53620865 ATAAATATATAAAATAATACAT-A-
1 ATAAAT-T-TAAAATAATATATAAG
*
53620888 ATAAATTT-GAATAATA-ATACATG
1 ATAAATTTAAAATAATATATA-A-G
*
53620911 A-AAAATTAAAATAAT-TATAAG
1 ATAAATTTAAAATAATATATAAG
**
53620932 ATAAATTTAAAATAATAATATGTG
1 ATAAATTTAAAATAAT-ATATAAG
53620956 ATAAATTTAAA
1 ATAAATTTAAA
53620967 CAAAATTCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.03
20 7 0.11
21 4 0.06
22 20 0.31
23 16 0.25
24 15 0.23
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (23 bp):
ATAAATTTAAAATAATATATAAG
Found at i:53622447 original size:143 final size:143
Alignment explanation
Indices: 53622200--53623323 Score: 1451
Period size: 143 Copynumber: 7.9 Consensus size: 143
53622190 TCTACCCTAT
* * * *
53622200 TGCAACGCTAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCGCTGTAACTTTAGGGAGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* * * * *
53622265 GCTGATGGTTTCAATCTGCTCCATTACAACTTCAAGAAGATAAGATTCGACATAACTTGTAGCTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
*
53622330 TAATCTATTCCAC
131 TAATCTGTTCCAC
* * ** * *
53622343 TGCAATGCTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCATTGCAACTTTAGGGGGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* * * * *
53622408 ACTGGTGGCTTCAATCTGTTCCACTACAACCTCAGGAAGATAAGATCCGCCATAATTTGTAGCTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
53622473 TAATCTGTTCCAC
131 TAATCTGTTCCAC
* * * *
53622486 TGCAACGCCAGGAAAATAAGATTCGCTGTCTTAAGTCTGCTCCGCTGCAACTTCAGAGAGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* * * *
53622551 GCTGATGGCTTCAATCTACTCCACTGCAACTTTAGGAAGATAAGATTCGCCATAATTTGTAACTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
53622616 TAATCTGTTCCAC
131 TAATCTGTTCCAC
** * * ** *
53622629 TGCAACGCCGGGGAAATAAGAATCGCTATCTTCAGTCTGCTCTACAGCAACTTCAGGGAGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* * * * * * *
53622694 ACTGGTGGCTTCAATATACTACACTGCAACTTCATGAAGATAAG-TTCTGCCATAATTTGTAGCT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTC-GCCATAATTTGTAGCT
53622758 TTAATCTGTTCCAC
130 TTAATCTGTTCCAC
* * * * *
53622772 TACAACACTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTTAGGAAGATTAA
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGA-TAA
* * * *
53622837 -GTTGACGGCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGATTTGCCATAATTTGTAGCT
65 GGCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCT
** *
53622901 TTAATCTGTTTTAT
130 TTAATCTGTTCCAC
* * * *
53622915 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTTTGCTCTGCTGCAGCTTTAGGGAGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* * * * *
53622980 ACTGGTGGCTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATAATTTGTAGCTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
*
53623045 TAATATGTTCCAC
131 TAATCTGTTCCAC
* * * * * * *
53623058 TGTAACGCCAGGGAAATAAGATTTGCTGTATTCAGTTTGCTCCGTTGCAACTTCAGGGAGGTAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
*
53623123 GCTGATGGCTTCAATCTGTTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
*
53623188 TAATCTGTTCTAC
131 TAATCTGTTCCAC
* * * * * * *
53623201 TGTAACGTTAGGGAAATAACATTCACTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAG
1 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
* ** *
53623266 GCTGATGGCTTCAATCTACTCCACTGTAACTTCAGGAAGATAAGATTCGCTATAATTT
66 GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTT
53623324 ATAATCCATG
Statistics
Matches: 847, Mismatches: 130, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
142 6 0.01
143 836 0.99
144 5 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAG
GCTGATGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTT
TAATCTGTTCCAC
Found at i:53623699 original size:22 final size:22
Alignment explanation
Indices: 53623674--53623715 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
53623664 TTGGGACATA
53623674 AAATTTGAACCATTTTCCTCTC
1 AAATTTGAACCATTTTCCTCTC
53623696 AAATTTGAACCATTTTCCTC
1 AAATTTGAACCATTTTCCTC
53623716 CCACTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.40
Consensus pattern (22 bp):
AAATTTGAACCATTTTCCTCTC
Found at i:53626400 original size:22 final size:23
Alignment explanation
Indices: 53626360--53626422 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
53626350 GGTCTCTCCT
*
53626360 TTTTC-TTTTCATTTTTTTCTTC-
1 TTTTCATTTTCA-TTTTTTCATCA
*
53626382 TCTTTCCTTTTC-TTTTTTCATCA
1 T-TTTCATTTTCATTTTTTCATCA
53626405 TTTTCATTTTCATTTTTT
1 TTTTCATTTTCATTTTTT
53626423 GAAATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 19 0.54
23 11 0.31
24 5 0.14
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTCATTTTCATTTTTTCATCA
Found at i:53631031 original size:18 final size:18
Alignment explanation
Indices: 53631008--53631053 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
53630998 AAAACAATTT
53631008 AAGTAAAAATAATAACAA
1 AAGTAAAAATAATAACAA
* * *
53631026 AAGTAAATATAATATCAT
1 AAGTAAAAATAATAACAA
53631044 AA-TAAAAATA
1 AAGTAAAAATA
53631054 TTGAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (18 bp):
AAGTAAAAATAATAACAA
Found at i:53632949 original size:21 final size:21
Alignment explanation
Indices: 53632925--53632967 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53632915 TATATGAATG
* * *
53632925 ACGATATAAAGAATAAAACAA
1 ACGAGATAAAAAAAAAAACAA
*
53632946 ACGAGCTAAAAAAAAAAACAA
1 ACGAGATAAAAAAAAAAACAA
53632967 A
1 A
53632968 ATGAATAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.09, T:0.09
Consensus pattern (21 bp):
ACGAGATAAAAAAAAAAACAA
Found at i:53635124 original size:46 final size:46
Alignment explanation
Indices: 53635060--53635394 Score: 156
Period size: 44 Copynumber: 7.5 Consensus size: 46
53635050 TGTAGCCCGT
* * *
53635060 CTTCAATCTGCTCTACTGCAACTTTAGAGAGATAAGATTGATTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGATTTAG
* * * * * *
53635106 CTGT-AGTCTGCTCCACTGCAACTTCAGGGGGATAAAATT-A-GTGG
1 CT-TCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGATTTAG
*
53635150 CTTCAATCTGATCCACTGCAACTTCAGAGAGATAAGATTGA--T--
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGATTTAG
*
53635192 -TT-AACCTGCTCCACTGCAACTTCA-AGGAGATAAG---G-TTT-G
1 CTTCAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATTGATTTAG
* * * * * *
53635231 ATAT-AATTTTCTCTACTGCAACTTTAGATAGATAAGATATGTTATTTATAG
1 CT-TCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TG--A-TT-TAG
* * * * * * * *
53635282 TTTCAATCTGTTCCATTGCAAGTTCAGGGAAATAAGATT--TGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGAT-TTAG
* * * *
53635327 CTCCAATCTGCTCCATTGCAACTTCAGGGAGATAAGACTTG---TAA
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGATTTAG
53635371 CTTCAA-CTTGCTCCACTGCAACTT
1 CTTCAATC-TGCTCCACTGCAACTT
53635395 TAGGGAAATA
Statistics
Matches: 221, Mismatches: 43, Indels: 52
0.70 0.14 0.16
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 1 0.00
40 29 0.13
41 27 0.12
42 1 0.00
43 2 0.01
44 56 0.25
45 38 0.17
46 33 0.15
47 1 0.00
49 2 0.01
50 3 0.01
51 26 0.12
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGATTTAG
Found at i:53635249 original size:41 final size:40
Alignment explanation
Indices: 53635161--53635268 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 40
53635151 TTCAATCTGA
*
53635161 TCCACTGCAACTTCAGAGAGATAAGATTGATTTAACCTGC
1 TCCACTGCAACTTCAGAGAGATAAGATTGATATAACCTGC
* ** *
53635201 TCCACTGCAACTTCA-AGGAGATAAGGTTTGATATAATTTTC
1 TCCACTGCAACTTCAGA-GAGATAA-GATTGATATAACCTGC
* * *
53635242 TCTACTGCAACTTTAGATAGATAAGAT
1 TCCACTGCAACTTCAGAGAGATAAGAT
53635269 ATGTTATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.02
40 24 0.43
41 30 0.54
42 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (40 bp):
TCCACTGCAACTTCAGAGAGATAAGATTGATATAACCTGC
Found at i:53635353 original size:45 final size:45
Alignment explanation
Indices: 53635285--53635415 Score: 158
Period size: 45 Copynumber: 2.9 Consensus size: 45
53635275 TTTATAGTTT
* *
53635285 CAATCTGTTCCATTGCAAGTTCAGGGAAATAAGATTTGCTATCTC
1 CAATCTGCTCCATTGCAACTTCAGGGAAATAAGATTTGCTATCTC
* * * *
53635330 CAATCTGCTCCATTGCAACTTCAGGGAGATAAGACTTG-TAACTT
1 CAATCTGCTCCATTGCAACTTCAGGGAAATAAGATTTGCTATCTC
* * *
53635374 CAA-CTTGCTCCACTGCAACTTTAGGGAAATAAGGTTTGCTAT
1 CAATC-TGCTCCATTGCAACTTCAGGGAAATAAGATTTGCTAT
53635416 ACAACTTTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
43 1 0.01
44 35 0.49
45 36 0.50
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (45 bp):
CAATCTGCTCCATTGCAACTTCAGGGAAATAAGATTTGCTATCTC
Found at i:53636378 original size:10 final size:9
Alignment explanation
Indices: 53636332--53636381 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
53636322 TGGCCTCTCA
53636332 TTTTTCTTT
1 TTTTTCTTT
**
53636341 TTCGTCTTT
1 TTTTTCTTT
*
53636350 TATTTT-TCT
1 T-TTTTCTTT
53636359 TTTTTCTTT
1 TTTTTCTTT
53636368 TTTTTCTTT
1 TTTTTCTTT
53636377 TTTTT
1 TTTTT
53636382 AAAGCATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 4 0.12
9 27 0.82
10 2 0.06
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:53639516 original size:24 final size:25
Alignment explanation
Indices: 53639489--53639541 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
53639479 GGATCTTTTG
* * *
53639489 TGAAATTTAATGCACATG-ATGCAA
1 TGAAATGTAATGCAAATGAATGAAA
53639513 TGAAATGTAATGCAAATGAATGAAA
1 TGAAATGTAATGCAAATGAATGAAA
53639538 TGAA
1 TGAA
53639542 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGAAA
Found at i:53640410 original size:30 final size:30
Alignment explanation
Indices: 53640349--53640426 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
53640339 CCTATGCCTT
* *
53640349 ATACAGTAGCAGTGTGT-GGCCATAGCCCA
1 ATACAGTAACAGAGTGTGGGCCATAGCCCA
53640378 ATACAGTAACAGAGTGTGGGCC-TAGCCCCA
1 ATACAGTAACAGAGTGTGGGCCATAG-CCCA
*
53640408 ATATAGTAACAGAGTGTGG
1 ATACAGTAACAGAGTGTGG
53640427 TGCAAGTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.41
30 26 0.59
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (30 bp):
ATACAGTAACAGAGTGTGGGCCATAGCCCA
Found at i:53640514 original size:30 final size:30
Alignment explanation
Indices: 53640474--53640589 Score: 178
Period size: 30 Copynumber: 3.9 Consensus size: 30
53640464 CCACTCGTAC
* * *
53640474 TAGCCTAATACAATAACAGAGTGTGGGCTT
1 TAGCCCAATACAGTAACAGAGTGTGGGCCT
*
53640504 TAGCCCAATACAGTAATAGAGTGTGGGCCT
1 TAGCCCAATACAGTAACAGAGTGTGGGCCT
*
53640534 TAACCCAATACAGTAACAGAGTGTGGGCCT
1 TAGCCCAATACAGTAACAGAGTGTGGGCCT
*
53640564 TAGCCCAATATAGTAACAGAGTGTGG
1 TAGCCCAATACAGTAACAGAGTGTGG
53640590 TGCAAGTAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (30 bp):
TAGCCCAATACAGTAACAGAGTGTGGGCCT
Found at i:53641109 original size:24 final size:24
Alignment explanation
Indices: 53641038--53641124 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
53641028 TCAGTTATAC
* *
53641038 AAATCATAGACAAATTAGTCATACT
1 AAATCACAGACAAATTAGTCAT-TT
* * **
53641063 -AATCACATACAAATCAACCATTT
1 AAATCACAGACAAATTAGTCATTT
*
53641086 AAATCACAGACAAATTAGTTATTT
1 AAATCACAGACAAATTAGTCATTT
*
53641110 ACATCAC-GAACAAAT
1 AAATCACAG-ACAAAT
53641125 CAATTGTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
23 2 0.04
24 46 0.96
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (24 bp):
AAATCACAGACAAATTAGTCATTT
Found at i:53641201 original size:27 final size:25
Alignment explanation
Indices: 53641170--53641270 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 25
53641160 TACCCTTTGA
*
53641170 GGGTATATCGGTCAGTTTACCTAACAG
1 GGGTATAT-GGTCATTTTACCT-ACAG
* * *
53641197 AGGTATTATAGTCATTTTGCCTACAG
1 GGGTA-TATGGTCATTTTACCTACAG
*
53641223 GGGCATCATGGTCATTTTACCTTACAG
1 GGGTAT-ATGGTCATTTTACC-TACAG
*
53641250 GGGTATTTCGGTCATTTTACC
1 GGGTATAT-GGTCATTTTACC
53641271 CTATAGAGGC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 20 0.33
27 36 0.60
28 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (25 bp):
GGGTATATGGTCATTTTACCTACAG
Found at i:53641324 original size:27 final size:27
Alignment explanation
Indices: 53641294--53641351 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
53641284 ATGATCATTA
53641294 TACCCCACAGGGGCATTACAATTATTT
1 TACCCCACAGGGGCATTACAATTATTT
** *
53641321 TACCTTACAGGGGCATTACGATTATTT
1 TACCCCACAGGGGCATTACAATTATTT
53641348 TACC
1 TACC
53641352 AATATTAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (27 bp):
TACCCCACAGGGGCATTACAATTATTT
Found at i:53642704 original size:43 final size:43
Alignment explanation
Indices: 53642632--53642922 Score: 392
Period size: 43 Copynumber: 6.8 Consensus size: 43
53642622 ATTTTTTTAA
*
53642632 AAAAGCGGCGCTAAA-GTCAGGGTCTTTAGCGGCGTTTGAGAG
1 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAG
53642674 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGTAGA-
1 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTG-AGAG
* * * *
53642717 AAAAGCACCCCTAAAGGTCAGGGTCTTTAGCAGTGTTTGTAG-G
1 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTG-AGAG
* *
53642760 AAAAGCGCTGCTAAAGGTCAGGGTCTTTAGTGGCGTTTGAGAG
1 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAG
* * *
53642803 AAAAGCGCCGCTAAAGGTTAGGGTCTTTAGCGGCATTTGTGAG
1 AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAG
* *
53642846 AAAAAGCGCCGCTAAAGGTCAGGGTCTTTAACGGCGTTTGTG-G
1 -AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAG
* *
53642889 AAAAAGCGCTGCTAAAGGTCAGCGTCTTTAGCGG
1 -AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGG
53642923 AATTTTTTGC
Statistics
Matches: 222, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
42 16 0.07
43 165 0.74
44 41 0.18
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAG
Found at i:53642891 original size:129 final size:130
Alignment explanation
Indices: 53642631--53642922 Score: 457
Period size: 130 Copynumber: 2.3 Consensus size: 130
53642621 CATTTTTTTA
53642631 AAAAAGCGGC-GCTAAA-GTCAGGGTCTTTAGCGGCGTTTGAGAGAAAAGCGCCGCTAAAGGTCA
1 AAAAAGC-GCTGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAGAAAAGCGCCGCTAAAGGTCA
* * *
53642694 GGGTCTTTAGCGGCGTTTGTAGAAAAAGCACCCCTAAAGGTCAGGGTCTTTAGCAGTGTTTGTAG
65 GGGTCTTTAGCGGCATTTGTAGAAAAAGCACCCCTAAAGGTCAGGGTCTTTAACAGCGTTTGTAG
53642759 G
130 G
* *
53642760 -AAAAGCGCTGCTAAAGGTCAGGGTCTTTAGTGGCGTTTGAGAGAAAAGCGCCGCTAAAGGTTAG
1 AAAAAGCGCTGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAGAAAAGCGCCGCTAAAGGTCAG
* * *
53642824 GGTCTTTAGCGGCATTTGTGAGAAAAAGCGCCGCTAAAGGTCAGGGTCTTTAACGGCGTTTGT-G
66 GGTCTTTAGCGGCATTTGT-AGAAAAAGCACCCCTAAAGGTCAGGGTCTTTAACAGCGTTTGTAG
53642888 G
130 G
*
53642889 AAAAAGCGCTGCTAAAGGTCAGCGTCTTTAGCGG
1 AAAAAGCGCTGCTAAAGGTCAGGGTCTTTAGCGG
53642923 AATTTTTTGC
Statistics
Matches: 149, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
127 2 0.01
128 12 0.08
129 66 0.44
130 69 0.46
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (130 bp):
AAAAAGCGCTGCTAAAGGTCAGGGTCTTTAGCGGCGTTTGAGAGAAAAGCGCCGCTAAAGGTCAG
GGTCTTTAGCGGCATTTGTAGAAAAAGCACCCCTAAAGGTCAGGGTCTTTAACAGCGTTTGTAGG
Found at i:53649566 original size:33 final size:33
Alignment explanation
Indices: 53649515--53649702 Score: 132
Period size: 27 Copynumber: 5.8 Consensus size: 33
53649505 ATTATCCGTT
*
53649515 ATCGGTGGATTCAGCACTTAGCAACCACCAATGA
1 ATCGG-GGAATCAGCACTTAGCAACCACCAATGA
*
53649549 ATCGGGGAAACAGCACTTAGCAACC-CC--T--
1 ATCGGGGAATCAGCACTTAGCAACCACCAATGA
* *
53649577 -T-GGGAGAATCAGCACTTAGCAACCCCCTTCACACTTAAA
1 ATCGGG-GAATCAGCACTTAGCAA-CCAC--CA-A--T-GA
*
53649616 ATACGGTGGAATCAGCACTTAGGAACCACCAATGA
1 AT-CGG-GGAATCAGCACTTAGCAACCACCAATGA
53649651 ATCGGGGAATCAGCACTTAGCAACC-CC--T--
1 ATCGGGGAATCAGCACTTAGCAACCACCAATGA
*
53649679 -TGGGGGAATCAGCACTTAGCAACC
1 ATCGGGGAATCAGCACTTAGCAACC
53649703 CCCTTTTTAT
Statistics
Matches: 129, Mismatches: 8, Indels: 41
0.72 0.04 0.23
Matches are distributed among these distances:
26 3 0.02
27 40 0.31
28 2 0.02
29 1 0.01
30 2 0.02
31 1 0.01
32 4 0.03
33 37 0.29
34 8 0.06
35 3 0.02
36 2 0.02
38 1 0.01
39 2 0.02
40 1 0.01
41 3 0.02
42 18 0.14
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.18
Consensus pattern (33 bp):
ATCGGGGAATCAGCACTTAGCAACCACCAATGA
Found at i:53649693 original size:102 final size:102
Alignment explanation
Indices: 53649517--53649707 Score: 346
Period size: 102 Copynumber: 1.9 Consensus size: 102
53649507 TATCCGTTAT
*
53649517 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAAACAGCACTTAGCAACCCCTTGGGA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAAACAGCACTTAGCAACCCCTTGGGA
53649582 GAATCAGCACTTAGCAACCCCCTTCACACTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTCACACTTAAAATA
* * *
53649619 CGGTGGAATCAGCACTTAGGAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAAACAGCACTTAGCAACCCCTTGGGA
53649684 GAATCAGCACTTAGCAACCCCCTT
66 GAATCAGCACTTAGCAACCCCCTT
53649708 TTTATTCAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.18
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAAACAGCACTTAGCAACCCCTTGGGA
GAATCAGCACTTAGCAACCCCCTTCACACTTAAAATA
Found at i:53656976 original size:33 final size:32
Alignment explanation
Indices: 53656934--53657284 Score: 110
Period size: 33 Copynumber: 10.4 Consensus size: 32
53656924 GTGGATTCAT
53656934 CACTTAGCAACCACCAGTGATTCGGGGAATCAG
1 CACTTAGCAACCACCA-TGATTCGGGGAATCAG
* *
53656967 CACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAG
1 CACTTAGCAA--CC--AC-CA--T--GATTCGG-GGAATCAG
* *
53657009 CACTTAGCAACCACCAATGAATCAGGGAATCAG
1 CACTTAGCAACCACC-ATGATTCGGGGAATCAG
*
53657042 CACTTAGCAACC-CC----TTGGGGGAATCAG
1 CACTTAGCAACCACCATGATTCGGGGAATCAG
** *
53657069 CACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATC-G
1 CACTTAGCAA---C---CAC-C--ATGATTCGG-GGAATCAG
53657110 ACACTTAGCAACCACCAATGAATT-GGGGAATCAG
1 -CACTTAGCAACCACC-ATG-ATTCGGGGAATCAG
*
53657144 CACTTAGCAACC-CC----TTGGGGGAATCAG
1 CACTTAGCAACCACCATGATTCGGGGAATCAG
** *
53657171 CACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATC-G
1 CACTTAGCAA---C---CAC-C--ATGATTCGG-GGAATCAG
53657212 ACACTTAGCAACCACCAATGAATT-GGGGAATCAG
1 -CACTTAGCAACCACC-ATG-ATTCGGGGAATCAG
*
53657246 CACTTAGCAACC-CC----TTGGGGGAATCAG
1 CACTTAGCAACCACCATGATTCGGGGAATCAG
53657273 CACTTAGCAACC
1 CACTTAGCAACC
53657285 CCCTTTTTGT
Statistics
Matches: 248, Mismatches: 22, Indels: 102
0.67 0.06 0.27
Matches are distributed among these distances:
26 4 0.02
27 62 0.25
30 2 0.01
32 6 0.02
33 68 0.27
34 14 0.06
35 10 0.04
36 7 0.03
37 2 0.01
38 4 0.02
39 3 0.01
40 2 0.01
41 14 0.06
42 50 0.20
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (32 bp):
CACTTAGCAACCACCATGATTCGGGGAATCAG
Found at i:53657063 original size:27 final size:27
Alignment explanation
Indices: 53657033--53657084 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
53657023 CAATGAATCA
53657033 GGGAATCAGCACTTAGCAACCCCTTGG
1 GGGAATCAGCACTTAGCAACCCCTTGG
53657060 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAGCACTTAGCAACCCCTT
53657085 TCACACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (27 bp):
GGGAATCAGCACTTAGCAACCCCTTGG
Found at i:53657075 original size:102 final size:102
Alignment explanation
Indices: 53656957--53657286 Score: 608
Period size: 102 Copynumber: 3.2 Consensus size: 102
53656947 CCAGTGATTC
* *
53656957 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATC-AGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGA-CACTTAGCAACC
**
53657021 ACCAATGAATCAGGGAATCAGCACTTAGCAACCCCTTG
65 ACCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
53657059 GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGACACTTAGCAACCA
53657124 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
53657161 GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGACACTTAGCAACCA
53657226 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
53657263 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
53657287 CTTTTTGTTC
Statistics
Matches: 223, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
102 222 1.00
103 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCACACTTAAAATACGGTGGAATCGACACTTAGCAACCA
CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:53657170 original size:27 final size:27
Alignment explanation
Indices: 53657134--53657186 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
53657124 CCAATGAATT
53657134 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
53657161 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
53657187 TCACACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:53662218 original size:41 final size:41
Alignment explanation
Indices: 53662161--53662268 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
53662151 TTAACATATT
*
53662161 CACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-AG
1 CACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT-CAGAG
* *
53662202 CACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGAT
1 CACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGAG
*
53662243 CACCGGCACTTAGCCTGCTAGACTTA
1 CACCGGCACTTAGCCTGCTAGGCTTA
53662269 AAGTCTGAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 2 0.03
41 59 0.97
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (41 bp):
CACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGAG
Found at i:53662303 original size:82 final size:81
Alignment explanation
Indices: 53662160--53662317 Score: 196
Period size: 82 Copynumber: 1.9 Consensus size: 81
53662150 TTTAACATAT
* *
53662160 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAAGCACCGGCACTTAGCCTGCTAGG-
1 TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATT-CAAGCACCGGCACTTAGCCTGCTAGGT
53662224 TTTATAACCTGATTCAGA
65 TTTA-AACCTGATTCAGA
* ** *
53662242 TCACCGGCACTTAGCCTGCTAGACTTAAAGTCTGAATT-ATTTCACCGGC-CTTAAGCTTGCTAG
1 TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTG-ATTCA-AGCACCGGCACTT-AGCCTGCTAG
53662305 GTTTTAAACCTGA
63 GTTTTAAACCTGA
53662318 AAATTTCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
81 4 0.06
82 55 0.83
83 7 0.11
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (81 bp):
TCACCGGCACTTAGCCTGCTAGACTTAAAGCCTGATTCAAGCACCGGCACTTAGCCTGCTAGGTT
TTAAACCTGATTCAGA
Found at i:53668726 original size:92 final size:90
Alignment explanation
Indices: 53668591--53668757 Score: 248
Period size: 92 Copynumber: 1.8 Consensus size: 90
53668581 CCGGCACCAC
* *
53668591 CTTTATTGGAATTTTTTTTACTTTTTTTGTGTCAATGGTAGGCACCAATATAC-AAAAATCAA-A
1 CTTTATTGGAATTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAATATACGAAAAA--AATA
53668654 AAAAAAATTTGGTGGTGGCTGGCATTT
64 AAAAAAATTTGGTGGTGGCTGGCATTT
* *
53668681 CTTTATTGGAATTTTTTTTTTACTTTTTTCGTTTCAATTGCAGGCACCAATATACGAAAAAAATA
1 CTTTATTGGAA--TTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAATATACGAAAAAAATA
53668746 AAAAAAATTTGG
64 AAAAAAATTTGG
53668758 AAAAAGATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
90 11 0.16
91 2 0.03
92 51 0.74
93 5 0.07
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (90 bp):
CTTTATTGGAATTTTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAATATACGAAAAAAATAAA
AAAAATTTGGTGGTGGCTGGCATTT
Found at i:53669124 original size:112 final size:112
Alignment explanation
Indices: 53668910--53669128 Score: 323
Period size: 112 Copynumber: 1.9 Consensus size: 112
53668900 TTTTTCAATT
* * * *
53668910 TTTTTTTACTTTTTTCGTATACTGGTGCCTGCCATTGACACGAAAAAAGTTAAAAAAAATTCCAA
1 TTTTTCTACTTCTTTCGTATACTGGTGCCTGCCATTGACACCAAAAAAGTAAAAAAAAATTCCAA
* *
53668975 TAAAGGTGGTGCCGGCAATTGGCAAGGCACCACCCAAAAAATATATA
66 TAAAGGTGGTGCCAGCAACTGGCAAGGCACCACCCAAAAAATATATA
*
53669022 TTTTTCTACTTCTTTCGTATACTGGTGCTTGCCATTGACACCAAAAAAGTAAAAAAAAAATTCCA
1 TTTTTCTACTTCTTTCGTATACTGGTGCCTGCCATTGACACCAAAAAAGT-AAAAAAAAATTCCA
* * *
53669087 ATAAAGGTGGTGTCAGCCACTGGC-AGGCCACCACCAAAAAAA
65 ATAAAGGTGGTGCCAGCAACTGGCAAGG-CACCACCCAAAAAA
53669129 AAGAATTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 49 0.52
113 46 0.48
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (112 bp):
TTTTTCTACTTCTTTCGTATACTGGTGCCTGCCATTGACACCAAAAAAGTAAAAAAAAATTCCAA
TAAAGGTGGTGCCAGCAACTGGCAAGGCACCACCCAAAAAATATATA
Found at i:53671215 original size:102 final size:102
Alignment explanation
Indices: 53671100--53671304 Score: 320
Period size: 102 Copynumber: 2.0 Consensus size: 102
53671090 TATATTTCTT
* * *
53671100 TTTGGTGTTGGCCTGCCAATGGCCGGCACCACCTTTATTGGAATTTTTTTTACTTTTTTCGTGTT
1 TTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATTGGAATTTTTTTTACTTTTTTCGTGTC
*
53671165 AATGGCAAGAACCAGTATACGAAAAAAACAAAAAAAA
66 AATGGCAAGAACCAGTATACAAAAAAAACAAAAAAAA
*
53671202 TTTGGTGGTGGCCTGCCAATGGTCGACACCACCTTTATTGGAATTTTTTTTACTTTTTTCGTGTC
1 TTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATTGGAATTTTTTTTACTTTTTTCGTGTC
* * * **
53671267 AATGGCAGGCACTAGTATACAAAAAAAAGTAAAAAAA
66 AATGGCAAGAACCAGTATACAAAAAAAACAAAAAAAA
53671304 T
1 T
53671305 GAGAAAAAGG
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (102 bp):
TTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATTGGAATTTTTTTTACTTTTTTCGTGTC
AATGGCAAGAACCAGTATACAAAAAAAACAAAAAAAA
Found at i:53676042 original size:22 final size:21
Alignment explanation
Indices: 53676017--53676057 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
53676007 AAAATGGTGA
53676017 AAAAAGAAAAGGAAAGAGAAGG
1 AAAAAGAAAAGGAAA-AGAAGG
53676039 AAAAAGAAAAGGAAAAGAA
1 AAAAAGAAAAGGAAAAGAA
53676058 AAAGGAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAGGAAAAGAAGG
Found at i:53676063 original size:12 final size:11
Alignment explanation
Indices: 53676018--53676059 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
53676008 AAATGGTGAA
53676018 AAAAGAAAAGG
1 AAAAGAAAAGG
*
53676029 -AAAGAGAAGG
1 AAAAGAAAAGG
53676039 AAAAAGAAAAGG
1 -AAAAGAAAAGG
53676051 AAAAGAAAA
1 AAAAGAAAA
53676060 AGGAGAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:53677099 original size:45 final size:43
Alignment explanation
Indices: 53677025--53677109 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 43
53677015 AGAAGGGACC
*
53677025 AAGGTGAAAACCCGCAAAGGGCACCTTGAGTCCTTAAAAAAAACT
1 AAGGTAAAAACCCGCAAAGGGCACCTTGAGT--TTAAAAAAAACT
** *
53677070 AAGGTAAAAACCCGCAAAGGGTGCTTTGAGTTTAAAAAAA
1 AAGGTAAAAACCCGCAAAGGGCACCTTGAGTTTAAAAAAA
53677110 TAAATGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 9 0.25
45 27 0.75
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (43 bp):
AAGGTAAAAACCCGCAAAGGGCACCTTGAGTTTAAAAAAAACT
Found at i:53679798 original size:285 final size:285
Alignment explanation
Indices: 53679184--53679972 Score: 1044
Period size: 285 Copynumber: 2.8 Consensus size: 285
53679174 GCTGTATTAT
* * * * *
53679184 AAATTATGGCGAATCTTATCTTCCTAAATTTACAGTGGAGTAGATTGATGCCATCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTGAA-TTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT
* * * * * * * * *
53679249 CCCTGAAGTTACAGTGGAACAGACTGAATATAGCGAATCTTATTTCCTTAGCGTTGTAGTGGAAT
65 CCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAAC
* * *
53679314 AGATTAAAGCTACAAATTATGGCGAATCTTATCTTCTTAAAGTTGTAGTGGAACAGATTGAAGCC
130 AGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCC
* * * * *
53679379 ATCAGCCTTATCTCCCTGAAGTTACAGCGGAGCAAACTAAAGACATCGAATCTTATTTCCTTGGT
195 GTCAGCCTTATCTCCCTGAAGTTACAGCAGAGCAAACTAAAGACAGCGAATCTTATTTCCTTAGC
*
53679444 GTTGTAGTGGAACAGATTAAAGCAAC
260 ATTGTAGTGGAACAGATTAAAGCAAC
* * * *
53679470 AAATTATGGCAAATCTTATCTTCCTGGCATTGCAGTGGAGCAGATTAAAACCACCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCT-GAATTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT
* * * *
53679535 CCCTGAAGATGTAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAAC
65 CCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAAC
* * * * * * *
53679600 AAATTAAAACTACAAATTATGGCAAATCTTATCTTCCTAAAGTTGCGGTGGAGTAGATTGAATCT
130 AGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCC
* * * *
53679665 GTCAG-CTTATTTCCCTGAAGTTACAGCAGAGCAGACTGAAGACAGCGAATCTTCTTTTCC-TAG
195 GTCAGCCTTATCTCCCTGAAGTTACAGCAGAGCAAACTAAAGACAGCGAATCTT-ATTTCCTTAG
*
53679728 CATTGTAGTGGAACAGATTAAAGCTAC
259 CATTGTAGTGGAACAGATTAAAGCAAC
* * *
53679755 AAATTATGGTGGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTGAA-TTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT
* *
53679820 CCCTAAAGTTGCAGCGGAGCAGACTTAAGACAGC-AATTCTTATTTCCCTGGCGTTGCAGTGGAA
65 CCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAA-TCTTATTTCCCTGGCGTTGCAGTGGAA
* * *
53679884 CAGATTAAAGTTACAAATAATGGCGAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGC
129 CAGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGC
*
53679949 CGTCAGCCTTATCTCTCTGAAGTT
194 CGTCAGCCTTATCTCCCTGAAGTT
53679973 GCAATGGAAC
Statistics
Matches: 430, Mismatches: 68, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
284 4 0.01
285 240 0.56
286 185 0.43
287 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (285 bp):
AAATTATGGCGAATCTTATCTTCCTGAATTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
GATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCG
TCAGCCTTATCTCCCTGAAGTTACAGCAGAGCAAACTAAAGACAGCGAATCTTATTTCCTTAGCA
TTGTAGTGGAACAGATTAAAGCAAC
Found at i:53679975 original size:143 final size:143
Alignment explanation
Indices: 53679184--53679972 Score: 999
Period size: 143 Copynumber: 5.5 Consensus size: 143
53679174 GCTGTATTAT
* * * *
53679184 AAATTATGGCGAATCTTATCTTCCTAAATTTACAGTGGAGTAGATTGATGCCATCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
* * * * * * *
53679249 CCCTGAAGTTACAGTGGAACAGACTGAATATAGCGAATCTTATTTCCTTAGCGTTGTAGTGGAAT
66 CCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAAC
53679314 AGATTAAAGCTAC
131 AGATTAAAGCTAC
* * *
53679327 AAATTATGGCGAATCTTATCTTCTTAAAGTTGTAGTGGAACAGATTGAAGCCATCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
* * * * *
53679392 CCCTGAAGTTACAGCGGAGCAAACTAAAGACATCGAATCTTATTTCCTTGGTGTTGTAGTGGAAC
66 CCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAAC
*
53679457 AGATTAAAGCAAC
131 AGATTAAAGCTAC
* ** * * *
53679470 AAATTATGGCAAATCTTATCTTCCTGGCA-TTGCAGTGGAGCAGATTAAAACCACCAGCCTTATC
1 AAATTATGGCGAATCTTATCTTCCT-AAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATC
* ** * * *
53679534 TCCCTGAAGATGTAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAA
65 TCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAA
* *
53679599 CAAATTAAAACTAC
130 CAGATTAAAGCTAC
* * * * ** *
53679613 AAATTATGGCAAATCTTATCTTCCTAAAGTTGCGGTGGAGTAGATTGAATCTGTCAG-CTTATTT
1 AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
* * * * *
53679677 CCCTGAAGTTACAGCAGAGCAGACTGAAGACAGCGAATCTTCTTTTCCTAGCATTGTAGTGGAAC
66 CCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAAC
53679742 AGATTAAAGCTAC
131 AGATTAAAGCTAC
* * * * *
53679755 AAATTATGGTGGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
* * * *
53679820 CCCTAAAGTTGCAGCGGAGCAGACTTAAGACAGC-AATTCTTATTTCCCTGGCGTTGCAGTGGAA
66 CCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAA-TCTTATTTCCCTGGCGTTGTAGTGGAA
*
53679884 CAGATTAAAGTTAC
130 CAGATTAAAGCTAC
* * *
53679898 AAATAATGGCGAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
*
53679963 CTCTGAAGTT
66 CCCTGAAGTT
53679973 GCAATGGAAC
Statistics
Matches: 547, Mismatches: 95, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
142 120 0.22
143 426 0.78
144 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (143 bp):
AAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCT
CCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGTAGTGGAAC
AGATTAAAGCTAC
Found at i:53679989 original size:98 final size:98
Alignment explanation
Indices: 53679872--53680067 Score: 270
Period size: 98 Copynumber: 2.0 Consensus size: 98
53679862 TTTCCCTGGC
* * *
53679872 GTTGCAGTGGAACAGATTAAAGTTACAAATAATGGCGAATCTTATCTTCCTAAAGTTACAGTGGA
1 GTTGCAATGGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGA
*
53679937 GCAGATTGAAG-C-CGTCAGCCTTATCTCTCTGAA
66 ACAGATTGAAGTCAC-T-AGCCTTATCTCTCTGAA
* * * * **
53679970 GTTGCAATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAGGTTGTAGTGGA
1 GTTGCAATGGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGA
53680035 ACAGATTGAAGTCACTAGCCTTATCTCTCTGAA
66 ACAGATTGAAGTCACTAGCCTTATCTCTCTGAA
53680068 ATTACAGCGG
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 83 0.97
99 2 0.02
100 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (98 bp):
GTTGCAATGGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGA
ACAGATTGAAGTCACTAGCCTTATCTCTCTGAA
Found at i:53680012 original size:241 final size:241
Alignment explanation
Indices: 53679736--53680187 Score: 676
Period size: 241 Copynumber: 1.9 Consensus size: 241
53679726 AGCATTGTAG
* * *
53679736 TGGAACAGATTAAAGCTACAAATTATGGTGGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATT
1 TGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAAGTTGCAGTAGAACAGATT
* *
53679801 GAAGCCACCAGCCTTATCTCCCT-AAAGTTGCAGCGGAGCAGACTTAAGACAGC-AATTCTTATT
66 GAAGCCACCAGCCTTATCTCCCTGAAA-TTACAGCGGAGCAGACTAAAGACAGCGAA-TCTTATT
* * *
53679864 TCC-CTGGCGTTGCAGTGGAACAGATTAAAGTTACAAATAATGGCGAATCTTATCTTCCTAAAGT
129 TCCAC-GGCATTGCAGTGGAACAAATTAAAGCTACAAATAATGGCGAATCTTATCTTCCTAAAGT
53679928 TACAGTGGAGCAGATTGAAGCCGTCAGCCTTATCTCTCTGAAGTTGCAA
193 TACAGTGGAGCAGATTGAAGCCGTCAGCCTTATCTCTCTGAAGTTGCAA
* * *
53679977 TGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAGGTTGTAGTGGAACAGATT
1 TGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAAGTTGCAGTAGAACAGATT
* * *
53680042 GAAGTCACTAGCCTTATCTCTCTGAAATTACAGCGGAGCAGACTAAAGACAGCGAATCTTATTTC
66 GAAGCCACCAGCCTTATCTCCCTGAAATTACAGCGGAGCAGACTAAAGACAGCGAATCTTATTTC
* * * * * *
53680107 CACGGCATTGCAGTGGAATAAATTAAAGCTACAAGTTATGGCGAATCTTATCTTCTTGAAGTTGC
131 CACGGCATTGCAGTGGAACAAATTAAAGCTACAAATAATGGCGAATCTTATCTTCCTAAAGTTAC
53680172 AGTGGAGCAGATTGAA
196 AGTGGAGCAGATTGAA
53680188 ACCTGTCATA
Statistics
Matches: 188, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
241 182 0.97
242 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (241 bp):
TGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAAGTTGCAGTAGAACAGATT
GAAGCCACCAGCCTTATCTCCCTGAAATTACAGCGGAGCAGACTAAAGACAGCGAATCTTATTTC
CACGGCATTGCAGTGGAACAAATTAAAGCTACAAATAATGGCGAATCTTATCTTCCTAAAGTTAC
AGTGGAGCAGATTGAAGCCGTCAGCCTTATCTCTCTGAAGTTGCAA
Found at i:53680083 original size:285 final size:280
Alignment explanation
Indices: 53679198--53680088 Score: 722
Period size: 285 Copynumber: 3.1 Consensus size: 280
53679188 TATGGCGAAT
* * * ** * * * *
53679198 CTTATCTTCCT-AAATTTACAGTGGAGTAGATTGATGCCATCAGCCTTATCTCCCTGAAGTTACA
1 CTTATCTTCCTGAAA-TTACAGCGGAGCAGATTAAAACCACCAGCCTTATCTCCCTAAAGATGCA
* * * * * * * * * * * *
53679262 GTGGAACAGACTGAATATAGCGAATCTTATTTCCTTAGCGTTGTAGTGGAATAGATTAAAGCTAC
65 GCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAACAAATTAAAACTAC
* * * ** * *
53679327 AAATTATGGCGAATCTTATCTTCTTAAAGTTGTAGTGGAACAGATTGAAGCCATCAGCCTTATCT
130 AAATAATGGCAAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAG-CTTATCT
* * * * * * * **
53679392 CCCTGAAGTTACAGCGGAGCAAACTAAAGACATCGAATCTTAT-TTCCTTGGTGTTGTAGTGGAA
194 CCCTGAAGTTACAACAGAACAGACTAAAGACAGCGAATCTTATCATCC-TAGCATTGTAGTGGAA
* * *
53679456 CAGATTAAAGCAACAAATTATGGCAAAT
258 CAGATTAAAGCTAC-AACTA-GG---AC
** * * * *
53679484 CTTATCTTCCTGGCATTGCAGTGGAGCAGATTAAAACCACCAGCCTTATCTCCCTGAAGATGTAG
1 CTTATCTTCCTGAAATTACAGCGGAGCAGATTAAAACCACCAGCCTTATCTCCCTAAAGATGCAG
53679549 CGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAACAAATTAAAACTACA
66 CGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAACAAATTAAAACTACA
* * * * * * *
53679614 AATTATGGCAAATCTTATCTTCCTAAAGTTGCGGTGGAGTAGATTGAATCTGTCAGCTTATTTCC
131 AATAATGGCAAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAGCTTATCTCC
* * * * **
53679679 CTGAAGTTACAGCAGAGCAGACTGAAGACAGCGAATCTTCTTTTCCTAGCATTGTAGTGGAACAG
196 CTGAAGTTACAACAGAACAGACTAAAGACAGCGAATCTTATCATCCTAGCATTGTAGTGGAACAG
* *
53679744 ATTAAAGCTACAAATTATGGTGGAT
261 ATTAAAGCTAC-AACTA----GGAC
* * ** * * *
53679769 CTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGCAG
1 CTTATCTTCCTGAAATTACAGCGGAGCAGATTAAAACCACCAGCCTTATCTCCCTAAAGATGCAG
* * * * **
53679834 CGGAGCAGACTTAAGACAGC-AATTCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGTTAC
66 CGGAGCAGACTGAAGACAACGAA-TCTTATTTCCCTGGCGTTGCAGTGAAACAAATTAAAACTAC
*
53679898 AAATAATGGCGAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAGCCTTATCT
130 AAATAATGGCAAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAG-CTTATCT
* * ** * * *
53679963 CTCTGAAGTTGCAATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAG-GTT
194 CCCTGAAGTTACAACAGAACAGACTAAAG--AC-----A--GCGAATCTTATCATCCT-AGCATT
*
53680027 GTAGTGGAACAGATTGAAG-T-C-ACTA-G-C
249 GTAGTGGAACAGATTAAAGCTACAACTAGGAC
*
53680054 CTTATC-TCTCTGAAATTACAGCGGAGCAGACTAAA
1 CTTATCTTC-CTGAAATTACAGCGGAGCAGATTAAA
53680089 GACAGCGAAT
Statistics
Matches: 500, Mismatches: 87, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
284 4 0.01
285 265 0.53
286 184 0.37
287 1 0.00
288 5 0.01
291 3 0.01
293 2 0.00
294 1 0.00
295 33 0.07
296 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (280 bp):
CTTATCTTCCTGAAATTACAGCGGAGCAGATTAAAACCACCAGCCTTATCTCCCTAAAGATGCAG
CGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGAAACAAATTAAAACTACA
AATAATGGCAAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGCCGTCAGCTTATCTCC
CTGAAGTTACAACAGAACAGACTAAAGACAGCGAATCTTATCATCCTAGCATTGTAGTGGAACAG
ATTAAAGCTACAACTAGGAC
Found at i:53680089 original size:98 final size:98
Alignment explanation
Indices: 53679880--53680089 Score: 253
Period size: 98 Copynumber: 2.1 Consensus size: 98
53679870 GCGTTGCAGT
* * *
53679880 GGAACAGATTAAAGTTACAAATAATGGCGAATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTG
1 GGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGAACAGATTG
* * *
53679945 AAGCCGTCAGCCTTATCTCTCTGAAGTTGCAAT
66 AAGCCGTCAGCCTTATCTCTCTGAAATTACAAC
* * * * **
53679978 GGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCATCCTGAGGTTGTAGTGGAACAGATTG
1 GGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGAACAGATTG
*
53680043 AAGTCAC-T-AGCCTTATCTCTCTGAAATTACAGC
66 AAG-C-CGTCAGCCTTATCTCTCTGAAATTACAAC
* *
53680076 GGAGCAGACTAAAG
1 GGAACAGATTAAAG
53680090 ACAGCGAATC
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
98 92 0.97
99 2 0.02
100 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (98 bp):
GGAACAGATTAAAGCTACAAATAATGGCGAATCTTATCATCCTAAAGTTACAGTGGAACAGATTG
AAGCCGTCAGCCTTATCTCTCTGAAATTACAAC
Found at i:53681455 original size:27 final size:26
Alignment explanation
Indices: 53681396--53681456 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
53681386 ATTTTTTAAA
*
53681396 TATTATTATTACTATTACTGTTATTG
1 TATTATTATTACTATTACTCTTATTG
53681422 TATTTATTATTACTACTTAC-CTTA-T-
1 TA-TTATTATTACTA-TTACTCTTATTG
53681447 TATTATTATT
1 TATTATTATT
53681457 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.25
25 2 0.06
26 3 0.09
27 15 0.47
28 4 0.12
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (26 bp):
TATTATTATTACTATTACTCTTATTG
Found at i:53681767 original size:4 final size:4
Alignment explanation
Indices: 53681758--53682624 Score: 1734
Period size: 4 Copynumber: 216.8 Consensus size: 4
53681748 TAATTTTCGT
53681758 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53681806 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53681854 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53681902 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53681950 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53681998 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682046 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682094 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682142 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682190 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682238 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682286 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682334 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682382 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682430 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682478 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682526 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682574 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53682622 ATA
1 ATA
53682625 TCTTTTTTGC
Statistics
Matches: 863, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 863 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:53686769 original size:16 final size:16
Alignment explanation
Indices: 53686748--53686787 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
53686738 CCCATGAGTT
*
53686748 TCAAAAAA-AAAAGAGA
1 TCAAAAAATAAAA-AAA
53686764 TCAAAAAATAAAAAAA
1 TCAAAAAATAAAAAAA
53686780 TCAAAAAA
1 TCAAAAAA
53686788 GGAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (16 bp):
TCAAAAAATAAAAAAA
Found at i:53689056 original size:88 final size:88
Alignment explanation
Indices: 53688896--53689056 Score: 223
Period size: 88 Copynumber: 1.8 Consensus size: 88
53688886 CCGGTGAAGA
* ** * * *
53688896 TATCTCCCTGAGAAATAGTAGAGTAGGTTGAAAATAGTAGGTCTTGTTTTCCTGTATTGGCAGCG
1 TATCTCCCTGAGAAACAGTAGAGTAGGTTGAAAATAACAGATCTTGTCTTCCTGTATTGACAGCG
*
53688961 AAGTAGATCAAAGATACCAGTCT
66 AAATAGATCAAAGATACCAGTCT
* * * *
53688984 TATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATAACAGATCTTGTCTTCCTGTATTGACATCG
1 TATCTCCCTGAGAAACAGTAGAGTAGGTTGAAAATAACAGATCTTGTCTTCCTGTATTGACAGCG
53689049 AAATAGAT
66 AAATAGAT
53689057 TGGAGATAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 62 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (88 bp):
TATCTCCCTGAGAAACAGTAGAGTAGGTTGAAAATAACAGATCTTGTCTTCCTGTATTGACAGCG
AAATAGATCAAAGATACCAGTCT
Found at i:53689066 original size:45 final size:45
Alignment explanation
Indices: 53688937--53689332 Score: 320
Period size: 45 Copynumber: 8.8 Consensus size: 45
53688927 AAATAGTAGG
* * * *
53688937 TCTTGTTTTCCTGTATTGGCAGCGAAGTAGATCAAAGATACCAG-
1 TCTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
* * *** * * *
53688981 TCTTATCTCCCTG-AGAAGCAGT-GGAGTAGGTTGAAGATAACAGA
1 TCTTGTCTTCCTGTATTGGCA-TCGAAGTAGATCGAAGATAACAGA
* * * *
53689025 TCTTGTCTTCCTGTATTGACATCGAAATAGATTGGAGATAACAGA
1 TCTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
* * * **
53689070 TCTTATCTTCCTGTACTGGCAGT-GAAGTAGATCAAAGATAGTAGA
1 TCTTGTCTTCCTGTATTGGCA-TCGAAGTAGATCGAAGATAACAGA
* * * *
53689115 TCTTGTCTTCCTATATTGGTAGT-GAAGTCGATCGAAGATAACATA
1 TCTTGTCTTCCTGTATTGGCA-TCGAAGTAGATCGAAGATAACAGA
* * * * **
53689160 TCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCAAATATAGTAGA
1 TCTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
* * *
53689205 TCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAGATATCAGA
1 TCTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
* * *
53689250 TCTTGT-TATCCTGTATTGGCAACAAAGTAGATCGAAGATAGCAGA
1 TCTTGTCT-TCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
* * * * *
53689295 TTTTGCCTTCATGTACTGACAGT-GAAGTAGATCGAAGA
1 TCTTGTCTTCCTGTATTGGCA-TCGAAGTAGATCGAAGA
53689333 CACCAGTCTT
Statistics
Matches: 276, Mismatches: 67, Indels: 17
0.77 0.19 0.05
Matches are distributed among these distances:
43 20 0.07
44 23 0.08
45 231 0.84
46 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (45 bp):
TCTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGATAACAGA
Found at i:53689118 original size:90 final size:90
Alignment explanation
Indices: 53688929--53689345 Score: 392
Period size: 90 Copynumber: 4.7 Consensus size: 90
53688919 TAGGTTGAAA
* * * * *
53688929 ATAGTAGGTCTTGTTTTCCTGTATTGGCAGCGAAGTAGATCAAAGATACCAG-TCTTATCTCCCT
1 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATCTTCCT
*** * * * **
53688993 G-AGAAGCAGTGGAGTAGGTTGAAG
66 GTATTGGCAGCGAAGTAGATCAAAG
** * * * * *
53689017 ATAACAGATCTTGTCTTCCTGTATTGACATCGAAATAGATTGGAGATAACAGATCTTATCTTCCT
1 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATCTTCCT
* *
53689082 GTACTGGCAGTGAAGTAGATCAAAG
66 GTATTGGCAGCGAAGTAGATCAAAG
* * * * * * *
53689107 ATAGTAGATCTTGTCTTCCTATATTGGTAGTGAAGTCGATCGAAGATAACATATCTTGTCTTTCT
1 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATCTTCCT
*
53689172 GTATTGGCAGCGAAGTAGATCAAAT
66 GTATTGGCAGCGAAGTAGATCAAAG
* * *
53689197 ATAGTAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAGATATCAGATCTTGT-TATCC
1 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATCT-TCC
* * *
53689261 TGTATTGGCAACAAAGTAGATCGAAG
65 TGTATTGGCAGCGAAGTAGATCAAAG
* * * * * * * * *
53689287 ATAGCAGATTTTGCCTTCATGTACTGACAGTGAAGTAGATCGAAGACACCAG-TCTTATC
1 ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATC
53689346 GCCTTGACGT
Statistics
Matches: 268, Mismatches: 57, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
88 41 0.15
89 18 0.07
90 209 0.78
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (90 bp):
ATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTATCTTCCT
GTATTGGCAGCGAAGTAGATCAAAG
Found at i:53689577 original size:50 final size:50
Alignment explanation
Indices: 53689525--53689892 Score: 315
Period size: 50 Copynumber: 7.4 Consensus size: 50
53689515 TTTGACATTA
* *
53689525 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTA
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * * * * *
53689575 TAGTGGAATAGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * ** *
53689625 CAGT-TAATAGATTGAAGCCACAATAGTGAATCTTACTTCCCTGGCAGTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * * * * * * *
53689674 TAGTGGAACAAATTGAAGTCACGACGGTGAATCTTGTTTCCTTGACATTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * ** * * * *
53689724 CAATTTAAAAGATTGAAGCCACAACGATGAATCTTACTTCCCTGGCGGTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * * * * * *
53689774 TAGTGGAATAGATTGAAGTCACGATGGCGAATCTTGTTTCCCTGACAATG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
* * ** * * * **
53689824 CAATTTAAAATATTGAAGCCACAACGGTGAATCTTGCTTCCCTAGTGGTG
1 TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
*
53689874 TAGTGGAACAGATTGAAGC
1 TAGTGGAATAGATTGAAGC
53689893 TACGACGGCA
Statistics
Matches: 233, Mismatches: 84, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
49 38 0.16
50 195 0.84
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (50 bp):
TAGTGGAATAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGCAGTG
Found at i:53689939 original size:100 final size:100
Alignment explanation
Indices: 53689534--53689941 Score: 527
Period size: 100 Copynumber: 4.1 Consensus size: 100
53689524 ATAGTGGAAT
* *
53689534 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTATAGTGGAATAGATTGAAG-CTACG
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGTC-ACG
* *
53689598 ACGGTGAATCTTGTTTCCCCGACATTGC-AGTTAAT
65 ACGGCGAATCTTGTTTCCCCGACATTGCAAGTTAAA
** *
53689633 AGATTGAAGCCACAATAGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAAATTGAAGTCACGA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGTCACGA
* ** *
53689698 CGGTGAATCTTGTTTCCTTGACATTGCAATTTAAA
66 CGGCGAATCTTGTTTCCCCGACATTGCAAGTTAAA
* * *
53689733 AGATTGAAGCCACAACGATGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGTCACGA
* * * *
53689798 TGGCGAATCTTGTTTCCCTGACAATGCAATTTAAA
66 CGGCGAATCTTGTTTCCCCGACATTGCAAGTTAAA
* * * **
53689833 ATATTGAAGCCACAACGGTGAATCTTGCTTCCCTAGTGGTGTAGTGGAACAGATTGAAG-CTACG
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGTC-ACG
* *
53689897 ACGGCAAATTTTGTTTCCCCGACATTGC-AGTTAAA
65 ACGGCGAATCTTGTTTCCCCGACATTGCAAGTTAAA
*
53689932 CAAATTGAAG
1 -AGATTGAAG
53689942 AAAATAATCC
Statistics
Matches: 273, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
99 90 0.33
100 183 0.67
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGTCACGA
CGGCGAATCTTGTTTCCCCGACATTGCAAGTTAAA
Found at i:53691727 original size:3 final size:3
Alignment explanation
Indices: 53691721--53691760 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
53691711 ATTATTATTA
53691721 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
53691761 ATTATTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:53694662 original size:24 final size:22
Alignment explanation
Indices: 53694630--53694731 Score: 75
Period size: 22 Copynumber: 4.5 Consensus size: 22
53694620 ATGAATTTTG
*
53694630 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
53694654 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
* * *
53694676 TTTAAGTTT-CCATGT-ATTAT
1 TTTAAATTTATCATATAATTAT
* *
53694696 TATTCAAATTTATTATGT-ATTAT
1 T-TT-AAATTTATCATATAATTAT
53694719 TTTACATATTTAT
1 TTTA-A-ATTTAT
53694732 ATGTAAACTT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.09
21 7 0.11
22 26 0.39
23 16 0.24
24 11 0.17
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:53694713 original size:23 final size:22
Alignment explanation
Indices: 53694687--53694736 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
53694677 TTAAGTTTCC
53694687 ATGTATTATTATT-CAAATTTATT
1 ATGTATTATT-TTACAAATTTA-T
*
53694710 ATGTATTATTTTACATATTTAT
1 ATGTATTATTTTACAAATTTAT
53694732 ATGTA
1 ATGTA
53694737 AACTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
ATGTATTATTTTACAAATTTAT
Found at i:53695979 original size:25 final size:25
Alignment explanation
Indices: 53695945--53695999 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
53695935 AATTGTCTTT
**
53695945 GATAGTATATCCTAAAACTACTATA
1 GATAGTATATAATAAAACTACTATA
*
53695970 GATAGTATATAATAATACTACTATA
1 GATAGTATATAATAAAACTACTATA
53695995 GATAG
1 GATAG
53696000 ACTATATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (25 bp):
GATAGTATATAATAAAACTACTATA
Found at i:53696016 original size:25 final size:24
Alignment explanation
Indices: 53695945--53696016 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
53695935 AATTGTCTTT
**
53695945 GATAGTATATCCTAAAACTACTATA
1 GATAGTATATAATAAAA-TACTATA
*
53695970 GATAGTATATAATAATACTACTATA
1 GATAGTATATAATAA-AATACTATA
*
53695995 GATAG-ACTATATTGAAAATACT
1 GATAGTA-TATAAT-AAAATACT
53696017 TAAAATAGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 35 0.90
26 3 0.08
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (24 bp):
GATAGTATATAATAAAATACTATA
Found at i:53700436 original size:27 final size:27
Alignment explanation
Indices: 53700406--53700468 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
53700396 TGCCCCAGTG
* * *
53700406 GGGTATAATGACCGTAATACCTCTGTA
1 GGGTAAAATGACCGAAATACCCCTGTA
*
53700433 GGGTAAAATGATCGAAATACCCCTGTA
1 GGGTAAAATGACCGAAATACCCCTGTA
*
53700460 AGGTAAAAT
1 GGGTAAAAT
53700469 AACCATGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCCTGTA
Found at i:53700607 original size:24 final size:24
Alignment explanation
Indices: 53700570--53700664 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
53700560 CCATCGAGGT
* *
53700570 TAAATGATTGATTTGT-TCGTGATG
1 TAAATGACTAATTTGTCT-GTGATG
*
53700594 TAAATGACTAATTTGTCTGTGATT
1 TAAATGACTAATTTGTCTGTGATG
** *
53700618 TAAATGGTTGATTTGTCTGTGATTGG
1 TAAATGACTAATTTGTCTGTGA-T-G
*
53700644 T--ATGACTGATTTGTCTGTGAT
1 TAAATGACTAATTTGTCTGTGAT
53700665 TTGTATGACT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.02
24 55 0.93
25 2 0.03
26 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.46
Consensus pattern (24 bp):
TAAATGACTAATTTGTCTGTGATG
Found at i:53700629 original size:48 final size:48
Alignment explanation
Indices: 53700569--53700666 Score: 130
Period size: 48 Copynumber: 2.0 Consensus size: 48
53700559 CCCATCGAGG
53700569 TTAAATGATTGATTTGT-TCGTGA-T-GTAAATGACTAATTTGTCTGTGAT
1 TTAAATGATTGATTTGTCT-GTGATTGGT--ATGACTAATTTGTCTGTGAT
* *
53700617 TTAAATGGTTGATTTGTCTGTGATTGGTATGACTGATTTGTCTGTGAT
1 TTAAATGATTGATTTGTCTGTGATTGGTATGACTAATTTGTCTGTGAT
53700665 TT
1 TT
53700667 GTATGACTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
48 41 0.91
49 2 0.04
50 2 0.04
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.48
Consensus pattern (48 bp):
TTAAATGATTGATTTGTCTGTGATTGGTATGACTAATTTGTCTGTGAT
Found at i:53700665 original size:24 final size:24
Alignment explanation
Indices: 53700597--53700678 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
53700587 CGTGATGTAA
* **
53700597 ATGACTAATTTGTCTGTGATTTAA
1 ATGACTGATTTGTCTGTGATTTGT
** *
53700621 ATGGTTGATTTGTCTGTGATTGGT
1 ATGACTGATTTGTCTGTGATTTGT
53700645 ATGACTGATTTGTCTGTGATTTGT
1 ATGACTGATTTGTCTGTGATTTGT
53700669 ATGACTGATT
1 ATGACTGATT
53700679 CTGAGCATGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTTGT
Found at i:53700666 original size:11 final size:11
Alignment explanation
Indices: 53700626--53700668 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
53700616 TTTAAATGGT
53700626 TGATTTGTCTG
1 TGATTTGTCTG
* *
53700637 TGATTGGTATG
1 TGATTTGTCTG
53700648 ACTGATTTGTCTG
1 --TGATTTGTCTG
53700661 TGATTTGT
1 TGATTTGT
53700669 ATGACTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.51
Consensus pattern (11 bp):
TGATTTGTCTG
Found at i:53700867 original size:32 final size:32
Alignment explanation
Indices: 53700826--53700979 Score: 193
Period size: 32 Copynumber: 4.8 Consensus size: 32
53700816 GCTGCGATGC
53700826 TACTGATGGCTTTGTGCTGATCATATTACCGT
1 TACTGATGGCTTTGTGCTGATCATATTACCGT
*
53700858 TACTGATGGCTTTGTG-TCGATCATATTACCTT
1 TACTGATGGCTTTGTGCT-GATCATATTACCGT
* * *
53700890 TATTGGTGGCATTGTGCTGATCATATTACCGT
1 TACTGATGGCTTTGTGCTGATCATATTACCGT
* ** *
53700922 TACTAATTACTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCTGATCATATTACCGT
* * *
53700954 TACTGATGGCTGTGTGCCGGTCATAT
1 TACTGATGGCTTTGTGCTGATCATAT
53700980 CACTGCTACT
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 1 0.01
32 101 0.98
33 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCTGATCATATTACCGT
Found at i:53700970 original size:64 final size:63
Alignment explanation
Indices: 53700826--53701030 Score: 223
Period size: 64 Copynumber: 3.2 Consensus size: 63
53700816 GCTGCGATGC
* * * *
53700826 TACTGATGGCTTTGTGCTGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATTACCTT
1 TACTGATGGC-TTGTGCTGATCATATTACCGTTACTAATTGCTTTGTGCCGATCATATTACCGT
* * *
53700890 TATTGGTGGCATTGTGCTGATCATATTACCGTTACTAATTACTTTGTGCCGATCATATTACCGT
1 TACTGATGGC-TTGTGCTGATCATATTACCGTTACTAATTGCTTTGTGCCGATCATATTACCGT
* * * * * * * * *
53700954 TACTGATGGCTGTGTGCCGGTCATATCACTGCTACTAATTGGTTTGAGCCAATCATATTACTG-
1 TACTGATGGCT-TGTGCTGATCATATTACCGTTACTAATTGCTTTGTGCCGATCATATTACCGT
*
53701017 TACTTATGGCTTGT
1 TACTGATGGCTTGT
53701031 AGCCATTCTA
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
62 3 0.03
63 11 0.09
64 105 0.88
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (63 bp):
TACTGATGGCTTGTGCTGATCATATTACCGTTACTAATTGCTTTGTGCCGATCATATTACCGT
Found at i:53701009 original size:96 final size:93
Alignment explanation
Indices: 53700835--53701014 Score: 209
Period size: 96 Copynumber: 1.9 Consensus size: 93
53700825 CTACTGATGG
* * * * *
53700835 CTTTGTGCTGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATATTACCTTTATTGGTGGC
1 CTTTGTGCCGATCATATTACCGTTACTGATGGCTGTGTGCCGATCATATCACCTTAATTGGT-G-
* **
53700900 ATTGTGCTGATCATATTACCGTTACTAATTA
64 -TTGAGCCAATCATATTACCGTTACTAATTA
*
53700931 CTTTGTGCCGATCATATTACCGTTACTGATGGCTGTGTGCCGGTCATATCACTGCTACTAATTGG
1 CTTTGTGCCGATCATATTACCGTTACTGATGGCTGTGTGCCGATCATATCAC--CT--TAATTGG
53700996 T-TTGAGCCAATCATATTAC
62 TGTTGAGCCAATCATATTAC
53701015 TGTACTTATG
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
96 62 0.87
98 2 0.03
100 7 0.10
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (93 bp):
CTTTGTGCCGATCATATTACCGTTACTGATGGCTGTGTGCCGATCATATCACCTTAATTGGTGTT
GAGCCAATCATATTACCGTTACTAATTA
Found at i:53701050 original size:22 final size:21
Alignment explanation
Indices: 53701020--53701081 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
53701010 ATTACTGTAC
53701020 TTATGGCTTGTAGCCATTCTAT
1 TTATGGCTT-TAGCCATTCTAT
* * * *
53701042 TTATAGCTTATAGCTATGCTGT
1 TTATGGCTT-TAGCCATTCTAT
53701064 TTATGGCTCTTAGCCATT
1 TTATGGCT-TTAGCCATT
53701082 TTGATTACTG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTAT
Found at i:53711368 original size:30 final size:30
Alignment explanation
Indices: 53711332--53711414 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
53711322 ACCAGTTATA
*
53711332 GTATTGGGATAAGGCCCACACTTTGTCACT
1 GTATTGGGATAAGGCCCACACTCTGTCACT
* *
53711362 GTATTGGGCTAAGGCCCACACTCTGTTACT
1 GTATTGGGATAAGGCCCACACTCTGTCACT
* *
53711392 GTATTAGGATATGGCCACACACT
1 GTATTGGGATAAGGCC-CACACT
53711415 ACTACTATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 40 0.87
31 6 0.13
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (30 bp):
GTATTGGGATAAGGCCCACACTCTGTCACT
Found at i:53712293 original size:24 final size:25
Alignment explanation
Indices: 53712256--53712308 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
53712246 TCTTTTTGCA
* *
53712256 TTCATTCCATTCATTTGCATTACAT
1 TTCATTCCATTCATGTGCATTAAAT
*
53712281 TTCATTGCA-TCATGTGCATTAAAT
1 TTCATTCCATTCATGTGCATTAAAT
53712305 TTCA
1 TTCA
53712309 CAAAAGATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (25 bp):
TTCATTCCATTCATGTGCATTAAAT
Found at i:53714689 original size:13 final size:13
Alignment explanation
Indices: 53714673--53714698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53714663 CCTTTTTGCG
53714673 TCATTTTACACTT
1 TCATTTTACACTT
53714686 TCATTTTACACTT
1 TCATTTTACACTT
53714699 CAAGAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (13 bp):
TCATTTTACACTT
Found at i:53721845 original size:27 final size:27
Alignment explanation
Indices: 53721814--53721867 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
53721804 GTTGATAAAC
*
53721814 ATTTATTTTAATTTTTTAATATATTTA
1 ATTTATTATAATTTTTTAATATATTTA
* *
53721841 ATTTATTATATTTTTTTAATCTATTTA
1 ATTTATTATAATTTTTTAATATATTTA
53721868 TATATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTATTATAATTTTTTAATATATTTA
Found at i:53721858 original size:18 final size:18
Alignment explanation
Indices: 53721814--53721870 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
53721804 GTTGATAAAC
*
53721814 ATTTATTTTAATTTTTTA-
1 ATTT-TTTTAATTTATTAT
* *
53721832 ATATATTTAATTTATTAT
1 ATTTTTTTAATTTATTAT
*
53721850 ATTTTTTTAATCTATTTAT
1 ATTTTTTTAATTTA-TTAT
53721869 AT
1 AT
53721871 ATAAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 11 0.35
18 14 0.45
19 6 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTTAATTTATTAT
Found at i:53728100 original size:18 final size:17
Alignment explanation
Indices: 53728056--53728108 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
53728046 AAATTAAAAA
53728056 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAA-TGAAT
***
53728074 AAAAATTTGTAAATGAAT
1 AATGTTTTG-AAATGAAT
53728092 AATGTTTTGAAAATGAA
1 AATGTTTTG-AAATGAA
53728109 CGACACGATT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (17 bp):
AATGTTTTGAAATGAAT
Found at i:53731395 original size:17 final size:19
Alignment explanation
Indices: 53731373--53731411 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
53731363 TATGAGTTTC
53731373 AAAAAAAATAA-AAAAT-A
1 AAAAAAAATAAGAAAATGA
*
53731390 AAAAAAATTAAGAAAATGA
1 AAAAAAAATAAGAAAATGA
53731409 AAA
1 AAA
53731412 TGAAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAAAAAATAAGAAAATGA
Found at i:53734245 original size:143 final size:143
Alignment explanation
Indices: 53733825--53734235 Score: 511
Period size: 143 Copynumber: 2.9 Consensus size: 143
53733815 GATGGATTAT
** * *
53733825 AAATTATGGTAAATATTATCTTCTTGAAGTTACAGTGGAGTAGATTGAAACCATCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTGAAACCATCAGCCTTATCT
* ** * * * **
53733890 CCCTGAAGTTACAGTGGAGCACTCTGAAGATA-TCGAATCTTATTTCCTTAGCGTTATAGTGGAA
66 CCCTGAAGTTACAGCGGAGCAAACTGAAGACAGT-GAATCTTATTTCCTTGGCATTGCAGTGGAA
*
53733954 CAGATTAAAGCTAC
130 TAGATTAAAGCTAC
* * ** * * *
53733968 AAATTATGGCGAATCTTATCTTCCTGAATTTGTAATGGAACAGATT-AAAGCCATCAGTCTTATC
1 AAATTATGGCGAATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTGAAA-CCATCAGCCTTATC
* * * * *
53734032 TCCCTGAAGTTGCAGCGGAACAAACTGAGGACAGCGAATCTTATTTCCCTGGCATTGCAGTGGAA
65 TCCCTGAAGTTACAGCGGAGCAAACTGAAGACAGTGAATCTTATTTCCTTGGCATTGCAGTGGAA
53734097 TAGATTAAAGCTAC
130 TAGATTAAAGCTAC
* *
53734111 AAGTTATGGCGAATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTGAAATCATCAGCCTTATCT
1 AAATTATGGCGAATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTGAAACCATCAGCCTTATCT
** * *
53734176 CTATAAAGTTACAGCGGAGCAGACTGAAGACAGTGAATCTTATTTCCTTGGCATTGCAGT
66 CCCTGAAGTTACAGCGGAGCAAACTGAAGACAGTGAATCTTATTTCCTTGGCATTGCAGT
53734236 AGGGTAGATT
Statistics
Matches: 222, Mismatches: 43, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
142 3 0.01
143 216 0.97
144 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (143 bp):
AAATTATGGCGAATCTTATCTTCTTGAAGTTACAGTGGAGCAGATTGAAACCATCAGCCTTATCT
CCCTGAAGTTACAGCGGAGCAAACTGAAGACAGTGAATCTTATTTCCTTGGCATTGCAGTGGAAT
AGATTAAAGCTAC
Found at i:53735736 original size:22 final size:21
Alignment explanation
Indices: 53735692--53735781 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 21
53735682 ATGAATTTTG
53735692 TTTAAATTTATCTCATATTATTAT
1 TTTAAATTTA--TCATA-TATTAT
53735716 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
* * *
53735738 TTGAAGTTT-TCATGTATTAT
1 TTTAAATTTATCATATATTAT
* *
53735758 TATTCAAATTTATTATGTATTAT
1 T-TT-AAATTTATCATATATTAT
53735781 T
1 T
53735782 CTACATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.11
21 7 0.12
22 22 0.39
23 11 0.20
24 10 0.18
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:53735775 original size:23 final size:22
Alignment explanation
Indices: 53735749--53735798 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
53735739 TGAAGTTTTC
*
53735749 ATGTATTATTATTCAAATTTATT
1 ATGTATTATTATACAAATTTA-T
* *
53735772 ATGTATTATTCTACATATTTAT
1 ATGTATTATTATACAAATTTAT
53735794 ATGTA
1 ATGTA
53735799 AACTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (22 bp):
ATGTATTATTATACAAATTTAT
Found at i:53737614 original size:25 final size:25
Alignment explanation
Indices: 53737580--53737648 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
53737570 AATTGTCTTT
* **
53737580 GATAGTATATCCTAAAACTGTTATA
1 GATAGTATATACTAAAACTACTATA
*
53737605 GATAGTATATACTAATACTACTATA
1 GATAGTATATACTAAAACTACTATA
**
53737630 GATAGGCTATACTGAAAAC
1 GATAGTATATACT-AAAAC
53737649 ACTTAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (25 bp):
GATAGTATATACTAAAACTACTATA
Found at i:53741974 original size:27 final size:27
Alignment explanation
Indices: 53741904--53741964 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
53741894 AAAATAATCG
* *
53741904 TAATACCCCTGTAGGGTAAAATGACTA
1 TAATGCCCCAGTAGGGTAAAATGACTA
* *
53741931 TAATGCCCCAGTGGGGTATAATGACTA
1 TAATGCCCCAGTAGGGTAAAATGACTA
53741958 TAATGCC
1 TAATGCC
53741965 TCTAGAGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (27 bp):
TAATGCCCCAGTAGGGTAAAATGACTA
Found at i:53742154 original size:24 final size:24
Alignment explanation
Indices: 53742102--53742223 Score: 111
Period size: 24 Copynumber: 5.1 Consensus size: 24
53742092 TCCATCGAGG
* *
53742102 TTAAATGATTGATTTGT-TCGTAAT
1 TTAAATGACTGATTTGTCT-GTGAT
* *
53742126 GTAAATGACTAATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
**
53742150 TTAAATGGTTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
***
53742174 TGGTATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*** *
53742198 TGGTATGACTGATTTGTGTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
53742222 TT
1 TT
53742224 GTACGACTGA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 81 0.99
25 1 0.01
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.48
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Done.