Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 10 of 311
Found at i:2845389 original size:16 final size:15
Alignment explanation
Indices: 2845346--2845391 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2845336 TTTTTTTATT
*
2845346 TTATTATTAAATT-A
1 TTATTATTATATTAA
2845360 TTA-TATTATATTAA
1 TTATTATTATATTAA
2845374 TATATTATTATATTAA
1 T-TATTATTATATTAA
2845390 TT
1 TT
2845392 TCTTAAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
15 3 0.11
16 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATATTAA
Found at i:2849536 original size:14 final size:15
Alignment explanation
Indices: 2849519--2849547 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2849509 TTATATCACG
2849519 AATCA-TATAAAATT
1 AATCATTATAAAATT
2849533 AATCATTATAAAATT
1 AATCATTATAAAATT
2849548 CAGTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AATCATTATAAAATT
Found at i:2850182 original size:18 final size:18
Alignment explanation
Indices: 2850159--2850194 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2850149 TCAGTAACAA
2850159 GCAAAATTTAAATCCAAT
1 GCAAAATTTAAATCCAAT
2850177 GCAAAATTTAAATCCAAT
1 GCAAAATTTAAATCCAAT
2850195 CTTTCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
GCAAAATTTAAATCCAAT
Found at i:2850986 original size:44 final size:44
Alignment explanation
Indices: 2850931--2851019 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
2850921 AAGTAACAAA
2850931 AACACTACGACAC-ACGAAGTGCCTCATCGACACAAAGTCGAAGT
1 AACACTACGACACTA-GAAGTGCCTCATCGACACAAAGTCGAAGT
* ** * *
2850975 AACAGTACGACACTATTAGTGCCTCATCGACTCAAGGTCGAAGT
1 AACACTACGACACTAGAAGTGCCTCATCGACACAAAGTCGAAGT
2851019 A
1 A
2851020 TCCCTATACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (44 bp):
AACACTACGACACTAGAAGTGCCTCATCGACACAAAGTCGAAGT
Found at i:2851831 original size:13 final size:14
Alignment explanation
Indices: 2851802--2851835 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2851792 AAAACCCTAA
*
2851802 TTTCCCCTTTTTCT
1 TTTCTCCTTTTTCT
2851816 TTTCTCCTTTTT-T
1 TTTCTCCTTTTTCT
2851829 TTTCTCC
1 TTTCTCC
2851836 CAATTTTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCTCCTTTTTCT
Found at i:2851914 original size:21 final size:21
Alignment explanation
Indices: 2851890--2851936 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2851880 TTTTCTTTTT
* *
2851890 TATTTTATTATTAAATTATTA
1 TATTATATTAATAAATTATTA
*
2851911 TATTATATTAATATATTATTA
1 TATTATATTAATAAATTATTA
2851932 TATTA
1 TATTA
2851937 ATTTCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATATTAATAAATTATTA
Found at i:2851930 original size:16 final size:15
Alignment explanation
Indices: 2851894--2851939 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2851884 CTTTTTTATT
*
2851894 TTATTATTAAATT-A
1 TTATTATTATATTAA
2851908 TTA-TATTATATTAA
1 TTATTATTATATTAA
2851922 TATATTATTATATTAA
1 T-TATTATTATATTAA
2851938 TT
1 TT
2851940 TCTTAAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
15 3 0.11
16 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATATTAA
Found at i:2855077 original size:40 final size:41
Alignment explanation
Indices: 2855033--2855125 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
2855023 ACTAGTTTGG
*
2855033 CACCCAGTGTCTTATCGGAT-AATTCGAAGTAGTAAATTAA
1 CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
* *
2855073 CACCCAGTGTCTTATCGAATAAATTCGAAGTCGTAAATTGA
1 CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
2855114 CACCCAGTGTCT
1 CACCCAGTGTCT
2855126 CATCAGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 19 0.39
41 30 0.61
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (41 bp):
CACCCAGTGTCTTATCGAATAAATTCGAAGTAGTAAATTAA
Found at i:2856152 original size:19 final size:19
Alignment explanation
Indices: 2856117--2856174 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2856107 ATATACTTAA
* *
2856117 ATATTAAGTAAACATAT-T
1 ATATTAAATATACATATGT
*
2856135 TTATTAATATATACATATGT
1 ATATTAA-ATATACATATGT
*
2856155 ATATTAAATTTACATATGT
1 ATATTAAATATACATATGT
2856174 A
1 A
2856175 ATCACTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATTAAATATACATATGT
Found at i:2858070 original size:50 final size:51
Alignment explanation
Indices: 2857996--2858128 Score: 205
Period size: 50 Copynumber: 2.6 Consensus size: 51
2857986 CACGGTCTTA
*
2857996 CACTGATCACTTATCACTTGTCACTGATCAGATAAGAGTAGCT-AAGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGAGTAGCTGAAGCTAC
* * * * *
2858046 CACTTATCATTTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGAGTAGCTGAAGCTAC
2858097 CACTTATCACTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTATCACTTGTCACTGATCAGA
2858129 AGTACTCAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 38 0.52
51 35 0.48
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
CACTTATCACTTATCACTTGTCACTGATCAGATAAGAGTAGCTGAAGCTAC
Found at i:2858745 original size:18 final size:19
Alignment explanation
Indices: 2858708--2858748 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2858698 ATTTAGAATC
2858708 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
2858727 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
2858745 AAAA
1 AAAA
2858749 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:2858750 original size:31 final size:31
Alignment explanation
Indices: 2858674--2858747 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
2858664 TCAAGTTATC
*
2858674 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
2858706 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
2858736 TTAAATATAAAA
1 TTAAATATAAAA
2858748 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:2863298 original size:224 final size:222
Alignment explanation
Indices: 2862901--2863332 Score: 581
Period size: 224 Copynumber: 1.9 Consensus size: 222
2862891 CAAACATATG
* * *
2862901 TAACTAAGCTCGGTCTTATTTAAGCCAACCATAAAGCTGCAAACCCTTAGTTTAGACGTTATGTA
1 TAACTAAGCTCAGTCTTATTTAAGCCAACCATAAAGCTACAAACCCTTAGTTTAGACATTATGTA
* ***
2862966 ACTCGTTAAATTGGGGCCTACCCCTAAGTTTTCTCGAGTTATGCTCACTTCTGGTCAAAACTCAA
66 ACTCATTAAATCAAGGCCTACCCCTAAGTTTTCTCGAGTTATGCTCACTTCTGGTCAAAACTCAA
*
2863031 ACATGGCGGTGGTATGGTAGATCAGTGTCAAATCATAAAACATATCA-TCAGACT-AGAAGAT-A
131 ACATGACGGTGGTATGGTAGATCAGTGTC-AATC--AAAACATATCATTC-GACTCA-AAGATAA
2863093 CATCTAGTCATTACAGGTCAAACATAGAGATA
191 CATCTAGTCATTACAGGTCAAACATAGAGATA
* *
2863125 TAACTAAGCTCAGTCTTATTTAAGCCAACCATAAAGGTACGAACCCTTAGTTTAGACATTATGTA
1 TAACTAAGCTCAGTCTTATTTAAGCCAACCATAAAGCTACAAACCCTTAGTTTAGACATTATGTA
*
2863190 ACTCATTAAATCAAGGCCTCACCCGCCCTCCTGAGTTTTCTCGAGTTATGCTCACTTCTGGTCAA
66 ACTCATTAAATCAAGGCCT-A-----CC-CCTAAGTTTTCTCGAGTTATGCTCACTTCTGGTCAA
* * *
2863255 AACTCAAACATGATGGT-GTATGGTAGATTAGTGTC-A-C-AAACATATCATTCGATTCAAAGAT
124 AACTCAAACATGACGGTGGTATGGTAGATCAGTGTCAATCAAAACATATCATTCGACTCAAAGAT
2863316 AACATCTAGTCATTACA
189 AACATCTAGTCATTACA
2863333 TTTCTTAACA
Statistics
Matches: 184, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
224 93 0.51
225 20 0.11
227 1 0.01
228 1 0.01
230 19 0.10
231 50 0.27
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (222 bp):
TAACTAAGCTCAGTCTTATTTAAGCCAACCATAAAGCTACAAACCCTTAGTTTAGACATTATGTA
ACTCATTAAATCAAGGCCTACCCCTAAGTTTTCTCGAGTTATGCTCACTTCTGGTCAAAACTCAA
ACATGACGGTGGTATGGTAGATCAGTGTCAATCAAAACATATCATTCGACTCAAAGATAACATCT
AGTCATTACAGGTCAAACATAGAGATA
Found at i:2864046 original size:41 final size:41
Alignment explanation
Indices: 2863972--2864049 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
2863962 TTTTTTTTAC
* *
2863972 GGCGTTTTCATTAAAAACGCCATTATAGCTTAATTTTTTGT
1 GGCGTTTTCATTAAAAACGCCACTATAGATTAATTTTTTGT
* *
2864013 GGCGTTTT-ACTTAAAAACGCTACTATTGATTAATTTT
1 GGCGTTTTCA-TTAAAAACGCCACTATAGATTAATTTT
2864050 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (41 bp):
GGCGTTTTCATTAAAAACGCCACTATAGATTAATTTTTTGT
Found at i:2864192 original size:8 final size:8
Alignment explanation
Indices: 2864181--2864276 Score: 90
Period size: 8 Copynumber: 11.9 Consensus size: 8
2864171 TACAATATTA
2864181 ATTTTTTT
1 ATTTTTTT
2864189 ATTTTTTT
1 ATTTTTTT
2864197 ATTTTTTT
1 ATTTTTTT
*
2864205 ATTTTTTA
1 ATTTTTTT
2864213 ATTTTAATTT
1 ATTTT--TTT
2864223 -TTTATTTT
1 ATTT-TTTT
2864231 -TTATTTTT
1 ATT-TTTTT
**
2864239 AAATTTTT
1 ATTTTTTT
**
2864247 AAATTTTT
1 ATTTTTTT
2864255 A-TTTTTT
1 ATTTTTTT
2864262 ATTTTTTT
1 ATTTTTTT
2864270 ATTTTTT
1 ATTTTTT
2864277 GAGTTTATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
7 6 0.08
8 64 0.83
9 4 0.05
10 3 0.04
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2864195 original size:7 final size:7
Alignment explanation
Indices: 2864183--2864293 Score: 109
Period size: 7 Copynumber: 15.4 Consensus size: 7
2864173 CAATATTAAT
2864183 TTTTTTA
1 TTTTTTA
2864190 TTTTTTTA
1 -TTTTTTA
2864198 TTTTTTTA
1 -TTTTTTA
2864206 TTTTTTA
1 TTTTTTA
* *
2864213 ATTTTAA
1 TTTTTTA
2864220 TTTTTTA
1 TTTTTTA
2864227 TTTTTTA
1 TTTTTTA
*
2864234 TTTTTAAA
1 TTTTT-TA
*
2864242 TTTTTAA
1 TTTTTTA
*
2864249 ATTTTTA
1 TTTTTTA
2864256 TTTTTTA
1 TTTTTTA
2864263 TTTTTTTA
1 -TTTTTTA
2864271 TTTTTTGA
1 TTTTTT-A
*
2864279 --GTTTA
1 TTTTTTA
2864284 TTTTTTA
1 TTTTTTA
2864291 TTT
1 TTT
2864294 CGGTTTAATG
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
5 1 0.01
6 3 0.03
7 55 0.62
8 29 0.33
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:2864223 original size:29 final size:28
Alignment explanation
Indices: 2864185--2864274 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 28
2864175 ATATTAATTT
*
2864185 TTTTATTTTTTTATTTTTTTATTTTTTAA
1 TTTTAATTTTTTA-TTTTTTATTTTTTAA
*
2864214 TTTTAATTTTTTATTTTTTATTTTTAAA
1 TTTTAATTTTTTATTTTTTATTTTTTAA
* *
2864242 TTTTTAAATTTTTATTTTTTATTTTTTTA
1 -TTTTAATTTTTTATTTTTTATTTTTTAA
2864271 TTTT
1 TTTT
2864275 TTGAGTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 18 0.33
29 37 0.67
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTAATTTTTTATTTTTTATTTTTTAA
Found at i:2864821 original size:15 final size:15
Alignment explanation
Indices: 2864798--2864848 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2864788 ATACCCATGG
*
2864798 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
2864813 CCATAAAACCGTAAA
1 CCATAAAACCTTAAA
* *
2864828 CTAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
2864842 CCTTAAA
1 CCATAAA
2864849 TATTAAACCG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:2865027 original size:37 final size:37
Alignment explanation
Indices: 2864971--2865043 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
2864961 ATGTGATGTT
*
2864971 TTTTGGGGTTTAGGGTTTTAAAAGTTATAGTTTAGTA
1 TTTTGGGGTTTAGAGTTTTAAAAGTTATAGTTTAGTA
* * *
2865008 TTTTGGGGTTTAGATTTTTAGAGGTTATAGTTTAGT
1 TTTTGGGGTTTAGAGTTTTAAAAGTTATAGTTTAGT
2865044 GTTCATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (37 bp):
TTTTGGGGTTTAGAGTTTTAAAAGTTATAGTTTAGTA
Found at i:2865131 original size:41 final size:41
Alignment explanation
Indices: 2865085--2865307 Score: 351
Period size: 41 Copynumber: 5.5 Consensus size: 41
2865075 AGGAGTAATA
*
2865085 TGACTTTTAGCGGCGTTTTAGCGAAAGCGCCGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
*
2865126 CGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
* *
2865167 TGACTTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGTTAC
1 TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCT-C
*
2865209 -GACTTTTAGCGGCGTTTTACCGAAAGCGCCACTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
* *
2865249 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
*
2865290 TG-TTTTTAGCGGCGTTTT
1 TGACTTTTAGCGGCGTTTT
2865308 TGATGAAACG
Statistics
Matches: 168, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
40 16 0.10
41 151 0.90
42 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTC
Found at i:2872931 original size:44 final size:43
Alignment explanation
Indices: 2872868--2873020 Score: 189
Period size: 44 Copynumber: 3.3 Consensus size: 43
2872858 CTGATCACAT
*
2872868 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTATCACTGATCAGATAAGTGTAGCT-AAGCTACCAC
* *
2872912 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCAC
1 TTATCACTTATCACTGATCAGATAAGTGTAGCTAAGCTACCAC
*
2872955 TTATCATTTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 -T-T-A----TCACTTATCACTGATCAGATAAGTGTAGCT-AAGCTACCAC
2873006 TTATCACTTATCACT
1 TTATCACTTATCACT
2873021 TGTCACTGAT
Statistics
Matches: 97, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
43 10 0.10
44 45 0.46
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 29 0.30
51 9 0.09
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (43 bp):
TTATCACTTATCACTGATCAGATAAGTGTAGCTAAGCTACCAC
Found at i:2873027 original size:51 final size:50
Alignment explanation
Indices: 2872868--2873034 Score: 213
Period size: 51 Copynumber: 3.4 Consensus size: 50
2872858 CTGATCACAT
*
2872868 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT---AC----CAC
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCAC
*
2872912 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAC
* * * *
2872962 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGAGTAGCT-AAGCTACCACTTATCAC
2873013 TTATCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
2873035 AGTACTCAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.05
44 32 0.30
46 2 0.02
50 32 0.30
51 35 0.33
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAC
Found at i:2882440 original size:19 final size:20
Alignment explanation
Indices: 2882407--2882453 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
2882397 CAGTAAAATA
*
2882407 TTTTCTGGAAAATGAATTCC
1 TTTTCTGGAAAATGAATTAC
*
2882427 TTTTCTGG-AAATGACTTAC
1 TTTTCTGGAAAATGAATTAC
2882446 TTTTCTGG
1 TTTTCTGG
2882454 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTTCTGGAAAATGAATTAC
Found at i:2882559 original size:20 final size:20
Alignment explanation
Indices: 2882534--2882573 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2882524 TTGTTTTTAC
2882534 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
2882554 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
2882574 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:2882578 original size:16 final size:18
Alignment explanation
Indices: 2882529--2882573 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
2882519 AAAAGTTGTT
* *
2882529 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
2882547 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
2882567 TTTATAT
1 TTTATAT
2882574 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:2883566 original size:24 final size:24
Alignment explanation
Indices: 2883534--2883586 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
2883524 GAGTACCTCA
2883534 CACACTCATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
2883558 CACACTCATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
2883582 CACAC
1 CACAC
2883587 CATAAGAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (24 bp):
CACACTCATCTCTAACATTCAACC
Found at i:2885457 original size:16 final size:16
Alignment explanation
Indices: 2885432--2885492 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
2885422 ATTATCATCA
2885432 TATA-AATTTTAATTT
1 TATACAATTTTAATTT
*
2885447 TATACAATTTT-A-TA
1 TATACAATTTTAATTT
* *
2885461 CATAAAATTTTAATTT
1 TATACAATTTTAATTT
* *
2885477 GATCCAATTTTAATTT
1 TATACAATTTTAATTT
2885493 AATATCATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
14 10 0.28
15 6 0.17
16 20 0.56
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (16 bp):
TATACAATTTTAATTT
Found at i:2885469 original size:30 final size:31
Alignment explanation
Indices: 2885430--2885488 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
2885420 AAATTATCAT
*
2885430 CATATAAATTTTAATTTTATACAATTTTATA
1 CATATAAATTTTAATTTGATACAATTTTATA
*
2885461 CATA-AAATTTTAATTTGATCCAATTTTA
1 CATATAAATTTTAATTTGATACAATTTTA
2885489 ATTTAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (31 bp):
CATATAAATTTTAATTTGATACAATTTTATA
Found at i:2885632 original size:31 final size:30
Alignment explanation
Indices: 2885578--2885667 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
2885568 ATTTTTTTAA
* **
2885578 ATATGTATAATTAAATTAAAATTAAAATTTC
1 ATATATATAATTAAA-CCAAATTAAAATTTC
* * *
2885609 A-AGTATATATTTAAACCATAATTAAAGTTTT
1 ATA-TATATAATTAAACCA-AATTAAAATTTC
*
2885640 ATATATATAATTACACCAAATTAAAATT
1 ATATATATAATTAAACCAAATTAAAATT
2885668 CATGTAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
30 11 0.23
31 35 0.74
32 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (30 bp):
ATATATATAATTAAACCAAATTAAAATTTC
Found at i:2894203 original size:90 final size:90
Alignment explanation
Indices: 2894050--2894225 Score: 298
Period size: 90 Copynumber: 2.0 Consensus size: 90
2894040 GAGTTTAGGT
* * * *
2894050 TACAAAATTAATGCGACGAATAACATGTAACTCATAAATGATAAGTTTTGAATGGTCGTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
2894115 CCAACATATGTTGCTTTTGTAGTCC
66 CCAACATATGTTGCTTTTGTAGTCC
* *
2894140 TACAAAATTAATGCAACAAATAACATATAACTCGTAAATGATAAGTTCTGAATGGTCTTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
2894205 CCAACATATGTTGCTTTTGTA
66 CCAACATATGTTGCTTTTGTA
2894226 ATCCGGGTAC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (90 bp):
TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
CCAACATATGTTGCTTTTGTAGTCC
Found at i:2897641 original size:15 final size:15
Alignment explanation
Indices: 2897621--2897698 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
2897611 TTTATGGAAA
2897621 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
2897636 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
2897650 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2897666 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2897680 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
2897696 ATC
1 ATC
2897699 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:2897658 original size:30 final size:30
Alignment explanation
Indices: 2897617--2897698 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
2897607 CATATTTATG
*
2897617 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
2897647 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
2897677 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
2897699 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:2903523 original size:50 final size:50
Alignment explanation
Indices: 2903404--2903652 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
2903394 GATAATAACA
* * * ** * *
2903404 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
2903455 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2903505 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2903555 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2903610 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
2903653 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2903581 original size:100 final size:104
Alignment explanation
Indices: 2903403--2903652 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
2903393 TGATAATAAC
* **
2903403 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
2903468 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
2903505 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
2903568 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
2903610 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2903653 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:2903768 original size:13 final size:13
Alignment explanation
Indices: 2903747--2903778 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2903737 GCTTGGATCA
*
2903747 TCATCAAATAAAT
1 TCATAAAATAAAT
2903760 TCATAAAATAAAT
1 TCATAAAATAAAT
2903773 TCATAA
1 TCATAA
2903779 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2904024 original size:30 final size:30
Alignment explanation
Indices: 2903990--2904047 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2903980 CCTCGACTCT
**
2903990 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
2904020 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
2904048 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2905093 original size:30 final size:30
Alignment explanation
Indices: 2905050--2905173 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
2905040 TCCATATTTA
* * *
2905050 TGGAAAATCAAAGATATGGGTATTAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2905080 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2905110 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2905140 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2905171 TGG
1 TGG
2905174 CATAATAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2905120 original size:15 final size:15
Alignment explanation
Indices: 2905102--2905151 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2905092 GATATGGGTA
2905102 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
* **
2905117 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
2905132 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
2905147 TCAAA
1 TCAAA
2905152 GATATGGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (15 bp):
TCAAATATTGGAAAG
Found at i:2906218 original size:33 final size:33
Alignment explanation
Indices: 2906181--2906256 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 33
2906171 ATGTAATATT
* * *
2906181 ATTTTATATGTGTATAATTACATTA-AAATTAAA
1 ATTTTATATGTATATAATTAAATCACAAA-TAAA
*
2906214 ATTTTATA--TATATACTTAAATCACAAATAAA
1 ATTTTATATGTATATAATTAAATCACAAATAAA
2906245 ATTTTATATGTA
1 ATTTTATATGTA
2906257 AAATTATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 23 0.64
32 3 0.08
33 10 0.28
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (33 bp):
ATTTTATATGTATATAATTAAATCACAAATAAA
Found at i:2906269 original size:29 final size:30
Alignment explanation
Indices: 2906210--2906275 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
2906200 ACATTAAAAT
* *
2906210 TAAAATTTTATATATATACTTAAATCACAAA
1 TAAAATTTTATATATAAAATTAAAT-ACAAA
* *
2906241 TAAAATTTTATATGTAAAATTATAT-CAAA
1 TAAAATTTTATATATAAAATTAAATACAAA
*
2906270 TCAAAT
1 TAAAAT
2906276 CAAAATTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 9 0.30
31 21 0.70
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAATTTTATATATAAAATTAAATACAAA
Found at i:2914708 original size:31 final size:30
Alignment explanation
Indices: 2914657--2914715 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
2914647 TGTGAAATGT
*
2914657 AAGACCATAATGGATCTATGGCATAGTGTGA
1 AAGACCATAATGGA-CTATGGCACAGTGTGA
2914688 AAGACCATAACTGAGA-TATGGCACAGTG
1 AAGACCATAA-TG-GACTATGGCACAGTG
2914716 AAAGTGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 21 0.84
32 2 0.08
33 2 0.08
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (30 bp):
AAGACCATAATGGACTATGGCACAGTGTGA
Found at i:2919329 original size:30 final size:31
Alignment explanation
Indices: 2919294--2919359 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2919284 CTACTTGGTA
* *
2919294 TTTTAGTTTGGGT-AATATTAGTCATTTTAT
1 TTTTAGATTCGGTCAATATTAGTCATTTTAT
* *
2919324 TTTTAGATTCGGTCAATTTTAGTCTTTTTAT
1 TTTTAGATTCGGTCAATATTAGTCATTTTAT
2919355 TTTTA
1 TTTTA
2919360 AAATTTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.21, C:0.06, G:0.14, T:0.59
Consensus pattern (31 bp):
TTTTAGATTCGGTCAATATTAGTCATTTTAT
Found at i:2921826 original size:100 final size:101
Alignment explanation
Indices: 2921710--2921911 Score: 388
Period size: 100 Copynumber: 2.0 Consensus size: 101
2921700 ATAATACATT
2921710 AAATGCACTAAAAGCATTAAAATAAATGCTTTCCAACAAATTGAAAATACA-TAAAAAAATATTT
1 AAATGCACTAAAAGCATTAAAATAAATGCTTTCCAACAAATTGAAAATACATTAAAAAAATATTT
2921774 ATACTTAAATAACACTAAAATATGTGCAATTTAACA
66 ATACTTAAATAACACTAAAATATGTGCAATTTAACA
2921810 AAATGCACTAAAAGCATTAAAATAAATGCTTTCCAACAAATTGAAAATACATTAAAAAAATATTT
1 AAATGCACTAAAAGCATTAAAATAAATGCTTTCCAACAAATTGAAAATACATTAAAAAAATATTT
*
2921875 ATACTTAAATAACACTAAGATATGTGCAATTTAACA
66 ATACTTAAATAACACTAAAATATGTGCAATTTAACA
2921911 A
1 A
2921912 TCAAATGTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 51 0.51
101 49 0.49
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (101 bp):
AAATGCACTAAAAGCATTAAAATAAATGCTTTCCAACAAATTGAAAATACATTAAAAAAATATTT
ATACTTAAATAACACTAAAATATGTGCAATTTAACA
Found at i:2922640 original size:23 final size:23
Alignment explanation
Indices: 2922605--2922649 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2922595 AAAAATAATT
*
2922605 TTTTTACTGTTTTCTTATTGTTG
1 TTTTTACTATTTTCTTATTGTTG
* *
2922628 TTTTTGCTATTTTCTTGTTGTT
1 TTTTTACTATTTTCTTATTGTT
2922650 TTCACTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.09, G:0.13, T:0.71
Consensus pattern (23 bp):
TTTTTACTATTTTCTTATTGTTG
Found at i:2922894 original size:13 final size:14
Alignment explanation
Indices: 2922873--2922907 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2922863 TATTTTTTAA
2922873 AAAAAAATAATA-T
1 AAAAAAATAATATT
*
2922886 AAAATAATAATATT
1 AAAAAAATAATATT
2922900 AAAAAAAT
1 AAAAAAAT
2922908 TTAACACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAAATAATATT
Found at i:2926477 original size:39 final size:39
Alignment explanation
Indices: 2926433--2926509 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
2926423 TGATAAACCT
2926433 TCAAAACAAAAAAATAAAGAAGGCTACCCATTTTCAGAA
1 TCAAAACAAAAAAATAAAGAAGGCTACCCATTTTCAGAA
2926472 TCAAAACAAAAAAATAAAGAAGGCTACCCATTTTCAGA
1 TCAAAACAAAAAAATAAAGAAGGCTACCCATTTTCAGA
2926510 CTCCCTTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.18
Consensus pattern (39 bp):
TCAAAACAAAAAAATAAAGAAGGCTACCCATTTTCAGAA
Found at i:2934386 original size:43 final size:42
Alignment explanation
Indices: 2934325--2934440 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 42
2934315 ATAATTTCGT
*
2934325 TGAACTTGAGTGATTCAGATTGTGATTAATATATATTTTCAGA
1 TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTT-AGA
* * *
2934368 TGAACTTAAGTGATTCAGATTGTGATCAAATATGTATTTTTGA
1 TGAACTTAAGTGATTCAGATTGTGAT-TAATATATATTTTAGA
*
2934411 TGAACTTTAAGTGATTCA-TTTGTGATTAAT
1 TGAAC-TTAAGTGATTCAGATTGTGATTAAT
2934441 TTTGGGGTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
42 3 0.05
43 39 0.60
44 23 0.35
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (42 bp):
TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTTAGA
Found at i:2941978 original size:15 final size:15
Alignment explanation
Indices: 2941958--2941997 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2941948 ACTTGAACAC
* *
2941958 CTGCAGCAGGAGGAG
1 CTGCAGCAGCAGCAG
2941973 CTGCAGCAGCAGCAG
1 CTGCAGCAGCAGCAG
*
2941988 CAGCAGCAGC
1 CTGCAGCAGC
2941998 TTTTCTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.38, T:0.05
Consensus pattern (15 bp):
CTGCAGCAGCAGCAG
Found at i:2952299 original size:29 final size:30
Alignment explanation
Indices: 2952252--2952319 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2952242 TGGCCCAAGA
* *
2952252 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
2952282 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
2952312 GCAAATAT
1 GTAAATAT
2952320 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:2954809 original size:46 final size:46
Alignment explanation
Indices: 2954742--2954829 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
2954732 AGTGTGCTCT
*
2954742 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAAAGACCATGGCAGC
2954788 CTGATATGAAATGTGTAAGACCATGGTTGAAAAAGACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAAAGACCATGG
2954830 TTGAAAGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAAAGACCATGGCAGC
Found at i:2954845 original size:16 final size:16
Alignment explanation
Indices: 2954804--2954835 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2954794 TGAAATGTGT
2954804 AAGACCATGGTTGAAA
1 AAGACCATGGTTGAAA
2954820 AAGACCATGGTTGAAA
1 AAGACCATGGTTGAAA
2954836 GATACTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
AAGACCATGGTTGAAA
Found at i:2954855 original size:62 final size:62
Alignment explanation
Indices: 2954758--2954891 Score: 223
Period size: 62 Copynumber: 2.2 Consensus size: 62
2954748 TGAAATGTGT
*
2954758 AAGACCATGGTTGAAAGAGACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGTTGAAA
1 AAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAA
* *
2954820 AAGACCATGGTTGAAAGATACTATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAA
1 AAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAA
* *
2954882 GATACCATGG
1 AAGACCATGG
2954892 CAACCTGATA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (62 bp):
AAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAA
Found at i:2954870 original size:46 final size:46
Alignment explanation
Indices: 2954820--2954985 Score: 244
Period size: 46 Copynumber: 3.6 Consensus size: 46
2954810 ATGGTTGAAA
*
2954820 AAGACCATGGTTGAAAGATACTATGGCAACCTGATATGAAATGTGT
1 AAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGT
2954866 AAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGT
1 AAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGT
* * *
2954912 AAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGT
1 AAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGT
* * * *
2954958 AAGGCCATAGTTGAAAGACACTATGGCA
1 AAGACCATGGTTGAAAGATACCATGGCA
2954986 TCATGTTAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
45 1 0.01
46 110 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
AAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGT
Found at i:2954935 original size:108 final size:108
Alignment explanation
Indices: 2954742--2954937 Score: 356
Period size: 108 Copynumber: 1.8 Consensus size: 108
2954732 AGTGTGCTCT
*
2954742 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAGCCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAG
2954807 ACCATGGTTGAAAAAGACCATGGTTGAAAGATACTATGGCAAC
66 ACCATGGTTGAAAAAGACCATGGTTGAAAGATACTATGGCAAC
*
2954850 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAG
* *
2954915 ACCATGGTTGAAAGATACCATGG
66 ACCATGGTTGAAAAAGACCATGG
2954938 CAACATGACA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (108 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAACCTGATATGAAATGTGTAAG
ACCATGGTTGAAAAAGACCATGGTTGAAAGATACTATGGCAAC
Found at i:2956334 original size:261 final size:261
Alignment explanation
Indices: 2955870--2956383 Score: 992
Period size: 261 Copynumber: 2.0 Consensus size: 261
2955860 GTTAAGCATA
*
2955870 GTTCGATTCGAGCTTTGCTTGGTATTGTGGCCATGCCTGATTTGGAGCTTGAGCAGTTAGATGTA
1 GTTCGATTCGAGCTTTGCTTGGTATTGTGGCCATGCATGATTTGGAGCTTGAGCAGTTAGATGTA
*
2955935 AAAACTGCATTTTTGCATGGAGAACTTGAGGAGGATACTTACATGCAACAACCAGAGGGTTTTAT
66 AAAACTGCATTTCTGCATGGAGAACTTGAGGAGGATACTTACATGCAACAACCAGAGGGTTTTAT
*
2956000 AGTCTCAGAAAAAGAGGACTATGTTTGCTTGCTGAAAAAGTCTCTTTACGATTTGAAACAGTCAC
131 AGTATCAGAAAAAGAGGACTATGTTTGCTTGCTGAAAAAGTCTCTTTACGATTTGAAACAGTCAC
2956065 CAAGACAGTGGTACAAGAGGTTTGATTCCTTTATGACTTCTCATGATTTCAAAAGAAGACAGTTG
196 CAAGACAGTGGTACAAGAGGTTTGATTCCTTTATGACTTCTCATGATTTCAAAAGAAGACAGTTG
2956130 T
261 T
*
2956131 GTTCGATTCGAGCTTTTCTTGGTATTGTGGCCATGCATGATTTGGAGCTTGAGCAGTTAGATGTA
1 GTTCGATTCGAGCTTTGCTTGGTATTGTGGCCATGCATGATTTGGAGCTTGAGCAGTTAGATGTA
2956196 AAAACTGCATTTCTGCATGGAGAACTTGAGGAGGATACTTACATGCAACAACCAGAGGGTTTTAT
66 AAAACTGCATTTCTGCATGGAGAACTTGAGGAGGATACTTACATGCAACAACCAGAGGGTTTTAT
2956261 AGTATCAGAAAAAGAGGACTATGTTTGCTTGCTGAAAAAGTCTCTTTACGATTTGAAACAGTCAC
131 AGTATCAGAAAAAGAGGACTATGTTTGCTTGCTGAAAAAGTCTCTTTACGATTTGAAACAGTCAC
2956326 CAAGACAGTGGTACAAGAGGTTTGATTCCTTTATGACTTCTCATGATTTCAAAAGAAG
196 CAAGACAGTGGTACAAGAGGTTTGATTCCTTTATGACTTCTCATGATTTCAAAAGAAG
2956384 TAGTTTTGAC
Statistics
Matches: 249, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
261 249 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (261 bp):
GTTCGATTCGAGCTTTGCTTGGTATTGTGGCCATGCATGATTTGGAGCTTGAGCAGTTAGATGTA
AAAACTGCATTTCTGCATGGAGAACTTGAGGAGGATACTTACATGCAACAACCAGAGGGTTTTAT
AGTATCAGAAAAAGAGGACTATGTTTGCTTGCTGAAAAAGTCTCTTTACGATTTGAAACAGTCAC
CAAGACAGTGGTACAAGAGGTTTGATTCCTTTATGACTTCTCATGATTTCAAAAGAAGACAGTTG
T
Found at i:2957841 original size:10 final size:11
Alignment explanation
Indices: 2957826--2957854 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2957816 TTATGTGTTC
2957826 TTTATTTTA-T
1 TTTATTTTATT
2957836 TTTATTTTATT
1 TTTATTTTATT
2957847 TTTATTTT
1 TTTATTTT
2957855 TTACAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2960597 original size:43 final size:43
Alignment explanation
Indices: 2960533--2960618 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
2960523 TATATGATTG
* *
2960533 ATATTGAAATGGTAAAGATGAGAAATGAATACGAGATGAGAAA
1 ATATTGAAATGGCAAAAATGAGAAATGAATACGAGATGAGAAA
*
2960576 ATATTGAAATGGCAAAAATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGCAAAAATGAGAAATGAATACGAGATGAGAAA
2960619 TGTAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.21
Consensus pattern (43 bp):
ATATTGAAATGGCAAAAATGAGAAATGAATACGAGATGAGAAA
Found at i:2960627 original size:19 final size:18
Alignment explanation
Indices: 2960591--2960641 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
2960581 GAAATGGCAA
2960591 AAATGAGAAATGAATATG
1 AAATGAGAAATGAATATG
*
2960609 AGATGAGAAATGTAATATG
1 AAATGAGAAATG-AATATG
2960628 AAATGATGAAATGA
1 AAATGA-GAAATGA
2960642 GATGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 12 0.41
20 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATGAGAAATGAATATG
Found at i:2961169 original size:24 final size:24
Alignment explanation
Indices: 2961123--2961169 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2961113 GGTTTAAGCT
*
2961123 ATGTTTTGGTATGTAGTTTAGTTA
1 ATGTTTTGGTATGTAGTTAAGTTA
*
2961147 ATGTTTTTGTATGT-GTATAAGTT
1 ATGTTTTGGTATGTAGT-TAAGTT
2961170 TTAAAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.55
Consensus pattern (24 bp):
ATGTTTTGGTATGTAGTTAAGTTA
Found at i:2964183 original size:44 final size:44
Alignment explanation
Indices: 2964103--2964193 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
2964093 AACTCTGTTT
* * *
2964103 TTAGTTTTCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATA
1 TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
* *
2964147 TTAGTTTCCCACTTAAACCCTGATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
2964191 TTA
1 TTA
2964194 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
Found at i:2965362 original size:97 final size:98
Alignment explanation
Indices: 2965195--2965476 Score: 433
Period size: 98 Copynumber: 2.9 Consensus size: 98
2965185 TTAAAAAGAG
*
2965195 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAACATAATTAATGCAGCTCAAATGTTCA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAACATAATTAATGCAGTTCAAATGTTCA
2965260 ATACAAGCATCTAAGCATAATAGAATAATCGAT
66 ATACAAGCATCTAAGCATAATAGAATAATCGAT
* * *
2965293 GCAAATGAGTTACCACAAAGGCATCTATGT-AAAGAAAACATAATTGATGCAGTTCAAATGTTCA
1 GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAACATAATTAATGCAGTTCAAATGTTCA
* **
2965357 ATACAAGCATTTAAGCATAATATCATAATCGAT
66 ATACAAGCATCTAAGCATAATAGAATAATCGAT
* * * * *
2965390 GCAAAATGAGTTAGCATAAAGG-ATTTAAGTAAAAAAAAACATAATTAATGCAATTCAAATGTTT
1 GC-AAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAACATAATTAATGCAGTTCAAATGTTC
2965454 AATACAAGCATCTAAGCATAATA
65 AATACAAGCATCTAAGCATAATA
2965477 CCATGATTGA
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
97 69 0.42
98 97 0.58
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (98 bp):
GCAAATGAGTTACCACAAAGGCATCTAAGTAAAAAAAAACATAATTAATGCAGTTCAAATGTTCA
ATACAAGCATCTAAGCATAATAGAATAATCGAT
Found at i:2965385 original size:49 final size:48
Alignment explanation
Indices: 2965329--2965496 Score: 121
Period size: 49 Copynumber: 3.4 Consensus size: 48
2965319 ATGTAAAGAA
2965329 AACATAATTGATGCAGTTCAAATGTTCAATACAAGCATTTAAGCATAAT
1 AACATAATTGATGCAGTTCAAATGTT-AATACAAGCATTTAAGCATAAT
* * * * * *
2965378 ATCATAATCGATGCA----AAATGAGTTAGCATA-AAGGATTTAAGTAAAAAAA
1 AACATAATTGATGCAGTTCAAAT--GTTA--ATACAAGCATTTAAG--CATAAT
* * *
2965427 AACATAATTAATGCAATTCAAATGTTTAATACAAGCATCTAAGCATAAT
1 AACATAATTGATGCAGTTCAAATG-TTAATACAAGCATTTAAGCATAAT
* * *
2965476 ACCATGATTGATGTAGTTCAA
1 AACATAATTGATGCAGTTCAA
2965497 TACAAGCATC
Statistics
Matches: 88, Mismatches: 19, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
45 4 0.05
46 1 0.01
47 13 0.15
48 3 0.03
49 47 0.53
50 3 0.03
51 10 0.11
52 3 0.03
53 4 0.05
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (48 bp):
AACATAATTGATGCAGTTCAAATGTTAATACAAGCATTTAAGCATAAT
Found at i:2966577 original size:15 final size:16
Alignment explanation
Indices: 2966547--2966579 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2966537 ATATTAATGT
*
2966547 TATTTAATCTTTAAAA
1 TATTTAATCATTAAAA
2966563 TATTTAAT-ATTAAAA
1 TATTTAATCATTAAAA
2966578 TA
1 TA
2966580 ATACAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATCATTAAAA
Found at i:2968614 original size:60 final size:62
Alignment explanation
Indices: 2968530--2968704 Score: 230
Period size: 60 Copynumber: 2.8 Consensus size: 62
2968520 CTACCGCTAT
* * * *
2968530 TATTTTTTTCGGGTAACTGTTTTGCTGTCTCTTCACGTCTCTTTGCAACCCTTGCTGCTATT-
1 TATTTTTTTC-GGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTGCTATTA
** * *
2968592 T-TTTTTTTTTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCTGCTATTA
1 TATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTGCTATTA
*
2968653 TATTTTTTTCGGCAACTACTTTGCTGCCTCTTCACGTCT-TTCTGCAACCCCT
1 TATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTT-TGCAACCCCT
2968705 ACTGATTTGC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
60 44 0.45
61 9 0.09
62 44 0.45
ACGTcount: A:0.13, C:0.29, G:0.14, T:0.45
Consensus pattern (62 bp):
TATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTTTGCAACCCCTGCTGCTATTA
Found at i:2968675 original size:62 final size:61
Alignment explanation
Indices: 2968525--2968704 Score: 238
Period size: 62 Copynumber: 3.0 Consensus size: 61
2968515 CTGCCCTACC
* * * * *
2968525 GCTA-TTATTTTTTTCGGGTAACTGTTTTGCTGTCTCTTCACGTCTCTTTGCAACCCTTGCT
1 GCTATTTATTTTTTTC-GGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
** *
2968586 GCTATTT-TTTTTTTTTGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGCT
1 GCTATTTATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
* *
2968646 GCTATTATATTTTTTTCGGCAACTACTTTGCTGCCTCTTCACGTCTTTCTGCAACCCCT
1 GCTATT-TATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCT
2968705 ACTGATTTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
60 44 0.43
61 12 0.12
62 47 0.46
ACGTcount: A:0.13, C:0.28, G:0.14, T:0.45
Consensus pattern (61 bp):
GCTATTTATTTTTTTCGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
Found at i:2971735 original size:46 final size:44
Alignment explanation
Indices: 2971631--2971738 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2971621 TGTCTTTGAC
** * * *
2971631 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2971675 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2971721 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2971739 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2978008 original size:3 final size:3
Alignment explanation
Indices: 2978000--2978484 Score: 203
Period size: 3 Copynumber: 163.3 Consensus size: 3
2977990 TAATGAGAAC
* * *
2978000 AAT AAT AAT AAT ATT AAT AAT AAT AAT AAC AAT AAT AGT AA- AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
2978046 AAT AAT ACT AAT GAT AAT AAT AAT AGT AAT AAT AAG AAT ATT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
2978094 AGT AAT AAT AAT GAT AAT AGT AAT AGAA AAG AAA AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* *
2978139 AAT -AT AAT AAT AAT AAT AGT AAAT AA- AAGT AA- AAGT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AA-T AAT AAT AAT
** * * * * *
2978184 AAT AAT GGT AAT AAT AAAT AGT AAT AAT AAC AAT AAC AAA AAT AGT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** * * * *
2978230 AAT AAT -GT ATT AAAT GGT AA- AAG AAT AAT AGT AAC AAT AAT -TT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
2978273 AA- AA- AAT GAT AAT AGT AAT AA- AAT AA- GAT TAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
2978317 AAT AAT AAA AAT GAA- CAT AAA AAA AGAT AGT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * * * * ** **
2978363 AAT AGT AAT AGT AA- AAGG AAT AAT AAT AGT AAT AAT AAG AGC GTT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * ** *
2978408 AAT TCT AAT AAA AAT ACA- AAT AAT AAT ATAT ATGT ACG AAA AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT
*
2978455 AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2978485 GAAGTAGTAA
Statistics
Matches: 350, Mismatches: 106, Indels: 52
0.69 0.21 0.10
Matches are distributed among these distances:
2 29 0.08
3 295 0.84
4 26 0.07
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2978466 original size:14 final size:14
Alignment explanation
Indices: 2978447--2978484 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2978437 ATATGTACGA
*
2978447 AAAATAATAATAGT
1 AAAATAATAATAAT
2978461 AAAATAATAATAAT
1 AAAATAATAATAAT
2978475 AATAATAATA
1 AA-AATAATA
2978485 GAAGTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:2978469 original size:17 final size:19
Alignment explanation
Indices: 2978422--2978475 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
2978412 CTAATAAAAA
2978422 TACAAATAATAATATATATG
1 TACAAATAATAATA-ATATG
2978442 TACGAAA-AATAATAATA-G
1 TAC-AAATAATAATAATATG
2978460 TA-AAATAATAATAATA
1 TACAAATAATAATAATA
2978476 ATAATAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 3 0.09
19 3 0.09
20 10 0.31
21 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (19 bp):
TACAAATAATAATAATATG
Found at i:2986569 original size:11 final size:11
Alignment explanation
Indices: 2986553--2986589 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2986543 ATTAAAGTAG
2986553 ATTTTAATGTA
1 ATTTTAATGTA
*
2986564 ATTTTAAAGTA
1 ATTTTAATGTA
2986575 GATTTTAATGTA
1 -ATTTTAATGTA
2986587 ATT
1 ATT
2986590 GTGTTGTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (11 bp):
ATTTTAATGTA
Found at i:2986571 original size:23 final size:23
Alignment explanation
Indices: 2986544--2986589 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2986534 AAACCTTATA
2986544 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2986567 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2986590 GTGTTGTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (23 bp):
TTAAAGTAGATTTTAATGTAATT
Found at i:2986581 original size:12 final size:12
Alignment explanation
Indices: 2986544--2986582 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2986534 AAACCTTATA
2986544 TTAAAGTAGATT
1 TTAAAGTAGATT
*
2986556 TTAATGTA-ATT
1 TTAAAGTAGATT
2986567 TTAAAGTAGATT
1 TTAAAGTAGATT
2986579 TTAA
1 TTAA
2986583 TGTAATTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (12 bp):
TTAAAGTAGATT
Found at i:2991640 original size:18 final size:18
Alignment explanation
Indices: 2991600--2991640 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2991590 CTAATTTTTT
2991600 AAAAATTATTAAAAATAA
1 AAAAATTATTAAAAATAA
*
2991618 TAAAATGTA-TAAAAATAA
1 AAAAAT-TATTAAAAATAA
2991636 AAAAA
1 AAAAA
2991641 ACAATACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAATTATTAAAAATAA
Found at i:2991834 original size:27 final size:26
Alignment explanation
Indices: 2991803--2991866 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
2991793 TTTATCAAGG
*
2991803 TTATTAGTTTATCGATAAA-TAAATATT
1 TTATTAATTTATCGATAAAGT-AATA-T
2991830 TTATTAATTTATCGATAAAGTAATAT
1 TTATTAATTTATCGATAAAGTAATAT
2991856 TTATTAATTTA
1 TTATTAATTTA
2991867 GAGAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 12 0.34
27 22 0.63
28 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (26 bp):
TTATTAATTTATCGATAAAGTAATAT
Found at i:2991901 original size:3 final size:3
Alignment explanation
Indices: 2991893--2991919 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2991883 TTATTCATGG
2991893 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2991920 CAAAATCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2993261 original size:182 final size:187
Alignment explanation
Indices: 2992945--2993296 Score: 633
Period size: 182 Copynumber: 1.9 Consensus size: 187
2992935 CATCCCAAGG
2992945 TTATTGAAGGCTTGAGAAATGTTGAATTATTCTTTTTGCCTCCAAAATCAACATAAAAAATTCAA
1 TTATTGAAGGCTTGAGAAATGTTGAATTATTCTTTTTGCCTCC---A-CAACATAAAAAATTCAA
2993010 TCATGTGATGCTAGAATTATTAGAGCAGTTAAGATTTATTATAGGCATCGCTTTTATTCTAGCAT
62 TCATGTGATGCTAGAATTATTAGAGCAGTTAAGATTTATTATAGGCATCGCTTTTATTCTAGCAT
2993075 CTTGGAAGTTTACAAGAAATGAGAAATAAATCCTAAAAAGTATACATTGCCCATGCATCCA
127 CTTGGAAGTTTACAAGAAATGAGAAATAAATCCTAAAAAGTATACATTGCCCATGCATCCA
2993136 TTATTGAAGGCTTGAGAAATGTTG-ATTATTCTTTTTGCCT-C-C-A-ATAAAAAATTCAATCAT
1 TTATTGAAGGCTTGAGAAATGTTGAATTATTCTTTTTGCCTCCACAACATAAAAAATTCAATCAT
2993196 GTGATGCTAGAATTATTAGAGCAGTTAAGATTTATTATAGGCATCGCTTTTATTCTAGCATCTTG
66 GTGATGCTAGAATTATTAGAGCAGTTAAGATTTATTATAGGCATCGCTTTTATTCTAGCATCTTG
2993261 GAAGTTTACAAGAAATGAGAAATAAATCCTAAAAAG
131 GAAGTTTACAAGAAATGAGAAATAAATCCTAAAAAG
2993297 ATTAATGTAT
Statistics
Matches: 161, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
182 118 0.73
183 1 0.01
184 1 0.01
189 1 0.01
190 16 0.10
191 24 0.15
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (187 bp):
TTATTGAAGGCTTGAGAAATGTTGAATTATTCTTTTTGCCTCCACAACATAAAAAATTCAATCAT
GTGATGCTAGAATTATTAGAGCAGTTAAGATTTATTATAGGCATCGCTTTTATTCTAGCATCTTG
GAAGTTTACAAGAAATGAGAAATAAATCCTAAAAAGTATACATTGCCCATGCATCCA
Found at i:2995659 original size:20 final size:20
Alignment explanation
Indices: 2995613--2995662 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2995603 TTAATTGATT
*
2995613 TATATTTTTTTTAAATTTAA
1 TATATTTTTTTTAAAATTAA
* *
2995633 GAGATTTTTTTTAAAAATT-A
1 TATATTTTTTTT-AAAATTAA
2995653 TATATTTTTT
1 TATATTTTTT
2995663 AATTTGCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TATATTTTTTTTAAAATTAA
Found at i:2996460 original size:29 final size:29
Alignment explanation
Indices: 2996428--2996490 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
2996418 TAGATTCCTC
* *
2996428 AAAAGTTGGGAAAAAAATTTAGGTCCCTT
1 AAAAGTAGGGAAAAAAATTTAGGGCCCTT
* *
2996457 AAAAGTAGGTAAAAAAATTTTGGGCCCTT
1 AAAAGTAGGGAAAAAAATTTAGGGCCCTT
2996486 AAAAG
1 AAAAG
2996491 CTAAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (29 bp):
AAAAGTAGGGAAAAAAATTTAGGGCCCTT
Found at i:3001925 original size:21 final size:21
Alignment explanation
Indices: 3001899--3001939 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3001889 ATCTGCTCAA
* *
3001899 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3001920 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3001940 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3020213 original size:17 final size:17
Alignment explanation
Indices: 3020191--3020234 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3020181 CCATGTGTGT
3020191 TGCCCGTGTGTGACATA
1 TGCCCGTGTGTGACATA
3020208 TGCCCGTGTGTGACATA
1 TGCCCGTGTGTGACATA
* *
3020225 CGCCCCTGTG
1 TGCCCGTGTG
3020235 GCCAGGCCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (17 bp):
TGCCCGTGTGTGACATA
Found at i:3021154 original size:16 final size:16
Alignment explanation
Indices: 3021133--3021197 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 16
3021123 ATCTCATAAT
3021133 CATTTCTCATATTTTC
1 CATTTCTCATATTTTC
*
3021149 CATTTC-AATATTTTC
1 CATTTCTCATATTTTC
3021164 TCA--TCTCATA--TT-
1 -CATTTCTCATATTTTC
* *
3021176 CATTTATCATCTTTTC
1 CATTTCTCATATTTTC
3021192 CATTTC
1 CATTTC
3021198 AAAATCAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
11 2 0.05
13 7 0.19
14 2 0.05
15 13 0.35
16 13 0.35
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.54
Consensus pattern (16 bp):
CATTTCTCATATTTTC
Found at i:3021169 original size:43 final size:43
Alignment explanation
Indices: 3021118--3021199 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
3021108 CATATTTCAA
*
3021118 TTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATATT
1 TTCTCATCTCATAATCATTTATCATATTTTCCATTTCAATATT
* *
3021161 TTCTCATCTCATATTCATTTATCATCTTTTCCATTTCAA
1 TTCTCATCTCATAATCATTTATCATATTTTCCATTTCAA
3021200 AATCAATCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (43 bp):
TTCTCATCTCATAATCATTTATCATATTTTCCATTTCAATATT
Found at i:3025059 original size:20 final size:20
Alignment explanation
Indices: 3025030--3025069 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3025020 CAAAGTGAAC
*
3025030 ATGGAGACTATGAGTGATAG
1 ATGGAAACTATGAGTGATAG
3025050 ATGGAAACTATGAGTGATAG
1 ATGGAAACTATGAGTGATAG
3025070 TGATGAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.25
Consensus pattern (20 bp):
ATGGAAACTATGAGTGATAG
Found at i:3027255 original size:16 final size:17
Alignment explanation
Indices: 3027224--3027257 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3027214 AATAAAAAAT
*
3027224 GAATACTACGATATAAA
1 GAATAATACGATATAAA
3027241 GAATAATAC-ATATAAA
1 GAATAATACGATATAAA
3027257 G
1 G
3027258 CAAAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
GAATAATACGATATAAA
Found at i:3027934 original size:17 final size:18
Alignment explanation
Indices: 3027914--3027950 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3027904 AGTAATTAAT
*
3027914 AAATATAAT-ATATGTGA
1 AAATATAATAATATATGA
3027931 AAATATAATAATATATGA
1 AAATATAATAATATATGA
3027949 AA
1 AA
3027951 GAGATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATAATAATATATGA
Found at i:3030158 original size:83 final size:83
Alignment explanation
Indices: 3029842--3030277 Score: 728
Period size: 83 Copynumber: 5.2 Consensus size: 83
3029832 TTCGATTTGT
* * * * *
3029842 AAGGATGTCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAATCATATCTGCAAGGTTCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
*
3029907 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
3029925 AAGGATGCCTAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCG
3029990 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* * *
3030009 AATGATGCCTAAACCATCTTGAGTCTATTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCG
3030074 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
3030093 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
3030158 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
3030176 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTTATATCTGCAACGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
3030241 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
3030259 AAGGATACCAAATCATCTT
1 AAGGATGCCAAACCATCTT
3030278 AGATCTGCTT
Statistics
Matches: 338, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 179 0.53
84 159 0.47
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:3030471 original size:202 final size:202
Alignment explanation
Indices: 3030119--3030521 Score: 662
Period size: 202 Copynumber: 2.0 Consensus size: 202
3030109 CTTGAGTCTG
* * *
3030119 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATCTGAGAGTCAAATCTGCAACGTCCTCGATTTGTCCCTTGTAAGCACAAGGATGC
* * * *
3030184 CAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTTATATCTGCAACGTCCTCGATTTGTTCC
66 CAAACCATCTTGAGTCTGTTTAAGAACATTTGAGAGTCATATCTACAACGTCCTCGATTTGTTCC
* * * *
3030249 TTGTAAGCACAAGGATACCAAATCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTTAGATC
131 TTGTAAACACAAGAATACCAAATCATCTTAGATCTGCCTCAGTATAAACATCTAAAGGTTAGATC
3030314 TGCTATA
196 TGCTATA
* * *
3030321 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTCCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATCTGAGAGTCAAATCTGCAACGTCCTCGATTTGTCCCTTGTAAGCACAAGGATGC
*
3030386 CAAACCATCTTGAGTTTGTTTAAGAACATTTGAGAGTCATATCTACAACGTCCTCGATTTGTTCC
66 CAAACCATCTTGAGTCTGTTTAAGAACATTTGAGAGTCATATCTACAACGTCCTCGATTTGTTCC
*
3030451 TTGTAAACACAAGAATACCAAATCATCTTGGATCTGCCTCAGTATAAACATCTAAAGGTTAGATC
131 TTGTAAACACAAGAATACCAAATCATCTTAGATCTGCCTCAGTATAAACATCTAAAGGTTAGATC
3030516 TGCTAT
196 TGCTAT
3030522 TTTCAATTTG
Statistics
Matches: 185, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
202 185 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (202 bp):
TTTGAGAACATCTGAGAGTCAAATCTGCAACGTCCTCGATTTGTCCCTTGTAAGCACAAGGATGC
CAAACCATCTTGAGTCTGTTTAAGAACATTTGAGAGTCATATCTACAACGTCCTCGATTTGTTCC
TTGTAAACACAAGAATACCAAATCATCTTAGATCTGCCTCAGTATAAACATCTAAAGGTTAGATC
TGCTATA
Found at i:3035096 original size:19 final size:19
Alignment explanation
Indices: 3035072--3035111 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3035062 AATATAGATG
3035072 AACATAAGCCTATTTTCGC
1 AACATAAGCCTATTTTCGC
3035091 AACATAAGCCTATTTTCGC
1 AACATAAGCCTATTTTCGC
3035110 AA
1 AA
3035112 ATGTAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (19 bp):
AACATAAGCCTATTTTCGC
Found at i:3041967 original size:16 final size:17
Alignment explanation
Indices: 3041936--3041969 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3041926 AATAAAAAAT
*
3041936 GAATACTACGATATAAA
1 GAATAATACGATATAAA
3041953 GAATAATAC-ATATAAA
1 GAATAATACGATATAAA
3041969 G
1 G
3041970 CAAAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
GAATAATACGATATAAA
Found at i:3042654 original size:17 final size:18
Alignment explanation
Indices: 3042634--3042670 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3042624 AGTAATTAAT
*
3042634 AAATATAAT-ATATGTGA
1 AAATATAATAATATATGA
3042651 AAATATAATAATATATGA
1 AAATATAATAATATATGA
3042669 AA
1 AA
3042671 GAGATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATAATAATATATGA
Found at i:3042912 original size:26 final size:25
Alignment explanation
Indices: 3042882--3042941 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3042872 TTTTGAAAGG
*
3042882 AATAAAACTGAATTAAGGATTAAAAT
1 AATAAAACT-AAGTAAGGATTAAAAT
*
3042908 AATAAATAATAAGTAAGGATTAAAAT
1 AATAAA-ACTAAGTAAGGATTAAAAT
3042934 --TAAAACTA
1 AATAAAACTA
3042942 GATAGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 3 0.10
24 4 0.13
26 21 0.70
27 2 0.07
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (25 bp):
AATAAAACTAAGTAAGGATTAAAAT
Found at i:3065701 original size:26 final size:26
Alignment explanation
Indices: 3065672--3065725 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
3065662 TAAACCAAAA
* *
3065672 TTTTTAAAAATATTTTTTAAAATCAC
1 TTTTTAAAAACATTTTTTAAAAGCAC
* *
3065698 TTTTTCACAACATTTTTTAAAAGCAC
1 TTTTTAAAAACATTTTTTAAAAGCAC
3065724 TT
1 TT
3065726 CTCAAAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTAAAAACATTTTTTAAAAGCAC
Found at i:3066997 original size:16 final size:16
Alignment explanation
Indices: 3066966--3066995 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3066956 TGTATCTTTC
3066966 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
3066982 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
3066996 TACTACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:3072124 original size:21 final size:21
Alignment explanation
Indices: 3072098--3072138 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3072088 AGACGAGCAA
* *
3072098 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3072119 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3072139 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3086684 original size:26 final size:25
Alignment explanation
Indices: 3086654--3086714 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
3086644 AATCATATAA
3086654 CATTTCAATAACCAT-ATAAACATATC
1 CATTTCAAT-ACC-TCATAAACATATC
* *
3086680 CATTTTCCATGCCTCATAAACATATC
1 CA-TTTCAATACCTCATAAACATATC
*
3086706 CTTTTCAAT
1 CATTTCAAT
3086715 TTATCTCATG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 7 0.24
26 16 0.55
27 6 0.21
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (25 bp):
CATTTCAATACCTCATAAACATATC
Found at i:3092506 original size:18 final size:17
Alignment explanation
Indices: 3092483--3092551 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
3092473 CCCAACTACT
*
3092483 GTATACGTGAACAGTGTC
1 GTATACGTGAATAGT-TC
*
3092501 GTATACGTGAATAGTACC
1 GTATACGTGAATAGT-TC
* *
3092519 ATATACGTAAATAGTTC
1 GTATACGTGAATAGTTC
3092536 TGTATACGTGAATAGT
1 -GTATACGTGAATAGT
3092552 ACCGTAAACG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 1 0.02
18 41 0.98
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (17 bp):
GTATACGTGAATAGTTC
Found at i:3092541 original size:36 final size:36
Alignment explanation
Indices: 3092484--3092554 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
3092474 CCAACTACTG
*
3092484 TATACGTGAACAGTGTCGTATACGTGAATAGTACCA
1 TATACGTAAACAGTGTCGTATACGTGAATAGTACCA
*
3092520 TATACGTAAATAGT-TCTGTATACGTGAATAGTACC
1 TATACGTAAACAGTGTC-GTATACGTGAATAGTACC
3092555 GTAAACGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (36 bp):
TATACGTAAACAGTGTCGTATACGTGAATAGTACCA
Found at i:3104107 original size:20 final size:21
Alignment explanation
Indices: 3104078--3104117 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3104068 ATTTTAGTCA
*
3104078 CACAATTTTTTTAAT-TTAAT
1 CACAAATTTTTTAATATTAAT
3104098 CACAAATTTTTTAATATTAA
1 CACAAATTTTTTAATATTAA
3104118 ATATTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
CACAAATTTTTTAATATTAAT
Found at i:3104107 original size:21 final size:21
Alignment explanation
Indices: 3104070--3104117 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
3104060 TTCGTTCTAT
*
3104070 TTTAGTCACACAATTTTTTTAA
1 TTTAATCACACAA-TTTTTTAA
3104092 TTTAATCACA-AATTTTTTAA
1 TTTAATCACACAATTTTTTAA
3104112 TATTAA
1 T-TTAA
3104118 ATATTTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAATCACACAATTTTTTAA
Found at i:3105446 original size:31 final size:29
Alignment explanation
Indices: 3105389--3105479 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
3105379 TATATATTTT
* * *
3105389 TAAAATTTTTATAGTTAGGACAAAATTGA
1 TAAATTTTTTATATTTAGGACTAAATTGA
*
3105418 TAAATTTTTTAAATATTTAGGACTAAATTTA
1 TAAATTTTTT--ATATTTAGGACTAAATTGA
** *
3105449 TTGATTTTTTATATTTATGA-TCAAATTGA
1 TAAATTTTTTATATTTAGGACT-AAATTGA
3105478 TA
1 TA
3105480 GAATGTGTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.02
29 25 0.50
31 24 0.48
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (29 bp):
TAAATTTTTTATATTTAGGACTAAATTGA
Found at i:3105617 original size:31 final size:30
Alignment explanation
Indices: 3105574--3105634 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
3105564 TTTTGTGATT
* *
3105574 AAATCGAAAAAAT-TAATAGTTGGGTAACCA
1 AAATAGAAAAAATGT-ATAGTTAGGTAACCA
*
3105604 AAATAGAATAAAATGTATAGTTAGGTGACCA
1 AAATAGAA-AAAATGTATAGTTAGGTAACCA
3105635 TTTTTATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 7 0.27
31 18 0.69
32 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (30 bp):
AAATAGAAAAAATGTATAGTTAGGTAACCA
Found at i:3110189 original size:22 final size:23
Alignment explanation
Indices: 3110164--3110222 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
3110154 CAACCAAATC
3110164 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3110186 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3110209 ACA-TCATCACATAT
1 A-ATTCAT-ACATAT
3110223 CTGAAATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 18 0.58
24 7 0.23
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3115275 original size:21 final size:21
Alignment explanation
Indices: 3115250--3115306 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3115240 AAAGTAGTAT
3115250 ACGACACATAAAGTGCCTAAA
1 ACGACACATAAAGTGCCTAAA
** * * *
3115271 ACGACACACGAGGTGCCTGAT
1 ACGACACATAAAGTGCCTAAA
*
3115292 ACGGCACATAAAGTG
1 ACGACACATAAAGTG
3115307 TCTGATCGGC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.14
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTAAA
Found at i:3116049 original size:30 final size:28
Alignment explanation
Indices: 3115994--3116055 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
3115984 ATTATTTAAT
3115994 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
*
3116022 TAATAAATATCTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTACTT-AATAATAAA
3116052 TAAT
1 TAAT
3116056 TTAAATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 7 0.23
30 12 0.39
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:3121758 original size:14 final size:14
Alignment explanation
Indices: 3121739--3121770 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3121729 CCCACCCACT
3121739 ATGCATATTTTCTA
1 ATGCATATTTTCTA
3121753 ATGCATATTTTCTA
1 ATGCATATTTTCTA
3121767 ATGC
1 ATGC
3121771 CTTCTGCTTA
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:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (14 bp):
ATGCATATTTTCTA
Found at i:3123429 original size:127 final size:127
Alignment explanation
Indices: 3123263--3123785 Score: 689
Period size: 126 Copynumber: 4.1 Consensus size: 127
3123253 GGCCAAACAT
* * * *
3123263 GAACTACTATAGAAAAAGAGCATCTACGTGGGGGCTTTTTTTAGT-AATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTA-TCAATTTTGCTGACAGTGCAT
* *
3123327 CTTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTTTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * *
3123390 AAACTACTGTAGAAAAAGAGCGTACACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCATC
* *
3123455 CTGCTTGAAGCG-TGTTTGACACTATTTGTTTAGAAACGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * *
3123516 GAACTATTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTAATCAATTTTGCTGACAGTACATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCATC
* * * * * *
3123581 CTGTTTGAAGCGTTTTTT-ATACTATTTGTTCAGAACCGCCTTCTCAAAATCATTTTTTTAG
66 CTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * * *
3123642 GAACTACTGTAGAAAAATAGCGTCCACATGGAAGCTTTTTTCATCAATTTGGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCATC
* * * * *
3123707 TTGCTTAAAGC-TTTTTTGACACTATTTATTCTGAACCGTCTTCTC-AAATT-TTCTTTTCCAG
66 CTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATT-TTTT-CAG
3123768 GAACTACTGTAGGAAAAA
1 GAACTACTGTA-GAAAAA
3123786 AACCAAAATT
Statistics
Matches: 347, Mismatches: 43, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
124 2 0.01
125 14 0.04
126 254 0.73
127 77 0.22
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (127 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:3123828 original size:7 final size:7
Alignment explanation
Indices: 3123817--3123850 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3123807 TATAGTTTTT
*
3123817 CCTAAAT
1 CCTAAAC
3123824 CCTAAAC
1 CCTAAAC
3123831 CCTAAAC
1 CCTAAAC
3123838 CCTAAA-
1 CCTAAAC
3123844 CCTAAAC
1 CCTAAAC
3123851 ACAATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (7 bp):
CCTAAAC
Found at i:3123912 original size:34 final size:32
Alignment explanation
Indices: 3123871--3123933 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
3123861 TTAAAAAAAA
3123871 CTAAACCCAAATTTAATTAATTAATTTAAAACCC
1 CTAAACCCAAATTTAATTAATT--TTTAAAACCC
*
3123905 CTAAACCCTAATTTAATTAATTTTTAAAA
1 CTAAACCCAAATTTAATTAATTTTTAAAA
3123934 AAGAACACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 7 0.25
34 21 0.75
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (32 bp):
CTAAACCCAAATTTAATTAATTTTTAAAACCC
Found at i:3124030 original size:41 final size:41
Alignment explanation
Indices: 3123980--3124061 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
3123970 TAAAACCGAA
* * *
3123980 AACCTTAAATTATTTTAACAAAACCTTAACCCTACAAACCT
1 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
3124021 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
1 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
3124062 TAAACTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (41 bp):
AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
Found at i:3124070 original size:41 final size:41
Alignment explanation
Indices: 3123985--3124070 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
3123975 CCGAAAACCT
* * *
3123985 TAAATTATTTTAACAAAACCTTAACCCTACAAACCTAACCC
1 TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTAACAC
3124026 TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTTAA-AC
1 TAAATTATTTTAACAAAACCCTAACCCTAAAAACC-TAACAC
3124067 TAAA
1 TAAA
3124071 AAACCTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.93
42 3 0.07
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (41 bp):
TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTAACAC
Found at i:3124379 original size:30 final size:31
Alignment explanation
Indices: 3124345--3124406 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
3124335 AGTATATATC
*
3124345 TTTATAACTTTTAAAAG-ATTAAAT-TAATTT
1 TTTATAA-TTTTAAAAGTATAAAATATAATTT
* *
3124375 TTTATTATTTTAAGAGTATAAAATATAATTT
1 TTTATAATTTTAAAAGTATAAAATATAATTT
3124406 T
1 T
3124407 AGCATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.30
30 12 0.44
31 7 0.26
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTATAATTTTAAAAGTATAAAATATAATTT
Found at i:3124633 original size:16 final size:18
Alignment explanation
Indices: 3124602--3124647 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
3124592 TAATATATTA
3124602 TATTTATTT-TGTATTT-
1 TATTTATTTATGTATTTG
3124618 TATTTATTTATG-ATTTG
1 TATTTATTTATGTATTTG
*
3124635 TGTTATATTTATG
1 TATT-TATTTATG
3124648 GTACTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (18 bp):
TATTTATTTATGTATTTG
Found at i:3124634 original size:22 final size:20
Alignment explanation
Indices: 3124595--3124646 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
3124585 ATATAATTAA
3124595 TATATTATATTTATTTTGTAT
1 TATATT-TATTTATTTTGTAT
* *
3124616 TTTATTTATTTATGATTTGTGT
1 TATATTTATTTAT--TTTGTAT
3124638 TATATTTAT
1 TATATTTAT
3124647 GGTACTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 5 0.19
22 14 0.54
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TATATTTATTTATTTTGTAT
Found at i:3129310 original size:21 final size:21
Alignment explanation
Indices: 3129273--3129313 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3129263 TTGCTGCTGC
*
3129273 TGCTGCTGTGGTGGTTGTTGT
1 TGCTGCTGTGCTGGTTGTTGT
3129294 TGCTGCTGCTGCT-GTTGTTG
1 TGCTGCTG-TGCTGGTTGTTG
3129314 AGGTTGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.00, C:0.15, G:0.39, T:0.46
Consensus pattern (21 bp):
TGCTGCTGTGCTGGTTGTTGT
Found at i:3129319 original size:30 final size:30
Alignment explanation
Indices: 3129262--3129320 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3129252 CGTGCCTGGG
*
3129262 GTTGCTGCTGCTGCTGCTGTGGTGGTTGTT
1 GTTGCTGCTGCTGCTGCTGTGGAGGTTGTT
* *
3129292 GTTGCTGCTGCTGCTGTTGTTGAGGTTGT
1 GTTGCTGCTGCTGCTGCTGTGGAGGTTGT
3129321 GAGGATTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.02, C:0.15, G:0.39, T:0.44
Consensus pattern (30 bp):
GTTGCTGCTGCTGCTGCTGTGGAGGTTGTT
Found at i:3130968 original size:6 final size:6
Alignment explanation
Indices: 3130953--3130982 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3130943 TAAGTAAACC
3130953 AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
3130983 GGGTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:3131540 original size:28 final size:26
Alignment explanation
Indices: 3131508--3131564 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
3131498 TATTAATTTT
* *
3131508 TATATTAGTTTTATATAATTTTAAAATA
1 TATATTA-TATTATA-AATTTTAAAAAA
3131536 TATATTATATTATAAATTTTAAAAAA
1 TATATTATATTATAAATTTTAAAAAA
3131562 TAT
1 TAT
3131565 GAATACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 14 0.52
27 6 0.22
28 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TATATTATATTATAAATTTTAAAAAA
Found at i:3131639 original size:30 final size:30
Alignment explanation
Indices: 3131605--3131666 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
3131595 ACTTAACAAG
*
3131605 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** *
3131635 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
3131665 CA
1 CA
3131667 GTATAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:3131722 original size:22 final size:22
Alignment explanation
Indices: 3131697--3131739 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3131687 TATCCAAATA
3131697 ATAACAACAAAAT-AGTAGCAAC
1 ATAACAACAAAATGA-TAGCAAC
* *
3131719 ATAATAATAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
3131740 AATAGGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAC
Found at i:3138210 original size:46 final size:46
Alignment explanation
Indices: 3138159--3138435 Score: 369
Period size: 46 Copynumber: 6.0 Consensus size: 46
3138149 GTGTGCTCTC
** *
3138159 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
** *
3138205 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
3138251 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*** ***
3138297 TGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGTG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*
3138343 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
3138389 TGA-A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
3138434 TG
1 TG
3138436 TCAAAGATAA
Statistics
Matches: 210, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
44 1 0.00
45 37 0.18
46 172 0.82
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Done.