Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 387 of 410
Found at i:117388493 original size:75 final size:74
Alignment explanation
Indices: 117388309--117388613 Score: 443
Period size: 75 Copynumber: 4.1 Consensus size: 74
117388299 AAAACACAAA
* * * *
117388309 AATTGACAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-ATTTTG
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
*
117388373 AAAAACAGA
66 AAAAACAGT
* *
117388382 AATTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
117388447 AACAAACAGT
66 AA-AAACAGT
* * *
117388457 AATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTTT
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
117388522 AACAAACAGT
66 AA-AAACAGT
* *
117388532 AATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACTCACCTCTTGCAATTATGAGTTGATTTTTT
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAA-TATGAGTTGATTTTTT
*
117388597 TGAAAACAG-
65 TAAAAACAGT
*
117388606 AAATGAAA
1 AATTGAAA
117388614 CATCCACATA
Statistics
Matches: 210, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
73 54 0.26
74 13 0.06
75 125 0.60
76 18 0.09
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (74 bp):
AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
AAAAACAGT
Found at i:117390092 original size:71 final size:68
Alignment explanation
Indices: 117390004--117390196 Score: 257
Period size: 68 Copynumber: 2.8 Consensus size: 68
117389994 CGATTTGTCT
* * * *
117390004 CGTAGCTCTCTTGTCTACATGGTG-TCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
1 CGTAGCTCTCTTGTCTACATGG-GATACATC-C--CGAATCACACATGCGACCTAGCTACATTTA
117390068 TCTTTCA
62 TCTTTCA
* *
117390075 CGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACATGTGACCTAGCTACATTTATCTT
1 CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCTACATTTATCTT
117390140 TCA
66 TCA
* *
117390143 CGTAGCTCTC-TGTCTACATGGGATACAT-CCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCTAC
117390197 TACAGGTGTC
Statistics
Matches: 115, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
66 26 0.23
67 18 0.16
68 43 0.37
70 2 0.02
71 26 0.23
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (68 bp):
CGTAGCTCTCTTGTCTACATGGGATACATCCCGAATCACACATGCGACCTAGCTACATTTATCTT
TCA
Found at i:117390136 original size:68 final size:66
Alignment explanation
Indices: 117390041--117390196 Score: 276
Period size: 68 Copynumber: 2.3 Consensus size: 66
117390031 TTCACTTGGA
* *
117390041 ATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTC-TGTCTACATGGGATACAT-C
117390106 CGT
64 CGT
117390109 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTGTCTACATGGGATACATCCG
1 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTGTCTACATGGGATACATCCG
117390174 T
66 T
117390175 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
117390197 TACAGGTGTC
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 26 0.30
67 18 0.21
68 42 0.49
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (66 bp):
ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTCTGTCTACATGGGATACATCCG
T
Found at i:117390228 original size:66 final size:67
Alignment explanation
Indices: 117390041--117390221 Score: 222
Period size: 68 Copynumber: 2.7 Consensus size: 67
117390031 TTCACTTGGA
* * ** * *
117390041 ATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATACAGCTGTCACGTAGCTCTCTTGTCTACATGGGATACAT-C
117390106 CGT
65 CGT
** * *
117390109 ATCACACATGTGACCTAGCTACATTTATCTTTCACGTAGCTCTC-TGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATACAGCTGTCACGTAGCTCTCTTGTCTACATGGGATACATCC
117390173 GT
66 GT
* * *
117390175 ATCACACATGTGACCTAGCTAC-TACAGGTGTCTCGTAGCTTTCTTGT
1 ATCACACATGTGACCTAGCTACATACAGCTGTCACGTAGCTCTCTTGT
117390222 ACACATGATG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
65 14 0.14
66 29 0.28
67 18 0.17
68 42 0.41
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (67 bp):
ATCACACATGTGACCTAGCTACATACAGCTGTCACGTAGCTCTCTTGTCTACATGGGATACATCC
GT
Found at i:117397671 original size:66 final size:66
Alignment explanation
Indices: 117397553--117397743 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 66
117397543 CGATTTGTCT
* * * * *
117397553 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGG-GTACATC-C---GTATCACACATGTGACCTAGCTACATTTAT
117397618 CTTTCA
61 CTTTCA
117397624 CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
1 CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
117397689 A
66 A
117397690 CGTAGCTCTC-TGTCTACATGGGATACATCCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGG-TACATCCGTATCACACATGTGACCTAGCTAC
117397744 TACAGGTGTC
Statistics
Matches: 114, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
65 12 0.11
66 74 0.65
69 1 0.01
70 5 0.04
71 22 0.19
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (66 bp):
CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
A
Found at i:117397775 original size:66 final size:66
Alignment explanation
Indices: 117397548--117397810 Score: 226
Period size: 66 Copynumber: 3.9 Consensus size: 66
117397538 CTAGCCGATT
* * * * * *
117397548 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
1 TGTCACGTAGCTCTCTTGTCTACATGG-GTACATC-C---GTATCACACATGTGACCTAGCTACA
** *
117397613 TTTATC
61 TACAGC
* ** *
117397619 TTTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTAT
1 TGTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATACAG
117397684 C
66 C
*
117397685 TTTCACGTAGCTCTC-TGTCTACATGGGATACATCCGTATCACACATGTGACCTAGCTAC-TACA
1 TGTCACGTAGCTCTCTTGTCTACATGGG-TACATCCGTATCACACATGTGACCTAGCTACATACA
*
117397748 GG
65 GC
* * * * * * *
117397750 TGTCTCGTAGCTTTCTTGTAC-ACATGATGTGCACTCAGCATCATACATGTGACCTAGCTAC
1 TGTCACGTAGCTCTCTTGT-CTACATG-GGTACA-TCCGTATCACACATGTGACCTAGCTAC
117397811 GCTCCCTCTA
Statistics
Matches: 168, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
65 26 0.15
66 85 0.51
67 26 0.15
69 1 0.01
70 5 0.03
71 25 0.15
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.33
Consensus pattern (66 bp):
TGTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATACAG
C
Found at i:117411484 original size:24 final size:25
Alignment explanation
Indices: 117411437--117411487 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
117411427 ACACATGTTC
*
117411437 ATAATATATAAAACATACATATAAT
1 ATAATATATAAAACATACACATAAT
**
117411462 ATAATAT-TAAAACATTTACATAAT
1 ATAATATATAAAACATACACATAAT
117411486 AT
1 AT
117411488 GTACACACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:117411584 original size:21 final size:21
Alignment explanation
Indices: 117411560--117411599 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
117411550 AAGATATACT
*
117411560 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
117411581 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
117411600 ATACATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:117411682 original size:20 final size:20
Alignment explanation
Indices: 117411654--117411691 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
117411644 TAAAAATAAT
* *
117411654 AATATACATAATATATACAA
1 AATACACATAATACATACAA
117411674 AATACACATAATACATAC
1 AATACACATAATACATAC
117411692 GTATATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (20 bp):
AATACACATAATACATACAA
Found at i:117413294 original size:5 final size:5
Alignment explanation
Indices: 117413284--117413309 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
117413274 TGATTTGCAT
117413284 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
117413310 GTTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:117415910 original size:35 final size:35
Alignment explanation
Indices: 117415864--117415934 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
117415854 TATGAAAGAA
*
117415864 CTTGGTGTTCTGTCTCCTTGGTGAATCCAATCCAT
1 CTTGGTGTTCTGTCTCCTCGGTGAATCCAATCCAT
117415899 CTTGGTGTTCTGTCTCCTCGGTGAATCCAATCCAT
1 CTTGGTGTTCTGTCTCCTCGGTGAATCCAATCCAT
117415934 C
1 C
117415935 CTAGATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (35 bp):
CTTGGTGTTCTGTCTCCTCGGTGAATCCAATCCAT
Found at i:117419078 original size:46 final size:46
Alignment explanation
Indices: 117419018--117419283 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
117419008 TTTGACATGA
* * * * * *
117419018 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
117419064 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117419110 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
117419156 TGCCATGGTA----T----CATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
117419194 TACCATGGTATCTTTCAACCAAGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117419240 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
117419284 AGAGCACACT
Statistics
Matches: 194, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
38 35 0.18
42 2 0.01
45 4 0.02
46 153 0.79
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:117419180 original size:38 final size:38
Alignment explanation
Indices: 117419129--117419251 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
117419119 ATCTTTCAAC
117419129 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
* *
117419167 CATGGTCTTACACATTTCATATCAGGCTACCATGGTATCTTT
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTA----T
*
117419209 CAACCAAGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
1 ----CATGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
117419251 C
1 C
117419252 TTTCAACCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
38 36 0.50
42 2 0.03
46 34 0.47
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (38 bp):
CATGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
Found at i:117419224 original size:84 final size:84
Alignment explanation
Indices: 117419095--117419251 Score: 278
Period size: 84 Copynumber: 1.9 Consensus size: 84
117419085 TGGTCTTGTT
* * *
117419095 CATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCC
1 CATTTCATATCACGCTACCATGGTATCTTTCAACCAAGGTCTTACACATTTCATATCAGGTTGCC
117419160 ATGGTATCATGGTCTTACA
66 ATGGTATCATGGTCTTACA
*
117419179 CATTTCATATCAGGCTACCATGGTATCTTTCAACCAAGGTCTTACACATTTCATATCAGGTTGCC
1 CATTTCATATCACGCTACCATGGTATCTTTCAACCAAGGTCTTACACATTTCATATCAGGTTGCC
117419244 ATGGTATC
66 ATGGTATC
117419252 TTTCAACCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (84 bp):
CATTTCATATCACGCTACCATGGTATCTTTCAACCAAGGTCTTACACATTTCATATCAGGTTGCC
ATGGTATCATGGTCTTACA
Found at i:117424349 original size:46 final size:46
Alignment explanation
Indices: 117424289--117424607 Score: 516
Period size: 46 Copynumber: 7.0 Consensus size: 46
117424279 TTTGACATGA
* * * * * *
117424289 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
117424335 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117424381 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
117424427 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117424473 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG-
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117424518 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
117424564 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
117424608 AGAGCACACT
Statistics
Matches: 260, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
45 49 0.19
46 211 0.81
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:117424581 original size:137 final size:138
Alignment explanation
Indices: 117424289--117424607 Score: 516
Period size: 137 Copynumber: 2.3 Consensus size: 138
117424279 TTTGACATGA
* * * * * * *
117424289 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGCTGCCATGGTATCTTTCAA
*** *
117424353 CCATGGTCTTGTTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
65 CCATGGTCTTACACATTTCATATCATGGTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
117424418 ATATCAGGT
130 ATATCAGGT
117424427 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
117424492 CATGGTCTTACACATTTCATATCA-GGTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTACACATTTCATATCATGGTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
117424556 TATCAGGT
131 TATCAGGT
117424564 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
117424608 AGAGCACACT
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
137 95 0.56
138 74 0.44
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCATGGTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGT
Found at i:117431614 original size:15 final size:15
Alignment explanation
Indices: 117431590--117431619 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
117431580 ATTAGTTATA
*
117431590 ATATATATTTTAATT
1 ATATAAATTTTAATT
117431605 ATATAAATTTTAATT
1 ATATAAATTTTAATT
117431620 TTTTATAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATAAATTTTAATT
Found at i:117436441 original size:31 final size:31
Alignment explanation
Indices: 117436400--117436463 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
117436390 CCTTTTCATA
*
117436400 TTTCATATTTTATGA-CACTGGGCCGAAGCCT
1 TTTCAAATTTTAT-ATCACTGGGCCGAAGCCT
* *
117436431 TTTCAAATTTTATATTACTGGGCTGAAGCCT
1 TTTCAAATTTTATATCACTGGGCCGAAGCCT
117436462 TT
1 TT
117436464 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTCAAATTTTATATCACTGGGCCGAAGCCT
Found at i:117436732 original size:23 final size:23
Alignment explanation
Indices: 117436678--117436773 Score: 131
Period size: 23 Copynumber: 4.1 Consensus size: 23
117436668 CCTAGCCTCT
* *
117436678 TTTAATAACTG-GGGAAAAGCCC
1 TTTAATAACTGAGGCATAAGCCC
117436700 TTTTTAATAACTGAGGCATAAGCCC
1 --TTTAATAACTGAGGCATAAGCCC
117436725 TTTAATAACTGAGGCATAAGCCC
1 TTTAATAACTGAGGCATAAGCCC
* *
117436748 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGAGGCATAAGCCC
117436771 TTT
1 TTT
117436774 TGCACTTCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 47 0.70
24 11 0.16
25 9 0.13
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGAGGCATAAGCCC
Found at i:117436849 original size:20 final size:20
Alignment explanation
Indices: 117436824--117436890 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
117436814 TTATAAATAC
117436824 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
117436844 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117436864 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117436884 ACCATGT
1 ATCATGT
117436891 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:117436855 original size:11 final size:11
Alignment explanation
Indices: 117436824--117436879 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
117436814 TTATAAATAC
117436824 ATCATGTGCAT
1 ATCATGTGCAT
*
117436835 ATCA--TACAT
1 ATCATGTGCAT
117436844 ATCATGTGCAT
1 ATCATGTGCAT
*
117436855 ATCA--TACAT
1 ATCATGTGCAT
*
117436864 GTCATGTGCAT
1 ATCATGTGCAT
117436875 ATCAT
1 ATCAT
117436880 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:117436959 original size:25 final size:25
Alignment explanation
Indices: 117436927--117436974 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
117436917 ATGTATAAAC
* * *
117436927 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
117436952 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
117436975 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:117444500 original size:30 final size:31
Alignment explanation
Indices: 117444460--117444522 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
117444450 CCTTTTCATA
117444460 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
117444491 TTTCA-ATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
117444521 TT
1 TT
117444523 ACTGTAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:117444810 original size:23 final size:23
Alignment explanation
Indices: 117444738--117444833 Score: 149
Period size: 24 Copynumber: 4.1 Consensus size: 23
117444728 CCTAGCCTCT
*
117444738 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
117444761 TTTTAATAACTGGGGCATAAAGCCC
1 -TTTAATAACTGGGGCAT-AAGCCC
117444786 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
117444809 TTTAATAACT-GGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
117444831 TTT
1 TTT
117444834 TGCACTTCCC
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
22 14 0.20
23 16 0.23
24 33 0.48
25 6 0.09
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:117444906 original size:19 final size:19
Alignment explanation
Indices: 117444878--117444939 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
117444868 TGCATTTATA
117444878 ATAC-ATCATGTGCATATC
1 ATACAATCATGTGCATATC
117444896 ATACAATCATGTGCATATC
1 ATACAATCATGTGCATATC
*
117444915 ATACATGTCATGTGCATATC
1 ATACA-ATCATGTGCATATC
117444935 ATACA
1 ATACA
117444940 TACCATGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
18 4 0.10
19 19 0.46
20 18 0.44
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
ATACAATCATGTGCATATC
Found at i:117444927 original size:20 final size:20
Alignment explanation
Indices: 117444882--117444947 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
117444872 TTTATAATAC
117444882 ATCATGTGCATATCATACA-
1 ATCATGTGCATATCATACAT
117444901 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117444921 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117444941 ACCATGT
1 ATCATGT
117444948 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 19 0.44
20 24 0.56
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:117445014 original size:25 final size:25
Alignment explanation
Indices: 117444982--117445029 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
117444972 TCATATAAAC
* * *
117444982 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
117445007 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
117445030 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:117453352 original size:23 final size:23
Alignment explanation
Indices: 117453298--117453393 Score: 140
Period size: 23 Copynumber: 4.1 Consensus size: 23
117453288 CCTAGCCTCT
*
117453298 TTTAATAACTGGGG-AAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
117453320 TTTTTAATAACTGGGGCATAAGCCC
1 --TTTAATAACTGGGGCATAAGCCC
117453345 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
117453368 TTTAATAACTGGGTCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
117453391 TTT
1 TTT
117453394 TGCACTTCCT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
23 47 0.69
24 14 0.21
25 7 0.10
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:117453469 original size:20 final size:20
Alignment explanation
Indices: 117453444--117453510 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
117453434 TTATAAATAC
117453444 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
117453464 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117453484 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117453504 ACCATGT
1 ATCATGT
117453511 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:117453475 original size:11 final size:11
Alignment explanation
Indices: 117453444--117453499 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
117453434 TTATAAATAC
117453444 ATCATGTGCAT
1 ATCATGTGCAT
*
117453455 ATCA--TACAT
1 ATCATGTGCAT
117453464 ATCATGTGCAT
1 ATCATGTGCAT
*
117453475 ATCA--TACAT
1 ATCATGTGCAT
*
117453484 GTCATGTGCAT
1 ATCATGTGCAT
117453495 ATCAT
1 ATCAT
117453500 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:117453579 original size:25 final size:25
Alignment explanation
Indices: 117453547--117453594 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
117453537 ATGTATAAAC
* * *
117453547 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
117453572 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
117453595 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:117461043 original size:26 final size:26
Alignment explanation
Indices: 117461009--117461116 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
117460999 TGAAATTCCC
117461009 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
117461035 ATCGTGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
117461061 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
117461087 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
117461113 ATCA
1 ATCA
117461117 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:117469210 original size:12 final size:13
Alignment explanation
Indices: 117469194--117469231 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
117469184 AAGTAATGCA
117469194 AGGTATAATATAT
1 AGGTATAATATAT
*
117469207 -GGTAAAATATAT
1 AGGTATAATATAT
117469219 AGTGTATAATATA
1 AG-GTATAATATA
117469232 ATTTGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 1 0.05
14 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (13 bp):
AGGTATAATATAT
Found at i:117469540 original size:28 final size:29
Alignment explanation
Indices: 117469484--117469556 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
117469474 CATAATTTAA
117469484 AATAAAAATAATATATATATGAAATATAT
1 AATAAAAATAATATATATATGAAATATAT
* *
117469513 AATAAAATATAATTTATA-AGTAAAATATAGAAT
1 AATAAAA-ATAATATATATA-TGAAATAT---AT
117469546 AATAAAAATAA
1 AATAAAAATAA
117469557 CATGATGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 8 0.22
30 16 0.43
32 4 0.11
33 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (29 bp):
AATAAAAATAATATATATATGAAATATAT
Found at i:117471139 original size:44 final size:44
Alignment explanation
Indices: 117471058--117471536 Score: 379
Period size: 44 Copynumber: 10.8 Consensus size: 44
117471048 ATGCTGATAT
* * * * * *
117471058 TTCGATCTGCTCTCCGTCGAACACAAAGACGCTAAATCTACTATC
1 TTCGATCTGCTCTCTGAC-AATACAGAGACGCCAAATCTGCTATC
* * * * *
117471103 TTCAATCTACTCTCTAACAATACAGAGACGCCAAATCTACTGTC
1 TTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC
* * *
117471147 TTCGATCTGCT-TCCTGACAATACAGGGATGCCAAATTTGCT-TC
1 TTCGATCTGCTCT-CTGACAATACAGAGACGCCAAATCTGCTATC
* * * * * *
117471190 TTGGA-CTTGCTC-CTCGTCGAATACAAAGATGTCAAATCTACTATC
1 TTCGATC-TGCTCTCT-GAC-AATACAGAGACGCCAAATCTGCTATC
* * *
117471235 -TCTGATTTGCTCTCTGACCATACAGAGATGCCAAATCTGCTATC
1 TTC-GATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC
* * * *
117471279 CTCGATCTGCTCCCTAACAAATACAGAGACGCCAAATCTACTATC
1 TTCGATCTGCTCTCTGAC-AATACAGAGACGCCAAATCTGCTATC
* * * *
117471324 TTTGACCTGCTCTCTGATAATACAGAGATGCCAAA--T-C-ATC
1 TTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC
* * * * *
117471364 TTAGATTTGCT-TCAG-CGTAA-ACATGTGAAAGCCAAATCTGCTATGTC
1 TTCGATCTGCTCTCTGAC--AATACA-GAG-ACGCCAAATCTGCTA--TC
* * *
117471411 TTCGATCTACTCCCTGACAATACAGGGACGCCAAATCTGCTATC
1 TTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC
*
117471455 TTCGATCTGCTCTCTGACAAATACAGAGACGTCAAATCTGCTATC
1 TTCGATCTGCTCTCTGAC-AATACAGAGACGCCAAATCTGCTATC
*
117471500 TTTGATCTGCTCTCTGACAATACAGAGACGCCAAATC
1 TTCGATCTGCTCTCTGACAATACAGAGACGCCAAATC
117471537 ATCTTAGATT
Statistics
Matches: 346, Mismatches: 63, Indels: 51
0.75 0.14 0.11
Matches are distributed among these distances:
39 6 0.02
40 15 0.04
41 8 0.02
42 4 0.01
43 14 0.04
44 160 0.46
45 103 0.30
46 16 0.05
47 14 0.04
48 5 0.01
49 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (44 bp):
TTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGCTATC
Found at i:117471319 original size:89 final size:89
Alignment explanation
Indices: 117471091--117471536 Score: 389
Period size: 89 Copynumber: 5.1 Consensus size: 89
117471081 CAAAGACGCT
* * * *
117471091 AAATCTACTATCTTCAATCTACTCTCTAAC-AATACAGAGACGCCAAATCTACTGTCT-TCGATC
1 AAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCTCT-GATC
*
117471154 TGCT-TCCTGACAATACAGGGATGCC
65 TGCTCT-CTGACAATACAGAGATGCC
* * * * * *
117471179 AAATTTGCT-TCTTGGA-CTTGCTCCTCGT--CGAATACAAAGATGTCAAATCTACTATCTCTGA
1 AAATCTGCTATCTTCGATC-TGCT-CTC-TAACAAATACAGAGACGCCAAATCTACTATCTCTGA
* *
117471240 TTTGCTCTCTGACCATACAGAGATGCC
63 TCTGCTCTCTGACAATACAGAGATGCC
* * * *
117471267 AAATCTGCTATCCTCGATCTGCTCCCTAACAAATACAGAGACGCCAAATCTACTATCTTTGACCT
1 AAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCTCTGATCT
*
117471332 GCTCTCTGATAATACAGAGATGCC
66 GCTCTCTGACAATACAGAGATGCC
* * * * * * * *
117471356 AAA--T-C-ATCTTAGATTTGCT-TC-AGCGTAA-ACATGTGAAAGCCAAATCTGCTATGTCTTC
1 AAATCTGCTATCTTCGATCTGCTCTCTAAC-AAATACA-GAG-ACGCCAAATCTACTATCTC-T-
* * * *
117471414 GATCTACTCCCTGACAATACAGGGACGCC
61 GATCTGCTCTCTGACAATACAGAGATGCC
* * * *
117471443 AAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGTCAAATCTGCTATCTTTGATCT
1 AAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCTCTGATCT
*
117471508 GCTCTCTGACAATACAGAGACGCC
66 GCTCTCTGACAATACAGAGATGCC
117471532 AAATC
1 AAATC
117471537 ATCTTAGATT
Statistics
Matches: 281, Mismatches: 55, Indels: 43
0.74 0.15 0.11
Matches are distributed among these distances:
83 5 0.02
84 5 0.02
85 26 0.09
86 3 0.01
87 37 0.13
88 67 0.24
89 98 0.35
90 3 0.01
91 27 0.10
92 6 0.02
93 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (89 bp):
AAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCTCTGATCT
GCTCTCTGACAATACAGAGATGCC
Found at i:117471484 original size:176 final size:175
Alignment explanation
Indices: 117471084--117471599 Score: 605
Period size: 176 Copynumber: 2.9 Consensus size: 175
117471074 TCGAACACAA
* * * * *
117471084 AGACGCTAAATCTACTATCTTCAATCTACTCTCTAAC-AATACAGAGACGCCAAATCTACTGTCT
1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCT
* * * * *
117471148 TCGATCTGCT-TCCTGACAATACAGGGATGCCAAATTTGCTTCTTGGACTTGCTCCTC-GTCG-A
66 TTGATCTGCTCT-CTGACAATACAGAGATGCCAAA--T-CATCTTAGATTTGCT--TCAG-CGTA
** * * * * * * * *
117471210 ATACAAAG-ATGTCAAATCTACTATCTC-T-GATTTGCTCTCTGACCATACAG
124 A-ACAGTGAAAGCCAAATCTGCTATGTCTTCGATCTACTCCCTGACAATACAG
* * *
117471260 AGATGCCAAATCTGCTATCCTCGATCTGCTCCCTAACAAATACAGAGACGCCAAATCTACTATCT
1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCT
* *
117471325 TTGACCTGCTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACATGT
66 TTGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA-GT
117471390 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCCTGACAATACAG
130 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCCTGACAATACAG
* * * *
117471436 GGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAAATACAGAGACGTCAAATCTGCTATCT
1 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCT
* *
117471501 TTGATCTGCTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTTAGCGTAAACAGGT
66 TTGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA-GT
*
117471566 GAAAGCTAAATCTGCTATGTCTTCGATCTACTCC
130 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCC
117471600 TTGTAAACAT
Statistics
Matches: 294, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
172 7 0.02
173 4 0.01
174 27 0.09
175 2 0.01
176 199 0.68
177 54 0.18
178 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (175 bp):
AGACGCCAAATCTGCTATCTTCGATCTGCTCTCTAACAAATACAGAGACGCCAAATCTACTATCT
TTGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAGTG
AAAGCCAAATCTGCTATGTCTTCGATCTACTCCCTGACAATACAG
Found at i:117473459 original size:46 final size:46
Alignment explanation
Indices: 117473383--117473546 Score: 265
Period size: 46 Copynumber: 3.6 Consensus size: 46
117473373 CGTTTTCCAT
** * * *
117473383 CCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
117473429 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
* *
117473475 CCAAGGTCTTACACATTTCATATCAGGTTGTCATGGTATCTTTCAA
1 CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
117473521 CCATGGTCTTACACATTTCATATCAG
1 CCATGGTCTTACACATTTCATATCAG
117473547 AGAGTACACT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 110 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
CCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAA
Found at i:117476922 original size:21 final size:21
Alignment explanation
Indices: 117476898--117476962 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
117476888 AAATCTAACT
117476898 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** *
117476919 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
117476937 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
117476958 GAAGC
1 GAAGC
117476963 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:117476927 original size:39 final size:39
Alignment explanation
Indices: 117476892--117476980 Score: 178
Period size: 39 Copynumber: 2.3 Consensus size: 39
117476882 AACCCGAAAT
117476892 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
117476931 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
117476970 CTAACTGAAGC
1 CTAACTGAAGC
117476981 TCATCAGAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.13
Consensus pattern (39 bp):
CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
Found at i:117487467 original size:20 final size:21
Alignment explanation
Indices: 117487414--117487489 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
117487404 CTAAATAATT
* *
117487414 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
117487433 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
117487454 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
117487475 TAATCATAAAATATC
1 -AATAATAAAATATC
117487490 ATCAAAATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:117489967 original size:20 final size:20
Alignment explanation
Indices: 117489927--117489967 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
117489917 AATAGATATT
*
117489927 TTATTATAACTATTATTAAG
1 TTATTATAACTATTATAAAG
117489947 TTATTATAA-TATATATAAAG
1 TTATTATAACTAT-TATAAAG
117489967 T
1 T
117489968 AAAAGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TTATTATAACTATTATAAAG
Found at i:117489987 original size:16 final size:17
Alignment explanation
Indices: 117489963--117490002 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
117489953 TAATATATAT
* *
117489963 AAAGTAAAAGAA-ATAA
1 AAAGAAAAAGAATAGAA
117489979 AAAGAAAAAGAATAGAA
1 AAAGAAAAAGAATAGAA
117489996 AAAGAAA
1 AAAGAAA
117490003 GAAAGGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAGAATAGAA
Found at i:117489997 original size:11 final size:10
Alignment explanation
Indices: 117489969--117490006 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
117489959 ATATAAAGTA
117489969 AAAGAAATAA-
1 AAAGAAA-AAG
117489979 AAAGAAAAAG
1 AAAGAAAAAG
117489989 AATAGAAAAAG
1 AA-AGAAAAAG
117490000 AAAGAAA
1 AAAGAAA
117490007 GGATGAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:117490060 original size:18 final size:18
Alignment explanation
Indices: 117490037--117490071 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
117490027 CAGGGGAAAG
*
117490037 AAAGAAGGAAGGAAAAAA
1 AAAGAAAGAAGGAAAAAA
117490055 AAAGAAAGAAGGAAAAA
1 AAAGAAAGAAGGAAAAA
117490072 GGGAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGGAAAAAA
Found at i:117491498 original size:259 final size:258
Alignment explanation
Indices: 117491039--117491550 Score: 952
Period size: 259 Copynumber: 2.0 Consensus size: 258
117491029 AGTATGACAC
117491039 AGATGGACAACTTGAATATTCATAAAAGTAAATAATAAAAATTATAGATAATGCTACTTACAAGT
1 AGATGGACAACTTGAATATTCATAAAAGTAAATAATAAAAATTATAGATAATGCTACTTACAAGT
117491104 GTGTTATATACACTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAAAATATGTATGAATATTCAT
66 GTGTTATATACACTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAAAATATGTATGAATATTCAT
* *
117491169 CTAGCATGGCTAATTTGCATGTTTTAGGCTCAGGGACTAAATTGAATAAAATTAAAACTTTATTG
131 CTAGCATGGCTAATTTGCATGTTTTAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTATGG
*
117491234 GTAATTTTGTAAAAATGTCAGAAATGACCAAATTGCATGAAATGGATTATTTTATTATTCTCAT
196 GTAATTTTCTAAAAA-GTCAGAAATGACCAAATTGCATGAAATGGATTATTTTATTATTCTCAT
* * *
117491298 AGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAAATTATAGATAATGTTATTTACAAGT
1 AGATGGACAACTTGAATATTCATAAAAGTAAATAATAAAAATTATAGATAATGCTACTTACAAGT
*
117491363 GTGTTATATACACTAAGGATGTGGAATGGAGAGGAGGAGGAGGAAAAATATGTATGAATATTCAT
66 GTGTTATATACACTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAAAATATGTATGAATATTCAT
117491428 CTAGCATGGCTAATTTGCATGTTTTAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTATGG
131 CTAGCATGGCTAATTTGCATGTTTTAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTATGG
117491493 GTAATTTTCTAAAAAGTCAGAAATGACCAAATTGCATGAAATGGATTATTTTATTATT
196 GTAATTTTCTAAAAAGTCAGAAATGACCAAATTGCATGAAATGGATTATTTTATTATT
117491551 TAAATTACAA
Statistics
Matches: 246, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
258 43 0.17
259 203 0.83
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (258 bp):
AGATGGACAACTTGAATATTCATAAAAGTAAATAATAAAAATTATAGATAATGCTACTTACAAGT
GTGTTATATACACTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAAAATATGTATGAATATTCAT
CTAGCATGGCTAATTTGCATGTTTTAGGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTATGG
GTAATTTTCTAAAAAGTCAGAAATGACCAAATTGCATGAAATGGATTATTTTATTATTCTCAT
Found at i:117492471 original size:46 final size:46
Alignment explanation
Indices: 117492415--117492736 Score: 443
Period size: 46 Copynumber: 7.0 Consensus size: 46
117492405 GCTTTCTGAA
*
117492415 ATAAAATGTGTAAGACCATGGTTCAAAGATACCATGGCAACATGAT
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
117492461 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG--
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
117492505 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
117492551 ATAAAATGTGTAAGCCCATGGTTGAAAGATACCATGGCAACATGAT
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
117492597 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGAC
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
117492643 ATGAAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 AT-AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
117492689 AGAAAATGAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATAAAATG--T--GTAAGACCATGGTTGAAAGATACCATGGCAACATG
117492737 TCAAAGATAA
Statistics
Matches: 247, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
44 42 0.17
45 4 0.02
46 167 0.68
47 4 0.02
50 30 0.12
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:117492533 original size:90 final size:90
Alignment explanation
Indices: 117492415--117492687 Score: 431
Period size: 90 Copynumber: 3.0 Consensus size: 90
117492405 GCTTTCTGAA
*
117492415 ATAAAATGTGTAAGACCATGGTTCAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCAT
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCAT
117492480 GGTTGAAAGATACCATGGCAACATG
66 GGTTGAAAGATACCATGGCAACATG
* * *
117492505 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGCCCAT
1 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCAT
117492570 GGTTGAAAGATACCATGGCAACATG
66 GGTTGAAAGATACCATGGCAACATG
** * **
117492595 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGACATGAAAA-GAATAAGAC
1 --ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT-AAAATGTGTAAGAC
117492659 CATGGTTGAAAGATACCATGGCAACATG
63 CATGGTTGAAAGATACCATGGCAACATG
117492687 A
1 A
117492688 CAGAAAATGA
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
90 87 0.52
92 77 0.46
93 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (90 bp):
ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCAT
GGTTGAAAGATACCATGGCAACATG
Found at i:117492743 original size:92 final size:90
Alignment explanation
Indices: 117492417--117492731 Score: 314
Period size: 90 Copynumber: 3.4 Consensus size: 90
117492407 TTTCTGAAAT
* * * * * **
117492417 AAAATGTGTAAGACCATGGTTCAAAGATACCATGGCAACATGATAT-AAAATGTGTAAGACCATG
1 AAAATGTGTAAGACCATAGTTGAAAGACACCATGGCAA-GT-ACATGAAAA-GAATAAGACCATG
*
117492481 GTTGAAAGATACCATGGCAACATGA-TG
63 GTTGAAAGATACCATGGCAACATGACAG
* * * * ** *
117492508 -AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGATAT-AAAATGTGTAAGCCCATG
1 AAAATGTGTAAGACCATAGTTGAAAGACACCATGGC-A-AGTACATGAAAA-GAATAAGACCATG
* *
117492571 GTTGAAAGATACCATGGCAACATGATAT
63 GTTGAAAGATACCATGGCAACATGACAG
* *
117492599 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGACATGAAAAGAATAAGACCATGG
1 AAAATGTGTAAGACCATAGTTGAAAGACACCATGGCAA-GT-ACATGAAAAGAATAAGACCATGG
117492664 TTGAAAGATACCATGGCAACATGACAG
64 TTGAAAGATACCATGGCAACATGACAG
*
117492691 AAAATGAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AAAATG--T--GTAAGACCATAGTTGAAAGACACCATGGCA
117492732 TCATGTCAAA
Statistics
Matches: 197, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
90 81 0.41
91 3 0.02
92 81 0.41
93 4 0.02
94 1 0.01
96 27 0.14
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (90 bp):
AAAATGTGTAAGACCATAGTTGAAAGACACCATGGCAAGTACATGAAAAGAATAAGACCATGGTT
GAAAGATACCATGGCAACATGACAG
Found at i:117496479 original size:35 final size:35
Alignment explanation
Indices: 117496425--117496494 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
117496415 AATCCTTGGC
117496425 CAGCTAGTTCTTTTCTGTTTATCCTCCAGCACACA
1 CAGCTAGTTCTTTTCTGTTTATCCTCCAGCACACA
117496460 CAGCTAGTTCCTTTT-TGTTTATCCTCCAGCACACA
1 CAGCTAGTT-CTTTTCTGTTTATCCTCCAGCACACA
117496495 TACTTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37
Consensus pattern (35 bp):
CAGCTAGTTCTTTTCTGTTTATCCTCCAGCACACA
Found at i:117502608 original size:28 final size:29
Alignment explanation
Indices: 117502552--117502624 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
117502542 CATAATTTAA
117502552 AATAAAAATAATATATATATGAAATATAT
1 AATAAAAATAATATATATATGAAATATAT
* *
117502581 AATAAAATATAATTTATA-AGTAAAATATAGAAT
1 AATAAAA-ATAATATATATA-TGAAATAT---AT
117502614 AATAAAAATAA
1 AATAAAAATAA
117502625 CATGATGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 8 0.22
30 16 0.43
32 4 0.11
33 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (29 bp):
AATAAAAATAATATATATATGAAATATAT
Found at i:117505182 original size:11 final size:11
Alignment explanation
Indices: 117505168--117505212 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
117505158 ATATAAATAT
117505168 TATTTTATTAA
1 TATTTTATTAA
*
117505179 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
117505192 TATTTTATTAT
1 TATTTTATTAA
117505203 TATTTTATTA
1 TATTTTATTA
117505213 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:117507066 original size:21 final size:21
Alignment explanation
Indices: 117507042--117507113 Score: 117
Period size: 21 Copynumber: 3.3 Consensus size: 21
117507032 TGAGGTTCGC
117507042 GGGTTTAGGGTTTAGGGTTTA
1 GGGTTTAGGGTTTAGGGTTTA
117507063 GGGTTTAGGGTTTAGGGTTTA
1 GGGTTTAGGGTTTAGGGTTTA
117507084 GGGTTTAGGGGTTTAGGGTTTTA
1 GGGTTTA-GGGTTTAGGG-TTTA
*
117507107 GGTTTTA
1 GGGTTTA
117507114 AAGATACCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 28 0.58
22 10 0.21
23 10 0.21
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (21 bp):
GGGTTTAGGGTTTAGGGTTTA
Found at i:117507113 original size:7 final size:7
Alignment explanation
Indices: 117507042--117507104 Score: 117
Period size: 7 Copynumber: 8.9 Consensus size: 7
117507032 TGAGGTTCGC
117507042 GGGTTTA
1 GGGTTTA
117507049 GGGTTTA
1 GGGTTTA
117507056 GGGTTTA
1 GGGTTTA
117507063 GGGTTTA
1 GGGTTTA
117507070 GGGTTTA
1 GGGTTTA
117507077 GGGTTTA
1 GGGTTTA
117507084 GGGTTTA
1 GGGTTTA
117507091 GGGGTTTA
1 -GGGTTTA
117507099 GGGTTT
1 GGGTTT
117507105 TAGGTTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 48 0.87
8 7 0.13
ACGTcount: A:0.13, C:0.00, G:0.44, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:117507203 original size:45 final size:46
Alignment explanation
Indices: 117507113--117507225 Score: 210
Period size: 45 Copynumber: 2.5 Consensus size: 46
117507103 TTTAGGTTTT
117507113 AAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTG
*
117507159 AAAGATACCATGGCAACATGATGGG-AATGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTG
117507204 AAAGATACCATGGCAACATGAC
1 AAAGATACCATGGCAACATGAC
117507226 ATGAGGTACC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 41 0.63
46 24 0.37
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (46 bp):
AAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTG
Found at i:117507286 original size:69 final size:68
Alignment explanation
Indices: 117507164--117507292 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 68
117507154 GGTTGAAAGA
** * *
117507164 TACCATGGCAACATGATGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
1 TACCATGGCAACATGATGAAAATGAATAAGACCATAGTTGAAAGACACCATGGCAACATGACATG
117507229 AGG
66 AGG
* * * *
117507232 TACCATGGCAACATGATAGAAAATGAGTAAGACCATAGTTGAAAGGCACTATGGCATCATG
1 TACCATGGCAACATGAT-GAAAATGAATAAGACCATAGTTGAAAGACACCATGGCAACATG
117507293 TCCAAGATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
68 17 0.33
69 35 0.67
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (68 bp):
TACCATGGCAACATGATGAAAATGAATAAGACCATAGTTGAAAGACACCATGGCAACATGACATG
AGG
Found at i:117510814 original size:19 final size:21
Alignment explanation
Indices: 117510759--117510815 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
117510749 AAAAAATAAT
117510759 AAAAATAAAAATAAAAGCTAAG
1 AAAAATAAAAATAAAAGC-AAG
* * * *
117510781 CATAATAATACTAAAA-C-AG
1 AAAAATAAAAATAAAAGCAAG
117510800 AAAAATAAAAATAAAA
1 AAAAATAAAAATAAAA
117510816 ATAAGAAGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
19 14 0.52
21 1 0.04
22 12 0.44
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAATAAAAGCAAG
Found at i:117510883 original size:4 final size:4
Alignment explanation
Indices: 117510874--117510900 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
117510864 AAATAAGAAA
117510874 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
117510901 AATAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:117513261 original size:15 final size:14
Alignment explanation
Indices: 117513237--117513267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
117513227 TTCATTCACA
117513237 TCTCCTTTCTCCTC
1 TCTCCTTTCTCCTC
117513251 TCTCACTTTCTCCTC
1 TCTC-CTTTCTCCTC
117513266 TC
1 TC
117513268 ATTTTTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (14 bp):
TCTCCTTTCTCCTC
Found at i:117525644 original size:14 final size:14
Alignment explanation
Indices: 117525627--117525670 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
117525617 ATTTTTTTAA
117525627 TAATTTTTTATATT
1 TAATTTTTTATATT
**
117525641 TAATTTTAAATATT
1 TAATTTTTTATATT
*
117525655 ATAATTTATTATATT
1 -TAATTTTTTATATT
117525670 T
1 T
117525671 TATAAGACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTTTATATT
Found at i:117539580 original size:24 final size:24
Alignment explanation
Indices: 117539529--117539743 Score: 344
Period size: 24 Copynumber: 9.0 Consensus size: 24
117539519 GCTTTATCAT
*
117539529 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
117539554 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
117539578 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
117539601 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
117539625 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
117539649 ATAACTGGGACATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
117539673 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
117539697 ATAACTGGGACATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
117539721 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
117539744 TCACTTCCTC
Statistics
Matches: 178, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 23 0.13
24 143 0.80
25 12 0.07
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:117539818 original size:20 final size:20
Alignment explanation
Indices: 117539793--117539893 Score: 184
Period size: 20 Copynumber: 5.0 Consensus size: 20
117539783 TTATGATTAC
117539793 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
117539813 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117539833 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
117539853 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
117539873 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
117539893 A
1 A
117539894 CCATATTTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:117544854 original size:50 final size:50
Alignment explanation
Indices: 117544779--117544955 Score: 291
Period size: 50 Copynumber: 3.5 Consensus size: 50
117544769 CCATGGCAAC
117544779 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
117544829 AAGTGATAAGTAATAGCTTTGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
117544879 AAGTGATAAGTGATAGCTTCGGCTACACTTATCCGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
117544929 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
117544956 CTGATCAGTG
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 93 0.79
51 24 0.21
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:117544969 original size:31 final size:31
Alignment explanation
Indices: 117544931--117545048 Score: 209
Period size: 31 Copynumber: 3.8 Consensus size: 31
117544921 ACAAATGACA
117544931 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
117544962 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
117544993 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
117545024 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
117545049 AAGTAACAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:117545136 original size:47 final size:46
Alignment explanation
Indices: 117545066--117545232 Score: 208
Period size: 47 Copynumber: 3.5 Consensus size: 46
117545056 AAGTGATTTC
* * *
117545066 CGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATATGCTA
1 CGTATAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATA
* * *
117545112 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATA
* *
117545159 CGTGTAAGACCATAGCTGGGATATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATAGCTGGGATATGGCATC-A-GTGTGATATGTGA-TA
* *
117545208 CGTGTAAGACCATAGCTGGGCTATG
1 CGTATAAGACCATAGCTGGGATATG
117545233 CTGTAACACT
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
46 28 0.26
47 43 0.40
48 11 0.10
49 25 0.23
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATAGCTGGGATATGGCATCAGTGTGATATGTGATA
Found at i:117547112 original size:39 final size:39
Alignment explanation
Indices: 117547049--117547208 Score: 266
Period size: 39 Copynumber: 4.1 Consensus size: 39
117547039 ATTACCAGCA
* *
117547049 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGACACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
117547088 CCAACACGAAACCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
117547127 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
117547166 CCAGCACGAAGCCTGTGGGACTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
117547205 CCAG
1 CCAG
117547209 TGTCTTGCAT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 113 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:117553069 original size:23 final size:22
Alignment explanation
Indices: 117553001--117553075 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
117552991 CCTGATCAGT
** *
117553001 ATACGACACATAAAGTGCCTAA
1 ATACGACACACGAGGTGCCTAA
* *
117553023 A-ACAACACACGAGGTGCCT-G
1 ATACGACACACGAGGTGCCTAA
117553043 ATACGACACACGAGGTGCCTAAA
1 ATACGACACACGAGGTGCCT-AA
117553066 ATACGACACA
1 ATACGACACA
117553076 TAAAGTGCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.02
21 31 0.72
22 1 0.02
23 10 0.23
ACGTcount: A:0.41, C:0.27, G:0.19, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTAA
Found at i:117553483 original size:15 final size:15
Alignment explanation
Indices: 117553458--117553515 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
117553448 TCATGTATAT
117553458 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
117553474 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
117553489 AATAATTTCAATCAA
1 TATAAATTCAATCAA
117553504 TATAAATTCAAT
1 TATAAATTCAAT
117553516 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:117554786 original size:5 final size:5
Alignment explanation
Indices: 117554778--117554807 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
117554768 AGTTTATATA
117554778 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
117554808 TAAAACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:117554791 original size:13 final size:13
Alignment explanation
Indices: 117554773--117554853 Score: 53
Period size: 15 Copynumber: 6.2 Consensus size: 13
117554763 TCTTTAGTTT
117554773 ATATAATAATATA
1 ATATAATAATATA
117554786 ATATAATATAATATA
1 ATAT-A-ATAATATA
*
117554801 ATATAAT--TAAA
1 ATATAATAATATA
*
117554812 ACATAA-AATAT-
1 ATATAATAATATA
* * *
117554823 CTTTATTATATAATA
1 ATATAATA-AT-ATA
117554838 ATATAATAATATA
1 ATATAATAATATA
117554851 ATA
1 ATA
117554854 ATATACTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
11 10 0.20
12 3 0.06
13 14 0.28
14 6 0.12
15 17 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:117561233 original size:26 final size:25
Alignment explanation
Indices: 117561197--117561280 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
117561187 CATGAAATTC
117561197 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAAC-CA
117561223 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
*
117561249 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACC-A
117561275 TTATCA
1 TTATCA
117561281 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
25 2 0.04
26 52 0.95
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:117562481 original size:23 final size:22
Alignment explanation
Indices: 117562429--117562503 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
117562419 CCTGATCAGT
** *
117562429 ATACGACACATAAAGTGCCTAA
1 ATACGACACACGAGGTGCCTAA
* *
117562451 A-ACAACACACGAGGTGTCT-A
1 ATACGACACACGAGGTGCCTAA
117562471 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCT-AA
117562494 ATACGACACA
1 ATACGACACA
117562504 TAAAGTGCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.05
21 29 0.67
22 1 0.02
23 11 0.26
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTAA
Found at i:117562515 original size:23 final size:22
Alignment explanation
Indices: 117562429--117562513 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
117562419 CCTGATCAGT
*
117562429 ATACGACACATAAAGTGCCTAA
1 ATACGACACACAAAGTGCCTAA
* * * *
117562451 A-ACAACACACGAGGTGTCT-A
1 ATACGACACACAAAGTGCCTAA
* *
117562471 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCT-AA
*
117562494 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
117562514 GATCGATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.04
21 29 0.58
22 1 0.02
23 18 0.36
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (22 bp):
ATACGACACACAAAGTGCCTAA
Found at i:117562911 original size:15 final size:15
Alignment explanation
Indices: 117562886--117562943 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
117562876 TCATGTATAT
117562886 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
117562902 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
117562917 AATAATTTCAATCAA
1 TATAAATTCAATCAA
117562932 TATAAATTCAAT
1 TATAAATTCAAT
117562944 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:117564219 original size:5 final size:5
Alignment explanation
Indices: 117564211--117564237 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
117564201 TCTTTAGTTT
117564211 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
117564238 TGTAAGGCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:117565485 original size:25 final size:26
Alignment explanation
Indices: 117565436--117565491 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
117565426 GTTTTACTTG
*
117565436 TTCATTTATTTATTGGTGAATATT-A
1 TTCATTTAATTATTGGTGAATATTAA
117565461 TTCATTTACATTATT-G-GAATCATTAA
1 TTCATTTA-ATTATTGGTGAAT-ATTAA
117565487 TTCAT
1 TTCAT
117565492 AATTCTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.15
25 12 0.44
26 11 0.41
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (26 bp):
TTCATTTAATTATTGGTGAATATTAA
Found at i:117565644 original size:3 final size:3
Alignment explanation
Indices: 117565638--117565736 Score: 114
Period size: 3 Copynumber: 33.0 Consensus size: 3
117565628 CATCATCATC
117565638 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
117565683 ATT ATTT ATT ATT ATT ATT ATT GTT ACTT -TT GTC ATT ATT A-T ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
*
117565728 ATT ACT ATT
1 ATT ATT ATT
117565737 GGTATTATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
2 5 0.06
3 72 0.87
4 6 0.07
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:117567704 original size:8 final size:8
Alignment explanation
Indices: 117567691--117567719 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
117567681 TATCTTTATT
117567691 ATATAATA
1 ATATAATA
117567699 ATATAATA
1 ATATAATA
117567707 ATATAATA
1 ATATAATA
117567715 ATATA
1 ATATA
117567720 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:117569790 original size:31 final size:30
Alignment explanation
Indices: 117569739--117569796 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
117569729 AGGGCAAACC
* *
117569739 TTTCAAAATGATTAAATAATGGCCAAATCT
1 TTTCAAAATGATCAAATAATGACCAAATCT
*
117569769 TTTCAAAATTGCTCAAATAATGACCAAA
1 TTTCAAAA-TGATCAAATAATGACCAAA
117569797 CAAGGATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.31
Consensus pattern (30 bp):
TTTCAAAATGATCAAATAATGACCAAATCT
Found at i:117575526 original size:10 final size:10
Alignment explanation
Indices: 117575511--117575569 Score: 84
Period size: 10 Copynumber: 5.9 Consensus size: 10
117575501 AATTTTAGCT
117575511 TTTATCTTTA
1 TTTATCTTTA
*
117575521 TTTATCCTTA
1 TTTATCTTTA
117575531 TTTATCTTTA
1 TTTATCTTTA
*
117575541 ATTATCTTTA
1 TTTATCTTTA
117575551 TTTAT-TTGTA
1 TTTATCTT-TA
117575561 TTTATCTTT
1 TTTATCTTT
117575570 TAGAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:117577108 original size:41 final size:35
Alignment explanation
Indices: 117577004--117577109 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
117576994 CACTTGCCTC
*
117577004 TTCCCACTCTCCCATGATGTCTGCCACCAGCACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
117577039 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
*
117577074 TTCCCATTCTCCCATGCTGTCTGCCACC-GACACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAG-CACCA
117577109 T
1 T
117577110 CACACACTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 1 0.01
35 67 0.99
ACGTcount: A:0.19, C:0.44, G:0.11, T:0.25
Consensus pattern (35 bp):
TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
Found at i:117577517 original size:12 final size:12
Alignment explanation
Indices: 117577488--117577541 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 12
117577478 ATTAAAACAT
117577488 AAAAAAATATAC
1 AAAAAAATATAC
117577500 ATAAAAAAATATAC
1 --AAAAAAATATAC
117577514 AAAAAAATAT--
1 AAAAAAATATAC
117577524 AAAAAAA-ATAC
1 AAAAAAATATAC
117577535 AAAAAAA
1 AAAAAAA
117577542 AAAATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.05
10 7 0.18
11 7 0.18
12 10 0.26
14 12 0.32
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:117577542 original size:12 final size:12
Alignment explanation
Indices: 117577488--117577543 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
117577478 ATTAAAACAT
*
117577488 AAAAAAATATAC
1 AAAAAAAAATAC
* *
117577500 ATAAAAAAATAT
1 AAAAAAAAATAC
*
117577512 ACAAAAAAATA-
1 AAAAAAAAATAC
*
117577523 TAAAAAAAATAC
1 AAAAAAAAATAC
117577535 AAAAAAAAA
1 AAAAAAAAA
117577544 AATTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATAC
Found at i:117577664 original size:11 final size:11
Alignment explanation
Indices: 117577648--117577682 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
117577638 CCGGATTCCC
117577648 CTCCCTTCTCT
1 CTCCCTTCTCT
117577659 CTCCCTTCTCT
1 CTCCCTTCTCT
117577670 CTTCCC-TCTCT
1 C-TCCCTTCTCT
117577681 CT
1 CT
117577683 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:117578170 original size:3 final size:3
Alignment explanation
Indices: 117578162--117578201 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
117578152 TGCATTTCAA
117578162 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
117578202 GAAATACATT
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:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:117578293 original size:3 final size:3
Alignment explanation
Indices: 117578265--117578307 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
117578255 TTCTATTACT
* *
117578265 TTA TT- TTA ATA TTT TTA TTAA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T
117578308 ATATCCTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:117579024 original size:16 final size:16
Alignment explanation
Indices: 117578988--117579026 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
117578978 ATATTTTTGC
*
117578988 ATATTATCTTATATAT
1 ATATTACCTTATATAT
117579004 ATATTACCTTATAT-T
1 ATATTACCTTATATAT
117579019 ATTATTAC
1 A-TATTAC
117579027 TAAATGTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTACCTTATATAT
Found at i:117591357 original size:115 final size:116
Alignment explanation
Indices: 117590961--117592411 Score: 2636
Period size: 116 Copynumber: 12.6 Consensus size: 116
117590951 CGTTGAGGTA
* *
117590961 TTTTTAATTGTTGTT-TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTCGGGGCACGC
1 TTTTT-ATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGC
117591025 TGAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
65 TGAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591076 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591141 GAGGTATTTTTAGTTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
66 GAGGTATTTTTAG-TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591192 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591257 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
** * *
117591307 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTATGAGAAGTGAGTTGAGCCT-TGGGCATGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591371 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
117591422 TTTTTATTTTTGTTGCTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591486 GA-GTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
117591535 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591600 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591651 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591716 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
117591766 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591831 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591882 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591947 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
117591997 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117592062 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117592113 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
*
117592178 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
*
117592229 TTTTTATTTTTATTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117592294 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* * *
117592345 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGGGCTTC-GGACACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117592409 GAG
66 GAG
117592412 TGAGTTGAGC
Statistics
Matches: 1295, Mismatches: 32, Indels: 18
0.96 0.02 0.01
Matches are distributed among these distances:
113 52 0.04
114 122 0.09
115 500 0.39
116 621 0.48
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (116 bp):
TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:117591828 original size:231 final size:231
Alignment explanation
Indices: 117590961--117592411 Score: 2698
Period size: 231 Copynumber: 6.3 Consensus size: 231
117590951 CGTTGAGGTA
* *
117590961 TTTTTAATTGTTGTT-TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTCGGGGCACGC
1 TTTTT-ATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGC
117591025 TGAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTT
65 TGAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTT
* *
117591090 GTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT
130 GTTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAG-
117591155 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C
194 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591192 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591257 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
* *
117591322 TTCAAAATCAACTCATATTATGAGAAGTGAGTTGAGCCTT-GGGCATGCTGAGGTATTTTTAGTT
131 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
117591386 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
196 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
117591422 TTTTTATTTTTGTTGCTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591486 GA-GTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
117591550 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
131 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
117591615 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
196 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591651 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591716 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
117591781 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
131 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
117591846 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
196 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117591882 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117591947 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
117592012 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
131 TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
117592077 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
196 TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
117592113 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
* *
117592178 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCCTTTTTATTTTTATT
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAG-CTTTTTATTTTTGTT
* *
117592243 GTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT
130 GTTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGT
117592308 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
195 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* * *
117592345 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGGGCTTC-GGACACGCT
1 TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
117592409 GAG
66 GAG
117592412 TGAGTTGAGC
Statistics
Matches: 1195, Mismatches: 19, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
228 101 0.08
229 159 0.13
230 94 0.08
231 674 0.56
232 167 0.14
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (231 bp):
TTTTTATTTTTGTTGTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCTTTTTATTTTTGTTG
TTCAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTTAGTT
TTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:117593116 original size:41 final size:35
Alignment explanation
Indices: 117593012--117593117 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
117593002 CACTTGCCTC
*
117593012 TTCCCACTCTCCCATGATGTCTGCCACCAGCACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
117593047 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
*
117593082 TTCCCATTCTCCCATGCTGTCTGCCACC-GACACCA
1 TTCCCATTCTCCCATGATGTCTGCCACCAG-CACCA
117593117 T
1 T
117593118 CACACACTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 1 0.01
35 67 0.99
ACGTcount: A:0.19, C:0.44, G:0.11, T:0.25
Consensus pattern (35 bp):
TTCCCATTCTCCCATGATGTCTGCCACCAGCACCA
Found at i:117593507 original size:13 final size:13
Alignment explanation
Indices: 117593489--117593527 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
117593479 ATATATTAAA
117593489 ACATAAAAAATAT
1 ACATAAAAAATAT
117593502 ACATAAAAAATAT
1 ACATAAAAAATAT
*
117593515 ACA-AAAATATAT
1 ACATAAAAAATAT
117593527 A
1 A
117593528 AAAAAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
ACATAAAAAATAT
Found at i:117593521 original size:12 final size:12
Alignment explanation
Indices: 117593493--117593533 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
117593483 ATTAAAACAT
117593493 AAAAAATATACA
1 AAAAAATATACA
117593505 TAAAAAATATACA
1 -AAAAAATATACA
*
117593518 AAAATATATA-A
1 AAAAAATATACA
117593529 AAAAA
1 AAAAA
117593534 TACAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 5 0.19
12 9 0.35
13 12 0.46
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAATATACA
Found at i:117593522 original size:10 final size:10
Alignment explanation
Indices: 117593507--117593541 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
117593497 AATATACATA
117593507 AAAAATATAC
1 AAAAATATAC
*
117593517 AAAAATATAT
1 AAAAATATAC
*
117593527 AAAAAAATAC
1 AAAAATATAC
117593537 AAAAA
1 AAAAA
117593542 AAAAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATATAC
Found at i:117593534 original size:12 final size:12
Alignment explanation
Indices: 117593493--117593544 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
117593483 ATTAAAACAT
*
117593493 AAAAAATATACA
1 AAAAAATATATA
*
117593505 TAAAAA-ATATA
1 AAAAAATATATA
*
117593516 CAAAAATATATA
1 AAAAAATATATA
*
117593528 AAAAAATACA-A
1 AAAAAATATATA
117593539 AAAAAA
1 AAAAAA
117593545 AATTATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 16 0.47
12 18 0.53
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAATATATA
Found at i:117593668 original size:11 final size:11
Alignment explanation
Indices: 117593652--117593686 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
117593642 CCGGATTCCC
117593652 CTCCCTTCTCT
1 CTCCCTTCTCT
117593663 CTCCCTTCTCT
1 CTCCCTTCTCT
117593674 CTTCCC-TCTCT
1 C-TCCCTTCTCT
117593685 CT
1 CT
117593687 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:117594172 original size:3 final size:3
Alignment explanation
Indices: 117594164--117594215 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
117594154 TGCATTTCAA
* *
117594164 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
117594212 TAT T
1 TAT T
117594216 GAAATACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:117594307 original size:3 final size:3
Alignment explanation
Indices: 117594279--117594324 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
117594269 TTCTATTACT
* *
117594279 TTA TT- TTA ATA TTT TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
117594324 T
1 T
117594325 ATATCCTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:117594575 original size:31 final size:30
Alignment explanation
Indices: 117594532--117594612 Score: 76
Period size: 33 Copynumber: 2.6 Consensus size: 30
117594522 TTCATATATA
* *
117594532 ATAT-TATGTATATATTTTAATATTATCAGT
1 ATATATATATATATATTTTAATACTATCA-T
*
117594562 -TATATATACTATATGATTTCTAATACTATTAT
1 ATATATATA-TATAT-ATTT-TAATACTATCAT
*
117594594 ATATATATATACATATTTT
1 ATATATATATATATATTTT
117594613 CTTAGTACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 3 0.07
30 4 0.10
31 9 0.21
32 9 0.21
33 17 0.40
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (30 bp):
ATATATATATATATATTTTAATACTATCAT
Found at i:117595036 original size:16 final size:16
Alignment explanation
Indices: 117595000--117595038 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
117594990 ATATTTTTGC
*
117595000 ATATTATCTTATATAT
1 ATATTACCTTATATAT
117595016 ATATTACCTTATAT-T
1 ATATTACCTTATATAT
117595031 ATTATTAC
1 A-TATTAC
117595039 TAAATGTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTACCTTATATAT
Found at i:117597435 original size:20 final size:19
Alignment explanation
Indices: 117597395--117597446 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
117597385 AACTGGAATT
*
117597395 AAATTTTATTTATGTTTCAAA
1 AAATTTT-TTTTTG-TTCAAA
117597416 AAATATTTTTTTTGTTCAAA
1 AAAT-TTTTTTTTGTTCAAA
*
117597436 TAATTTTTTTT
1 AAATTTTTTTT
117597447 GTAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 9 0.32
22 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
AAATTTTTTTTTGTTCAAA
Found at i:117597460 original size:18 final size:18
Alignment explanation
Indices: 117597415--117597460 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
117597405 TATGTTTCAA
117597415 AAAAT-ATTTTTTTTGTT
1 AAAATAATTTTTTTTGTT
*
117597432 CAAATAATTTTTTTTG-T
1 AAAATAATTTTTTTTGTT
*
117597449 AAAATTATTTTT
1 AAAATAATTTTT
117597461 CAAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
AAAATAATTTTTTTTGTT
Found at i:117601591 original size:39 final size:39
Alignment explanation
Indices: 117601546--117601622 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
117601536 TCTATATTCA
117601546 ATAATTACTATAAATTTCAAGAGCAAATTAGGAATTAAT
1 ATAATTACTATAAATTTCAAGAGCAAATTAGGAATTAAT
117601585 ATAATTACTATAAATTTCAAGAGCAAATTAGGAATTAA
1 ATAATTACTATAAATTTCAAGAGCAAATTAGGAATTAA
117601623 ATCGAATCCT
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:0.49, C:0.08, G:0.10, T:0.32
Consensus pattern (39 bp):
ATAATTACTATAAATTTCAAGAGCAAATTAGGAATTAAT
Found at i:117605083 original size:18 final size:17
Alignment explanation
Indices: 117605053--117605086 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
117605043 TTGAATTAAT
*
117605053 GAAATTATGAATTAAAG
1 GAAATTATAAATTAAAG
117605070 GAAATTTATAAATTAAA
1 GAAA-TTATAAATTAAA
117605087 TAAGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (17 bp):
GAAATTATAAATTAAAG
Found at i:117606405 original size:53 final size:54
Alignment explanation
Indices: 117606286--117606444 Score: 225
Period size: 53 Copynumber: 3.0 Consensus size: 54
117606276 GATATGTGCG
* * * *
117606286 CCCGTATAAGACCATATCTGAGCTATGGCATCGGTGTAATGTGAT-ATGTG-TT
1 CCCGTATAAGACCATAGCTGGGCTATGGCGTCGGTGTGATGTGATAATGTGATT
* *
117606338 CCCGTATAAGACCATAGCTGGGCTATGGCGCCGGTATGATGTGATAATGTGATT
1 CCCGTATAAGACCATAGCTGGGCTATGGCGTCGGTGTGATGTGATAATGTGATT
* *
117606392 -CTGTATAAGACCATAGCTGGGCTATAGCGTCGGTGTGATGTGATAATGTGATT
1 CCCGTATAAGACCATAGCTGGGCTATGGCGTCGGTGTGATGTGATAATGTGATT
117606445 GTAATAGCCT
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
52 39 0.41
53 54 0.57
54 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (54 bp):
CCCGTATAAGACCATAGCTGGGCTATGGCGTCGGTGTGATGTGATAATGTGATT
Found at i:117613409 original size:3 final size:3
Alignment explanation
Indices: 117613401--117613441 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
117613391 TTAGGATGCA
117613401 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
117613442 AGACTTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:117616491 original size:51 final size:51
Alignment explanation
Indices: 117616410--117616576 Score: 289
Period size: 51 Copynumber: 3.3 Consensus size: 51
117616400 ACTTCTGATC
* *
117616410 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
117616461 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
117616512 AGTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
117616563 AGTGACAAGTGATA
1 AGTGACAAGTGATA
117616577 CATGTGATCA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 109 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:117618644 original size:3 final size:3
Alignment explanation
Indices: 117618631--117618715 Score: 80
Period size: 3 Copynumber: 28.0 Consensus size: 3
117618621 AAATTAATTA
* * * * *
117618631 ATT ACT ATT ATT ATTT CTT ATT ATT GTT ATC ATT ATT ATT ATT AGT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
117618677 ATT ATT ATT ATC ATT ATC ATT ATT GTT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
117618716 CTTAAAACTA
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
3 61 0.97
4 2 0.03
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:117619075 original size:3 final size:3
Alignment explanation
Indices: 117619061--117619150 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
117619051 CAAAAATTCA
* *
117619061 TAT TAT TCAT TAT TAT TAC TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
117619107 TAC TAT TAC GAT T-T CTAT TAT TAT TAT TAC TAT TAT TTT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
117619151 ACATTTTTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
2 1 0.01
3 65 0.93
4 4 0.06
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:117619089 original size:15 final size:15
Alignment explanation
Indices: 117619064--117619150 Score: 108
Period size: 15 Copynumber: 5.9 Consensus size: 15
117619054 AAATTCATAT
117619064 TATTCATTATTATTAC
1 TATT-ATTATTATTAC
*
117619080 TATTATTATTATTAA
1 TATTATTATTATTAC
117619095 TATTATTATTATTAC
1 TATTATTATTATTAC
**
117619110 TATTACGA-T-TT-C
1 TATTATTATTATTAC
117619122 TATTATTATTATTAC
1 TATTATTATTATTAC
*
117619137 TATTATTTTTATTA
1 TATTATTATTATTA
117619151 ACATTTTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
12 7 0.11
13 3 0.05
14 3 0.05
15 44 0.72
16 4 0.07
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:117619278 original size:32 final size:32
Alignment explanation
Indices: 117619242--117619316 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
117619232 TTTCACTAGA
* *
117619242 ATTTTTTTATT-TTATTTATTTATTTCATT-TTT
1 ATTTTTTTATTATTA-TTA-TTATCTCATTATAT
*
117619274 ATTTTGTTATTATTATTATTATCTCATTATAT
1 ATTTTTTTATTATTATTATTATCTCATTATAT
*
117619306 ATTTATTTATT
1 ATTTTTTTATT
117619317 CATTTATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.25
32 24 0.67
33 3 0.08
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (32 bp):
ATTTTTTTATTATTATTATTATCTCATTATAT
Found at i:117622948 original size:30 final size:30
Alignment explanation
Indices: 117622912--117622972 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
117622902 GAACATAATG
117622912 AATATATATTAAGAACCGAGGAACTGTCTT
1 AATATATATTAAGAACCGAGGAACTGTCTT
117622942 AATATATATTAAGAACCGAGGAACTGTCTT
1 AATATATATTAAGAACCGAGGAACTGTCTT
117622972 A
1 A
117622973 CTGGTGCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (30 bp):
AATATATATTAAGAACCGAGGAACTGTCTT
Found at i:117625996 original size:6 final size:7
Alignment explanation
Indices: 117625980--117626009 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
117625970 TTTTTTCATA
117625980 TTAATTT
1 TTAATTT
*
117625987 TTTATTT
1 TTAATTT
117625994 TTAATTT
1 TTAATTT
117626001 TTAATTT
1 TTAATTT
117626008 TT
1 TT
117626010 TTTGACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTAATTT
Found at i:117627269 original size:6 final size:6
Alignment explanation
Indices: 117627258--117627282 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
117627248 AATGAAGAAT
117627258 ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA A
117627283 AAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:117628738 original size:23 final size:22
Alignment explanation
Indices: 117628695--117628738 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
117628685 ATCCATATAT
*
117628695 ATTTTATACTTTCTCTTTTTTA
1 ATTTTATACTTTCTCTATTTTA
117628717 ATTTTCATACTTT-TCATATTTT
1 ATTTT-ATACTTTCTC-TATTTT
117628739 TCTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTATACTTTCTCTATTTTA
Found at i:117631949 original size:16 final size:17
Alignment explanation
Indices: 117631916--117631949 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
117631906 GTAAAATTTT
*
117631916 AATCTTAAATATAATAA
1 AATCTTAAATAAAATAA
117631933 AATCTTAAA-AAAATAA
1 AATCTTAAATAAAATAA
117631949 A
1 A
117631950 GAGAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AATCTTAAATAAAATAA
Found at i:117631992 original size:68 final size:68
Alignment explanation
Indices: 117631903--117632058 Score: 267
Period size: 68 Copynumber: 2.3 Consensus size: 68
117631893 GTAGAATAAA
* *
117631903 GGTGTAAAATTTTAATCTTAAATATAATAAAATCTTAAAAAAATAAAGAGAAATAATCTACTTAA
1 GGTGTAAAATTTTAATTTTAAATATAATAAAATATTAAAAAAATAAAGAGAAATAATCTACTTAA
117631968 ATT
66 ATT
* * *
117631971 GTTGTAAAATTTTAATTTTAAATATAATAAAATATTAAAAAAGTAAAGAGAAATAATCTATTTAA
1 GGTGTAAAATTTTAATTTTAAATATAATAAAATATTAAAAAAATAAAGAGAAATAATCTACTTAA
117632036 ATT
66 ATT
117632039 GGTGTAAAATTTTAATTTTA
1 GGTGTAAAATTTTAATTTTA
117632059 TATAATTTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 82 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (68 bp):
GGTGTAAAATTTTAATTTTAAATATAATAAAATATTAAAAAAATAAAGAGAAATAATCTACTTAA
ATT
Found at i:117635349 original size:29 final size:30
Alignment explanation
Indices: 117635301--117635359 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
117635291 AAGACATTCA
*
117635301 TTTAACAGAGATAGCCACAAATG-CATCCT
1 TTTAACAGAGATAGCCACAAAGGACATCCT
**
117635330 TTTAACAGAGATAGTTACAAAGGACATCCT
1 TTTAACAGAGATAGCCACAAAGGACATCCT
117635360 AATTATAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (30 bp):
TTTAACAGAGATAGCCACAAAGGACATCCT
Found at i:117639190 original size:31 final size:32
Alignment explanation
Indices: 117639159--117639217 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
117639149 AAATTAAATT
117639159 TTTAACATA-AAG-ATTAATTTAT-TATTTAA
1 TTTAACATATAAGAATTAATTTATCTATTTAA
*
117639188 TTTAATATATAAGAATTAATTTATCTATTT
1 TTTAACATATAAGAATTAATTTATCTATTT
117639218 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 3 0.12
31 10 0.38
32 5 0.19
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
TTTAACATATAAGAATTAATTTATCTATTTAA
Found at i:117649169 original size:34 final size:34
Alignment explanation
Indices: 117649109--117649175 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
117649099 TTAGGATTTT
* *
117649109 AATTAAATTAGGATTTATGGTGTTTAAATAAATA
1 AATTAAATCAGGATTTAGGGTGTTTAAATAAATA
*
117649143 AATTAAATCAGGGTTCTAGGGT-TTTAAATAAAT
1 AATTAAATCAGGATT-TAGGGTGTTTAAATAAAT
117649176 TAAACTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (34 bp):
AATTAAATCAGGATTTAGGGTGTTTAAATAAATA
Found at i:117649215 original size:28 final size:29
Alignment explanation
Indices: 117649109--117649216 Score: 92
Period size: 28 Copynumber: 3.6 Consensus size: 29
117649099 TTAGGATTTT
*
117649109 AATTAAATTAGGATTTATGGTGTTTAAATAAATA
1 AATTAAATTAGGGTTTA-GG-GTTT--A-AAATA
* *
117649143 AATTAAATCAGGGTTCTAGGGTTTTAAATA
1 AATTAAATTAGGGTT-TAGGGTTTAAAATA
* * * *
117649173 AATTAAACTAAGGTTTAGTG-TTAAAATT
1 AATTAAATTAGGGTTTAGGGTTTAAAATA
117649201 AATTAAATTAGGGTTT
1 AATTAAATTAGGGTTT
117649217 TGTTTTTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
28 20 0.32
29 4 0.06
30 17 0.27
33 4 0.06
34 15 0.24
35 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.40
Consensus pattern (29 bp):
AATTAAATTAGGGTTTAGGGTTTAAAATA
Done.