Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold330
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: 1763736
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:1447699 original size:23 final size:24
Alignment explanation
Indices: 1447672--1447718 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1447662 TTGTTGAAAA
*
1447672 TTTAT-TTTCAATTG-ATTTGTGTT
1 TTTATGTTT-AATTGAATTTATGTT
1447695 TTTATGTTTAATTGAATTTATGTT
1 TTTATGTTTAATTGAATTTATGTT
1447719 CAATTCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.21, C:0.02, G:0.13, T:0.64
Consensus pattern (24 bp):
TTTATGTTTAATTGAATTTATGTT
Found at i:1449872 original size:20 final size:20
Alignment explanation
Indices: 1449827--1449878 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1449817 GTAGCCAAAC
**
1449827 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
1449847 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1449866 TTGTATCGATACA
1 TTGTATCGATACA
1449879 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1452140 original size:79 final size:79
Alignment explanation
Indices: 1452057--1452239 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 79
1452047 TAAAGCATCG
* * * ***
1452057 ATTTTCCACAATCGGGGATACTCTAACCCTGTTATTTTCGAGGGGATACTCCAACCTTGATTTTA
1 ATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCAAGGGGATACTCCAACCCCAATTTTA
*
1452122 TTTTCAAAACCCCA
66 TTTTCAAAACACCA
* ** * * *
1452136 ATTTTCTATAATCATGGATACTCCAACCCTATTATTTTTAAGGGGATACTCTAACCCCAATTTTA
1 ATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCAAGGGGATACTCCAACCCCAATTTTA
* **
1452201 TTTTCAGAACACTG
66 TTTTCAAAACACCA
1452215 ATTTTCCATAATCGGGGATACTCTA
1 ATTTTCCATAATCGGGGATACTCTA
1452240 GCCCCGTTGT
Statistics
Matches: 84, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
79 84 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
ATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCAAGGGGATACTCCAACCCCAATTTTA
TTTTCAAAACACCA
Found at i:1462731 original size:84 final size:84
Alignment explanation
Indices: 1462558--1462718 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 84
1462548 ACTCAAAGAA
* * * *
1462558 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
1462623 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
1462642 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
1462705 AA-AAGAAATGAGTT
64 AATAAGAAA-GAGTT
1462719 GCAAGTGGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 56 0.85
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:1465804 original size:20 final size:20
Alignment explanation
Indices: 1465759--1465810 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1465749 GTAGCCAAAC
**
1465759 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
1465779 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1465798 TTGTATCGATACA
1 TTGTATCGATACA
1465811 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1468057 original size:79 final size:78
Alignment explanation
Indices: 1467974--1468173 Score: 197
Period size: 79 Copynumber: 2.5 Consensus size: 78
1467964 AACCCCGGCC
* * *
1467974 TTATTTCTAAAGAATCGATTTTCCACAATCGGGGATACTCTAACCCTGTTATTTTCGAGGGGATA
1 TTATTT-TAAAGAAACGATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCGAGGGGATA
***
1468039 CTCCAACCTTGATT
65 CTCCAACCCCAATT
** * * ** * *
1468053 TTATTTTCAAA-ACCCCAATTTTCTATAATCATGGATACTCCAACCCTATTATTTTTGAGGGGAT
1 TTATTTT-AAAGA-AACGATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCGAGGGGAT
*
1468117 ACTCTAACCCCAATT
64 ACTCCAACCCCAATT
*
1468132 TTATTTT-CAGAACACTGATTTTCCATAATCGGGGATACTCTA
1 TTATTTTAAAGAA-AC-GATTTTCCATAATCGGGGATACTCTA
1468174 GCCCCGTTGT
Statistics
Matches: 94, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
77 1 0.01
78 4 0.04
79 89 0.95
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (78 bp):
TTATTTTAAAGAAACGATTTTCCATAATCGGGGATACTCTAACCCTATTATTTTCGAGGGGATAC
TCCAACCCCAATT
Found at i:1476081 original size:28 final size:28
Alignment explanation
Indices: 1476009--1476580 Score: 166
Period size: 28 Copynumber: 20.2 Consensus size: 28
1475999 AATACGATCT
* ** *
1476009 CTTTTCAAAGCCCATGAGTTAGTGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * *
1476038 CTTGT-AAAGTCC-ACCAGTTAGTGGTAC
1 CTTTTCAAAG-CCTACCAGTCAGTGGCAC
*
1476065 CTTTTCTAAGCCTACCAGTCAGTGGCAC
1 CTTTTCAAAGCCTACCAGTCAGTGGCAC
* ** *
1476093 TTTTTCAAAGCGGACAAAGTCAGTGGCATC
1 CTTTTCAAAGCCTAC-CAGTCAGTGGCA-C
* * * ** *
1476123 C-TTCCAAAACCCATAAGTCAGTGGTATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * * *
1476151 C-TTCCAAAGCCCACGAGTCAGTGTCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * * *
1476179 C-TTCCAAAGCCCACGAGTTAGTGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* *
1476207 CTTTT-AAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * *
1476235 C-TTTCAAAGCCCACGAGTGAGTGGCA-
1 CTTTTCAAAGCCTACCAGTCAGTGGCAC
* * **
1476261 TTTGTTCGAAAGCCCATGAGTCAGTGGCATC
1 CTT-TTC-AAAGCCTACCAGTCAGTGGCA-C
* * * *
1476292 C-TTCCAAATCCCACGAGTCAGTGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * * * * *
1476320 C-TTCCAATGCCCACAAGTTAATGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* * * *
1476348 C-TTCCAAAGCCCACAAGTGAGTGGCATC
1 CTTTTCAAAGCCTACCAGTCAGTGGCA-C
* **
1476376 C-TTCCAAAGCCTAGGAGTCAGTGGCAC
1 CTTTTCAAAGCCTACCAGTCAGTGGCAC
* * * *
1476403 ATTTTTAAAGTCC-ACAAGTCAATGGCAC
1 CTTTTCAAAG-CCTACCAGTCAGTGGCAC
** * * * *
1476431 CGCTTCAAAGCCCACAAGTCAATAGCAC
1 CTTTTCAAAGCCTACCAGTCAGTGGCAC
* * * * *
1476459 C-TTTCCAAGCCCACAAGTCAATAGCAC
1 CTTTTCAAAGCCTACCAGTCAGTGGCAC
*
1476486 CTTTTCGAAGCCTA-CATGTCAGTGGCAC
1 CTTTTCAAAGCCTACCA-GTCAGTGGCAC
* * * *
1476514 CCTTTCAAAGCCCACACAAGTCGGTGCCAAC
1 CTTTTCAAAGCCTAC-C-AGTCAGTGGC-AC
* *
1476545 TCTTTTCAAAGCCCACACAAGTTAGTGGCAC
1 -CTTTTCAAAGCCTAC-C-AGTCAGTGGCAC
*
1476576 TTTTT
1 CTTTT
1476581 TTTTAAAGCC
Statistics
Matches: 442, Mismatches: 79, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
27 40 0.09
28 309 0.70
29 50 0.11
30 14 0.03
31 5 0.01
32 24 0.05
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCTACCAGTCAGTGGCAC
Found at i:1476181 original size:56 final size:56
Alignment explanation
Indices: 1476110--1476528 Score: 364
Period size: 56 Copynumber: 7.5 Consensus size: 56
1476100 AAGCGGACAA
* ** *
1476110 AGTCAGTGGCATCCTTCCAAAACCCATAAGTCAGTGGTATCCTTCCAAAGCCCACG
1 AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACG
* * ** *
1476166 AGTCAGTGTCATCCTTCCAAAGCCCACGAGTTAGTGGCATCCTTTTAAAGCCCACA
1 AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACG
* * ** * *
1476222 AGTCAGTGGCATCCTTTCAAAGCCCACGAGTGAGTGGCATTTGTTCGAAAGCCCATG
1 AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCA-TCCTTCCAAAGCCCACG
* * *
1476279 AGTCAGTGGCATCCTTCCAAATCCCACGAGTCAGTGGCATCCTTCCAATGCCCACA
1 AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACG
* * * * * *
1476335 AGTTAATGGCATCCTTCCAAAGCCCACAAGTGAGTGGCATCCTTCCAAAGCCTAGG
1 AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACG
* ** * * * * *
1476391 AGTCAGTGGCA-CATTTTTAAAGTCCACAAGTCAATGGCACCGCTT-CAAAGCCCACA
1 AGTCAGTGGCATC-CTTCCAAAGCCCACGAGTCAGTGGCATC-CTTCCAAAGCCCACG
* * * * * * * *
1476447 AGTCAATAGCA-CCTTTCC-AAGCCCACAAGTCAATAGCA-CCTTTTCGAAGCCTAC-
1 AGTCAGTGGCATCC-TTCCAAAGCCCACGAGTCAGTGGCATCC-TTCCAAAGCCCACG
* *
1476501 ATGTCAGTGGCACCCTTTCAAAGCCCAC
1 A-GTCAGTGGCATCCTTCCAAAGCCCAC
1476529 ACAAGTCGGT
Statistics
Matches: 294, Mismatches: 60, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
53 1 0.00
54 4 0.01
55 38 0.13
56 201 0.68
57 50 0.17
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (56 bp):
AGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACG
Found at i:1476273 original size:113 final size:113
Alignment explanation
Indices: 1476109--1476476 Score: 406
Period size: 113 Copynumber: 3.3 Consensus size: 113
1476099 AAAGCGGACA
* * * *
1476109 AAGTCAGTGGCATCCTTCCAAAACCCATAAGTCAGTGGTA-TCCTTCCAAAGCCCACGAGTCAGT
1 AAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGAGTGGCATTCCTTCCAAAGCCCACGAGTCAGT
* * **
1476173 GTCATCCTTCCAAAGCCCACGAGTTAGTGGCATCCTTTTAAAGCCCAC
66 GGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCAC
* * ** * *
1476221 AAGTCAGTGGCATCCTTTCAAAGCCCACGAGTGAGTGGCATTTGTTCGAAAGCCCATGAGTCAGT
1 AAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGAGTGGCATTCCTTCCAAAGCCCACGAGTCAGT
* *
1476286 GGCATCCTTCCAAATCCCACGAGTCAGTGGCATCCTTCCAATGCCCAC
66 GGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCAC
* * * *
1476334 AAGTTAATGGCATCCTTCCAAAGCCCACAAGTGAGTGGCA-TCCTTCCAAAGCCTAGGAGTCAGT
1 AAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGAGTGGCATTCCTTCCAAAGCCCACGAGTCAGT
* ** * * * *
1476398 GGCA-CATTTTTAAAGTCCACAAGTCAATGGCACCGCTT-CAAAGCCCAC
66 GGCATC-CTTCCAAAGCCCACGAGTCAGTGGCATC-CTTCCAAAGCCCAC
* *
1476446 AAGTCAATAGCA-CCTTTCC-AAGCCCACAAGT
1 AAGTCAGTGGCATCC-TTCCAAAGCCCACAAGT
1476477 CAATAGCACC
Statistics
Matches: 216, Mismatches: 36, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
111 15 0.07
112 100 0.46
113 101 0.47
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (113 bp):
AAGTCAGTGGCATCCTTCCAAAGCCCACAAGTGAGTGGCATTCCTTCCAAAGCCCACGAGTCAGT
GGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCAC
Found at i:1476277 original size:141 final size:139
Alignment explanation
Indices: 1476014--1476528 Score: 486
Period size: 141 Copynumber: 3.7 Consensus size: 139
1476004 GATCTCTTTT
* * ** * * * * * *
1476014 CAAAGCCCATGAGTTAGTGGCATCCTTGTAAAGTCCACCAGTTAGTGGTACCTTTTCTAAGCCTA
1 CAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACAAGTTAATGGCACCTTTTCAAAGCCCA
* * ** * * * *
1476079 CCAGTCAGTGGCA-CTTTTTCAAAGCGGACAAAGTCAGTGGCATCCTTCCAAAACCCATAAGTCA
66 CAAGTCAGTGGCATC-CTTTCAAAGCCCAC-GAGTCAGTGGCAT-TTTTCAAAGCCCATAAGTCA
*
1476143 GTGGTATCCTTC
128 GTGGCATCCTTC
* * *
1476155 CAAAGCCCACGAGTCAGTGTCATCCTTCCAAAGCCCACGAGTTAGTGGCATCCTTTT-AAAGCCC
1 CAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACAAGTTAATGGCA-CCTTTTCAAAGCCC
* *
1476219 ACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTGAGTGGCATTTGTTCGAAAGCCCATGAGTCA
65 ACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCATTT-TTC-AAAGCCCATAAGTCA
1476284 GTGGCATCCTTC
128 GTGGCATCCTTC
* * *
1476296 CAAATCCCACGAGTCAGTGGCATCCTTCCAATGCCCACAAGTTAATGGCATCC-TTCCAAAGCCC
1 CAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACAAGTTAATGGCA-CCTTTTCAAAGCCC
* * * * * *
1476360 ACAAGTGAGTGGCATCCTTCCAAAGCCTAGGAGTCAGTGGCACATTTTT-AAAGTCCACAAGTCA
65 ACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGG--CATTTTTCAAAGCCCATAAGTCA
* *
1476424 ATGGCACCGCTT-
128 GTGGCATC-CTTC
* * * * * * *
1476436 CAAAGCCCACAAGTCAATAGCA-CCTTTCC-AAGCCCACAAGTCAATAGCACCTTTTCGAAGCCT
1 CAAAGCCCACGAGTCAGTGGCATCC-TTCCAAAGCCCACAAGTTAATGGCACCTTTTCAAAGCCC
* *
1476499 ACATGTCAGTGGCACCCTTTCAAAGCCCAC
65 ACAAGTCAGTGGCATCCTTTCAAAGCCCAC
1476529 ACAAGTCGGT
Statistics
Matches: 311, Mismatches: 53, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
138 2 0.01
139 52 0.17
140 55 0.18
141 188 0.60
142 9 0.03
143 5 0.02
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (139 bp):
CAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACAAGTTAATGGCACCTTTTCAAAGCCCA
CAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCATTTTTCAAAGCCCATAAGTCAGTG
GCATCCTTC
Found at i:1476293 original size:169 final size:168
Alignment explanation
Indices: 1476014--1476430 Score: 471
Period size: 169 Copynumber: 2.5 Consensus size: 168
1476004 GATCTCTTTT
* * * * * * * *
1476014 CAAAGCCCATGAGTTAGTGGCATCCTTGTAAAGTCCACCAGTTAGTGGTACCTTTTCTAAGCCTA
1 CAAAGCCCACGAGTTAGTGGCATCCTTCTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
*
1476079 CCAGTCAGTGGCACTTTTTCAAAGCGGACAAAGTCAGTGGCATCCTTCCAAAACCCATAAGTCAG
66 CCAGTCAGTGGCACTTTTTCAAAGC-GACAAAGTCAGTGGCATCCTTCCAAAACCCACAAGTCAG
* * * *
1476144 TGGTATCCTTCCAAAGCCCACGAGTCAGTGTCATCCTTC
130 TGGCATCCTTCCAAAGCCCACAAGTCAATGGCATCCTTC
*
1476183 CAAAGCCCACGAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCC
1 CAAAGCCCACGAGTTAGTGGCATCCTTCTAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCC
* * * * * *
1476247 ACGAGTGAGTGGCA-TTTGTTCGAAAGC-CCATGAGTCAGTGGCATCCTTCCAAATCCCACGAGT
65 ACCAGTCAGTGGCACTTT-TTC-AAAGCGACA-AAGTCAGTGGCATCCTTCCAAAACCCACAAGT
* *
1476310 CAGTGGCATCCTTCCAATGCCCACAAGTTAATGGCATCCTTC
127 CAGTGGCATCCTTCCAAAGCCCACAAGTCAATGGCATCCTTC
* * * * ** * * *
1476352 CAAAGCCCACAAGTGAGTGGCATCCTTCCAAAGCCTAGGAGTCAGTGGCACATTTTTAAAGTCCA
1 CAAAGCCCACGAGTTAGTGGCATCCTTCTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
* *
1476417 CAAGTCAATGGCAC
66 CCAGTCAGTGGCAC
1476431 CGCTTCAAAG
Statistics
Matches: 208, Mismatches: 34, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
168 6 0.03
169 195 0.94
170 7 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (168 bp):
CAAAGCCCACGAGTTAGTGGCATCCTTCTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
CCAGTCAGTGGCACTTTTTCAAAGCGACAAAGTCAGTGGCATCCTTCCAAAACCCACAAGTCAGT
GGCATCCTTCCAAAGCCCACAAGTCAATGGCATCCTTC
Found at i:1476552 original size:32 final size:32
Alignment explanation
Indices: 1476503--1476619 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 32
1476493 AAGCCTACAT
*
1476503 GTCAGTGGC-AC-CCTTTCAAAGCCCACACAA
1 GTCAGTGGCAACTCTTTTCAAAGCCCACACAA
* *
1476533 GTCGGTGCCAACTCTTTTCAAAGCCCACACAA
1 GTCAGTGGCAACTCTTTTCAAAGCCCACACAA
* * * *
1476565 GTTAGTGGC-ACTTTTTTTTTAAAGCCCATACAA
1 GTCAGTGGCAAC--TCTTTTCAAAGCCCACACAA
*
1476598 GTCAGTGGCAACCCTTTTCAAA
1 GTCAGTGGCAACTCTTTTCAAA
1476620 TCACCACTGT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
30 7 0.10
31 4 0.06
32 31 0.45
33 25 0.36
34 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (32 bp):
GTCAGTGGCAACTCTTTTCAAAGCCCACACAA
Found at i:1476757 original size:49 final size:45
Alignment explanation
Indices: 1476647--1476770 Score: 131
Period size: 49 Copynumber: 2.7 Consensus size: 45
1476637 TTAAAGTCCG
* * *
1476647 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTAGCCCA
1 ATATCGCTGGCCTTGAATCAGAACATTGGCACCTTTATTAACCCA
* * * * *
1476692 ATGTCCCTGGCCTTGAATCAGTACATTGGTCCACTTTTCTCTTAACCCA
1 ATATCGCTGGCCTTGAATCAGAACATTGG--CAC-CTT-TATTAACCCA
*
1476741 ATATCGCTGGCCTTGAATTAGAACATTGGC
1 ATATCGCTGGCCTTGAATCAGAACATTGGC
1476771 TCCGTTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 25 0.39
47 4 0.06
48 2 0.03
49 33 0.52
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (45 bp):
ATATCGCTGGCCTTGAATCAGAACATTGGCACCTTTATTAACCCA
Found at i:1477465 original size:20 final size:20
Alignment explanation
Indices: 1477440--1477557 Score: 94
Period size: 20 Copynumber: 5.7 Consensus size: 20
1477430 TTTTACCTAG
1477440 ATGTATCGATACATGTTTCA
1 ATGTATCGATACATGTTTCA
* *
1477460 ATGTATTGATACATTTTTACCTA
1 ATGTATCGATACATGTTT--C-A
* * *
1477483 GATGTATGGATGCATTTTTCA
1 -ATGTATCGATACATGTTTCA
* * *
1477504 ATGTATCGATATATGTATGA
1 ATGTATCGATACATGTTTCA
* *
1477524 ATGTCTGGATACAT-TCTTCA
1 ATGTATCGATACATGT-TTCA
1477544 ATGTATCGATACAT
1 ATGTATCGATACAT
1477558 TCTGTCTTTT
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
19 1 0.01
20 55 0.72
21 1 0.01
22 2 0.03
23 1 0.01
24 16 0.21
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCA
Found at i:1477498 original size:24 final size:24
Alignment explanation
Indices: 1477428--1477501 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
1477418 GAAAAGTCAT
1477428 ATTTTTACCTAGATGTATCGATAC
1 ATTTTTACCTAGATGTATCGATAC
* *
1477452 ATGTTT--C-A-ATGTATTGATAC
1 ATTTTTACCTAGATGTATCGATAC
* *
1477472 ATTTTTACCTAGATGTATGGATGC
1 ATTTTTACCTAGATGTATCGATAC
1477496 ATTTTT
1 ATTTTT
1477502 CAATGTATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 16 0.39
21 1 0.02
22 2 0.05
23 1 0.02
24 21 0.51
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (24 bp):
ATTTTTACCTAGATGTATCGATAC
Found at i:1477503 original size:44 final size:44
Alignment explanation
Indices: 1477428--1477514 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
1477418 GAAAAGTCAT
*
1477428 ATTTTTACCTAGATGTATCGATACATGTTTCAATGTATTGATAC
1 ATTTTTACCTAGATGTATCGATACATGTTTCAATGTATCGATAC
* * *
1477472 ATTTTTACCTAGATGTATGGATGCATTTTTCAATGTATCGATA
1 ATTTTTACCTAGATGTATCGATACATGTTTCAATGTATCGATA
1477515 TATGTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.44
Consensus pattern (44 bp):
ATTTTTACCTAGATGTATCGATACATGTTTCAATGTATCGATAC
Found at i:1482193 original size:166 final size:168
Alignment explanation
Indices: 1481897--1482242 Score: 414
Period size: 166 Copynumber: 2.1 Consensus size: 168
1481887 TCAATTGAGC
* * * ***
1481897 CCCTAAACTTTTAAAAATTTAAATTTCATACCCAAT-GAAAAACGAAGAGGATAAGAAAAGTCTT
1 CCCTAAACTTTTGAAACTTT-TATTTCATACTTGATAGAAAAACGAAGAGGATAAGAAAAGTCTT
* * * *
1481961 GAAAATTTTTATACCTCTATAGAAGGCCATAGGAATAATAGAAATATTTAAAAATAATTGAAATG
65 AAAAATTTTTATACCTCTATAGAAAGCCATAGGAATAATAGAAATATTTAAAAATAACTAAAATG
*
1482026 ATGATTTTACCTCT-AAAAACTAAAATTTGGTATTTAAT
130 ATGATTTTACCTCTAAAAAACTAAAATTTGATATTTAAT
* * ** *
1482064 CCTTAAACTTTTGAAACTTTTATTTCATACTTGATAGAAAATCG-AGAGGATATTAAAAGTTTTA
1 CCCTAAACTTTTGAAACTTTTATTTCATACTTGATAGAAAAACGAAGAGGATAAGAAAAGTCTTA
* * * * *
1482128 AAAATTTTTATACC-CTTATGGAAAGCTATAGGAATTATA-AAGATCTTTAAAAATGACTAAAAT
66 AAAATTTTTATACCTC-TATAGAAAGCCATAGGAATAATAGAA-ATATTTAAAAATAACTAAAAT
* *
1482191 GATGATTTTACCTTTAAAAAACTAAAATTTTATATTTAAT
129 GATGATTTTACCTCTAAAAAACTAAAATTTGATATTTAAT
*
1482231 CCCTAAGCTTTT
1 CCCTAAACTTTT
1482243 AAAAATGTTC
Statistics
Matches: 150, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
165 3 0.02
166 91 0.61
167 56 0.37
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (168 bp):
CCCTAAACTTTTGAAACTTTTATTTCATACTTGATAGAAAAACGAAGAGGATAAGAAAAGTCTTA
AAAATTTTTATACCTCTATAGAAAGCCATAGGAATAATAGAAATATTTAAAAATAACTAAAATGA
TGATTTTACCTCTAAAAAACTAAAATTTGATATTTAAT
Found at i:1484146 original size:23 final size:23
Alignment explanation
Indices: 1484100--1484142 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1484090 GAAATAAAAT
1484100 TTCATATAATCAAATTAATTTAA
1 TTCATATAATCAAATTAATTTAA
1484123 TTCA-ATAA-CAAATTCAATTT
1 TTCATATAATCAAATT-AATTT
1484143 TAATGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (23 bp):
TTCATATAATCAAATTAATTTAA
Found at i:1484764 original size:20 final size:21
Alignment explanation
Indices: 1484739--1484787 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1484729 ATTTAAAAAA
1484739 AATAAAAATAACATA-ATAAT
1 AATAAAAATAACATATATAAT
* *
1484759 AAT-AAAATAATATATATTAT
1 AATAAAAATAACATATATAAT
1484779 AATTAAAAA
1 AA-TAAAAA
1484788 AAGAGCCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 1 0.04
22 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAAAATAACATATATAAT
Found at i:1485504 original size:7 final size:7
Alignment explanation
Indices: 1485494--1485518 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1485484 AAGAAGAGAG
1485494 AAGAGGA
1 AAGAGGA
1485501 AAGAGGA
1 AAGAGGA
1485508 AAGAGGA
1 AAGAGGA
1485515 AAGA
1 AAGA
1485519 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAGAGGA
Found at i:1485864 original size:26 final size:30
Alignment explanation
Indices: 1485830--1485885 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1485820 GCAAAGAGAG
1485830 AAAGTAG-AAAT-GAAAC-AACAAGAAAAA
1 AAAGTAGAAAATAGAAACGAACAAGAAAAA
*
1485857 AAAG-AGAAAATAGAACCGAACAAGAAAAA
1 AAAGTAGAAAATAGAAACGAACAAGAAAAA
1485886 GAAAAGCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 8 0.32
28 4 0.16
29 11 0.44
ACGTcount: A:0.70, C:0.09, G:0.16, T:0.05
Consensus pattern (30 bp):
AAAGTAGAAAATAGAAACGAACAAGAAAAA
Found at i:1491893 original size:62 final size:62
Alignment explanation
Indices: 1491754--1492006 Score: 260
Period size: 62 Copynumber: 4.1 Consensus size: 62
1491744 TTTTCCTTCC
** * * * * * *
1491754 AAAGCCCACAAAAGTTGGTGGTACCTTTCAGTCCTCAAAG-GCAGGACGCCATTTTCCTTTT
1 AAAGCCCACATGAGTTGGTAGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTTCTTTTT
* * *
1491815 AAAGCCCACACGAGTTGGTAGCACCTTTCAGTCCTCAAAGAGGAGGACTCCTTTTTCTTTTT
1 AAAGCCCACATGAGTTGGTAGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTTCTTTTT
* * * * *
1491877 AAAGCCCACATGAGTTGGTGGCACCTTTTAGCCCTCAAAAAGCAAGACACCTTTTTCTTTTT
1 AAAGCCCACATGAGTTGGTAGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTTCTTTTT
* * ** * * * *
1491939 AAAGCCCGCATGAGTTTGTCA-CATTTTTTAGTTCGCAAAGAGCAAGA-TGCTTTTTCTTTTT
1 AAAGCCCACATGAGTTGGT-AGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTTCTTTTT
1492000 AAAGCCC
1 AAAGCCC
1492007 TTTTAGTCCT
Statistics
Matches: 163, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
61 55 0.34
62 108 0.66
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (62 bp):
AAAGCCCACATGAGTTGGTAGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTTCTTTTT
Found at i:1492031 original size:43 final size:44
Alignment explanation
Indices: 1491964--1492047 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
1491954 TTGTCACATT
* *
1491964 TTTTAGTTCGCAAAGAGCAAGATG-CTTTTTCTTTTTAAAGCCC
1 TTTTAGTCCGCAAAGAGCAAGATGCCTTTTTCCTTTTAAAGCCC
* * *
1492007 TTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCCTTTTAAAG
1 TTTTAGTCCGCAAAGAGCAAGATGCCTTTTTCCTTTTAAAG
1492048 GCCACAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 20 0.57
44 15 0.43
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (44 bp):
TTTTAGTCCGCAAAGAGCAAGATGCCTTTTTCCTTTTAAAGCCC
Found at i:1492106 original size:61 final size:62
Alignment explanation
Indices: 1492005--1492160 Score: 206
Period size: 61 Copynumber: 2.5 Consensus size: 62
1491995 TTTTTAAAGC
** **
1492005 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCCTTTTAAAGGCCACA-AAATTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCAGTTTAAAACCCACACAAATTAGTGGCA
* * * *
1492066 TCTTTTAGTCCTTAAAGAGTAGGATGCCTTTTTCAGTTTAAAACCCACACGAGTTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCAGTTTAAAACCCACACAAATTAGTGGCA
* * *
1492128 CCTTTTAGTTCTCAAAGAGCAGGATGCTTTTTT
1 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTT
1492161 TTTTTCATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 43 0.53
62 38 0.47
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (62 bp):
CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCAGTTTAAAACCCACACAAATTAGTGGCA
Found at i:1492146 original size:166 final size:167
Alignment explanation
Indices: 1491838--1492165 Score: 381
Period size: 166 Copynumber: 2.0 Consensus size: 167
1491828 GTTGGTAGCA
* * * *
1491838 CCTTTCAGTCCTCAAAGAGGAGGACTCCTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACCT
1 CCTTTCAGTCCTCAAAGAGGAGGACTCCTTTTTCCTTTTAAAGCCCACATAAATTAGTGGCACCT
** * * * * **
1491903 TTTAGCCCTCAAAAAGCAAGACACCTTTTTCTTTTTAAAGCCCGCATGAGTTTGTCACATTTTTT
66 TTTAGCCCTCAAAAAGCAAGACACCTTTTTCAGTTTAAAACCCACACGAGTTAGTCACACCTTTT
1491968 AGTTCGCAAAGAGCAAGATGCTTTTTCTTTTTAAAGC
131 AGTTCGCAAAGAGCAAGATGCTTTTTCTTTTTAAAGC
* * * *
1492005 CCTTTTAGTCCTCAAAGAGTAGGA-TGCCTTTTTCCTTTTAAAGGCCACA-AAATTAGTGGCATC
1 CCTTTCAGTCCTCAAAGAGGAGGACT-CCTTTTTCCTTTTAAAGCCCACATAAATTAGTGGCACC
* * * * * ** **
1492068 TTTTAGTCCTTAAAGAGTAGGATGCCTTTTTCAGTTTAAAACCCACACGAGTTAGTGGCACCTTT
65 TTTTAGCCCTCAAAAAGCAAGACACCTTTTTCAGTTTAAAACCCACACGAGTTAGTCACACCTTT
* * *
1492133 TAGTTCTCAAAGAGCAGGATGCTTTTTTTTTTT
130 TAGTTCGCAAAGAGCAAGATGCTTTTTCTTTTT
1492166 CATTTATCCT
Statistics
Matches: 132, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
166 89 0.67
167 43 0.33
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (167 bp):
CCTTTCAGTCCTCAAAGAGGAGGACTCCTTTTTCCTTTTAAAGCCCACATAAATTAGTGGCACCT
TTTAGCCCTCAAAAAGCAAGACACCTTTTTCAGTTTAAAACCCACACGAGTTAGTCACACCTTTT
AGTTCGCAAAGAGCAAGATGCTTTTTCTTTTTAAAGC
Found at i:1493040 original size:20 final size:21
Alignment explanation
Indices: 1492995--1493045 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1492985 GCCAAAGAAA
*
1492995 TGTATCGATATATTTTCTATT
1 TGTATCGATATATTTTCCATT
1493016 TGTATCGATATATTTTCCA-T
1 TGTATCGATATATTTTCCATT
1493036 TGTATCGATA
1 TGTATCGATA
1493046 CATTCTAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (21 bp):
TGTATCGATATATTTTCCATT
Found at i:1510014 original size:20 final size:20
Alignment explanation
Indices: 1509989--1510126 Score: 145
Period size: 20 Copynumber: 6.9 Consensus size: 20
1509979 GTAAAAAGAT
*
1509989 AGAATGTATCGATACGTTGA
1 AGAATGTATCGATACATTGA
*
1510009 AGAATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
* *
1510029 AGAATGCATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
1510049 TA-CATGTATTGATACATTGA
1 -AGAATGTATCGATACATTGA
* * *
1510069 AGAAAGCATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1510089 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1510109 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
1510127 TGGGTAAAAG
Statistics
Matches: 95, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.02
20 91 0.96
21 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1510056 original size:40 final size:40
Alignment explanation
Indices: 1510012--1510126 Score: 194
Period size: 40 Copynumber: 2.9 Consensus size: 40
1510002 ACGTTGAAGA
1510012 ATGTATTGATACATTGAAGAATGCATCGATACATTCATAC
1 ATGTATTGATACATTGAAGAATGCATCGATACATTCATAC
*
1510052 ATGTATTGATACATTGAAGAAAGCATCGATACATTCATAC
1 ATGTATTGATACATTGAAGAATGCATCGATACATTCATAC
* * *
1510092 ATGTATCGATACATTGAAAAATGTATCGATACATT
1 ATGTATTGATACATTGAAGAATGCATCGATACATT
1510127 TGGGTAAAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (40 bp):
ATGTATTGATACATTGAAGAATGCATCGATACATTCATAC
Found at i:1510188 original size:24 final size:20
Alignment explanation
Indices: 1509991--1510172 Score: 141
Period size: 20 Copynumber: 8.6 Consensus size: 20
1509981 AAAAAGATAG
* *
1509991 AATGTATCGATACGTTGAAG
1 AATGTATCGATACATTGAAA
* *
1510011 AATGTATTGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
1510031 AATGCATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
1510051 CATGTATTGATACATTGAAGA
1 AATGTATCGATACATTGAA-A
* * *
1510072 AA-GCATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
1510091 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
1510111 AATGTATCGATACATTTGGGTAAAAGACAA
1 AATGTATCGATACA--T---T----GA-AA
1510141 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
1510161 AATGTATCGATA
1 AATGTATCGATA
1510173 TATCTAGGTA
Statistics
Matches: 128, Mismatches: 22, Indels: 24
0.74 0.13 0.14
Matches are distributed among these distances:
19 2 0.02
20 100 0.78
21 4 0.03
22 1 0.01
25 2 0.02
28 1 0.01
29 2 0.02
30 16 0.12
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1520874 original size:27 final size:27
Alignment explanation
Indices: 1520836--1520898 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
1520826 AATAAGGTTA
1520836 GAGTATCCCCTCGGAAGAAT-GGTGTTG
1 GAGTATCCCCTCGGAAGAATAGGT-TTG
1520863 GAGTATCCCCTCGGAAGAATAGGTTTG
1 GAGTATCCCCTCGGAAGAATAGGTTTG
1520890 GAGTATCCC
1 GAGTATCCC
1520899 GATAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (27 bp):
GAGTATCCCCTCGGAAGAATAGGTTTG
Found at i:1523352 original size:20 final size:21
Alignment explanation
Indices: 1523309--1523361 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1523299 GACATGGCCT
1523309 TGTATCGATACATTTCAAACA
1 TGTATCGATACATTTCAAACA
***
1523330 TGTATCGATACA-TTCATTTA
1 TGTATCGATACATTTCAAACA
1523350 TGTATCGATACA
1 TGTATCGATACA
1523362 AATTATAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTCAAACA
Found at i:1524262 original size:3 final size:3
Alignment explanation
Indices: 1524256--1524287 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1524246 TGGTATTTAT
1524256 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1524288 TATTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1525315 original size:10 final size:10
Alignment explanation
Indices: 1525302--1525349 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
1525292 TTTAGCTTAG
1525302 TTTTTTCTTTT
1 TTTTTTC-TTT
1525313 TTTCTTTCTTT
1 TTT-TTTCTTT
*
1525324 TTCTTTCTTT
1 TTTTTTCTTT
*
1525334 TTTCTTCTTT
1 TTTTTTCTTT
1525344 TTTTTT
1 TTTTTT
1525350 TCACTTGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 20 0.62
11 8 0.25
12 4 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1525346 original size:21 final size:20
Alignment explanation
Indices: 1525302--1525351 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
1525292 TTTAGCTTAG
1525302 TTTTTTCTTT-TTTTCTTTC
1 TTTTTTCTTTCTTTTCTTTC
*
1525321 -TTTTTCTTTCTTTTTTCTTC
1 TTTTTTCTTTCTTTTCT-TTC
*
1525341 TTTTTTTTTTC
1 TTTTTTCTTTC
1525352 ACTTGCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 9 0.35
19 5 0.19
20 3 0.12
21 9 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTCTTTCTTTTCTTTC
Found at i:1525348 original size:14 final size:14
Alignment explanation
Indices: 1525302--1525351 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1525292 TTTAGCTTAG
1525302 TTTTTTCTT-TTTT
1 TTTTTTCTTCTTTT
* *
1525315 TCTTTCTTTTTCTTTC
1 T-TTT-TTCTTCTTTT
1525331 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
1525345 TTTTTTC
1 TTTTTTC
1525352 ACTTGCCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 7 0.23
16 4 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:1526175 original size:166 final size:164
Alignment explanation
Indices: 1525971--1526362 Score: 500
Period size: 166 Copynumber: 2.4 Consensus size: 164
1525961 TTAGGGGTAG
*
1525971 GAAAATTTTAAAGAAAAAATGAAAAACTTATAAAAATAAATGAATTTTTCAAAACTGATTTACTA
1 GAAAATTTT-AAGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTT-AAAACTGATTTACTA
* * *
1526036 TTAATTAAATGATGTTATTTGATGAATATCAAAATTTTGAACCGAG-AAAATCTCCCC-CGAAAA
64 TGAATTAAATGATGATATTTGATGAATATCAAAATTTTAAACCGAGAAAAATC-CCCCTCGAAAA
* * *
1526099 TATTTGTGGAGTAGAAAACTCCATTGTTCAAAAATAA
128 CATTTATGGAGTAGAAAACTCAATTGTTCAAAAATAA
* * * * *
1526136 GAAAATTTTAAGGAAAAAAATGAAATACTTATGAAAATAAATGAAATTTTAAAAATTAATTTATT
1 GAAAATTTTAA-G-AAAAAATGAAAAACTTATGAAAATAAATG-AATTTTTAAAACTGATTTACT
* * * ** *
1526201 GTGAATTAAATGATGATATTTGATGAGTATTAAAATTTTAAATTGAGAAAAATCCCCCTCGGAAA
63 ATGAATTAAATGATGATATTTGATGAATATCAAAATTTTAAACCGAGAAAAATCCCCCTCGAAAA
* *
1526266 CATTTATGGAGTAGAAAACTCAATTTTTCGAAAATAA
128 CATTTATGGAGTAGAAAACTCAATTGTTCAAAAATAA
* * * *
1526303 GAGAATTTTAAGAAAAAATGAAAAACTCATGAAAATAAATAAATTTTTTAAACTGATTTA
1 GAAAATTTTAAGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTTAAAACTGATTTA
1526363 ATGGTAATTA
Statistics
Matches: 194, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
164 17 0.09
165 36 0.19
166 82 0.42
167 59 0.30
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (164 bp):
GAAAATTTTAAGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTTAAAACTGATTTACTATG
AATTAAATGATGATATTTGATGAATATCAAAATTTTAAACCGAGAAAAATCCCCCTCGAAAACAT
TTATGGAGTAGAAAACTCAATTGTTCAAAAATAA
Found at i:1527167 original size:43 final size:41
Alignment explanation
Indices: 1527069--1527212 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 41
1527059 CGCCCGAACC
* * *
1527069 AGGGCATAACCATCACGTCAAACAAAAGTGAAAGGAGTTTGACCA
1 AGGGCA-AACCATCATGTCAAAC-GAAG-GAAAGGAGTTTGA-CT
** *
1527114 AGGTAAAACCATCATGTCAAACGAAGGAAAAAGAGTTTGACT
1 AGGGCAAACCATCATGTCAAACGAAGG-AAAGGAGTTTGACT
* * *
1527156 AGGGCAGAACCATCATTTCAAATGAAGGAAAGGAGTTTGAAT
1 AGGGCA-AACCATCATGTCAAACGAAGGAAAGGAGTTTGACT
1527198 AGGGCCAAACCATCA
1 AGGG-CAAACCATCA
1527213 CGTTAGTTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
42 30 0.36
43 35 0.42
44 15 0.18
45 4 0.05
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (41 bp):
AGGGCAAACCATCATGTCAAACGAAGGAAAGGAGTTTGACT
Found at i:1527209 original size:42 final size:42
Alignment explanation
Indices: 1527119--1527212 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
1527109 GACCAAGGTA
*
1527119 AAACCATCATGTCAAACGAAGGAAAAAGAGTTTGACTAGGGC
1 AAACCATCATGTCAAACGAAGGAAAAAGAGTTTGAATAGGGC
* * *
1527161 AGAACCATCATTTCAAATGAAGG-AAAGGAGTTTGAATAGGGCC
1 A-AACCATCATGTCAAACGAAGGAAAAAGAGTTTGAATAGGG-C
1527204 AAACCATCA
1 AAACCATCA
1527213 CGTTAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 25 0.54
43 21 0.46
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
AAACCATCATGTCAAACGAAGGAAAAAGAGTTTGAATAGGGC
Found at i:1527221 original size:28 final size:28
Alignment explanation
Indices: 1527189--1527243 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1527179 GAAGGAAAGG
1527189 AGTTTGAA-TAGGGCCA-AACCATCACGTT
1 AGTTT-AACTAGGG-CAGAACCATCACGTT
1527217 AGTTTAACTAGGGCAGAACCATCACGT
1 AGTTTAACTAGGGCAGAACCATCACGT
1527244 CAAATGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (28 bp):
AGTTTAACTAGGGCAGAACCATCACGTT
Found at i:1527326 original size:44 final size:44
Alignment explanation
Indices: 1527262--1527654 Score: 236
Period size: 44 Copynumber: 8.9 Consensus size: 44
1527252 AGTGAAAGGA
* * *
1527262 AACCATCATGTCAAAGGAAAGTGAAACAAGTTTGACTAGGATAG
1 AACCATCACGTCAAAAGAAAGTGAAAGAAGTTTGACTAGGATAG
* * * **
1527306 AACCATCACATCAAAAGAAAGTGAAAGGAGTTTGACCAGGGCAG
1 AACCATCACGTCAAAAGAAAGTGAAAGAAGTTTGACTAGGATAG
* * **
1527350 AACCATCACGT-AAAATGAAAGCGAAAAAAGTTTGA-TCAGGGCAG
1 AACCATCACGTCAAAA-GAAAGTGAAAGAAGTTTGACT-AGGATAG
* * ** * * *
1527394 AACCATCATGTCAAACGAAA-ACAAAAAGAGTTTGACCAGGGTAG
1 AACCATCACGTCAAAAGAAAGTGAAAGA-AGTTTGACTAGGATAG
* *
1527438 AACCATCACGT-AAAACAAAAGTGAAA-AGAGTTTGACCA-GAGTAG
1 AACCATCACGTCAAAA-GAAAGTGAAAGA-AGTTTGACTAGGA-TAG
* * * *
1527482 AACCATCATGTCAAACA-AAAGCGAAA-AGAGTTTGACTCGGGTAG
1 AACCATCACGTCAAA-AGAAAGTGAAAGA-AGTTTGACTAGGATAG
* * * * *
1527526 AACCATCACAT-TAAACAAAGCGAAATG-AGTTTAACTAAGGCA-A-
1 AACCATCACGTCAAAAGAAAGTGAAA-GAAGTTTGACT-AGG-ATAG
* * * *
1527569 AACCATCACATCAAACA-AAAGTGAAAGGAGTTTGACCAGGACAG
1 AACCATCACGTCAAA-AGAAAGTGAAAGAAGTTTGACTAGGATAG
* * *
1527613 AACCATCATGTCAAATGAATGTGAAATGAAGTTTGACGTAGG
1 AACCATCACGTCAAAAGAAAGTGAAA-GAAGTTTGAC-TAGG
1527655 TCTAAAGATT
Statistics
Matches: 279, Mismatches: 46, Indels: 46
0.75 0.12 0.12
Matches are distributed among these distances:
42 2 0.01
43 48 0.17
44 205 0.73
45 20 0.07
46 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (44 bp):
AACCATCACGTCAAAAGAAAGTGAAAGAAGTTTGACTAGGATAG
Found at i:1527425 original size:88 final size:88
Alignment explanation
Indices: 1527262--1527654 Score: 346
Period size: 88 Copynumber: 4.5 Consensus size: 88
1527252 AGTGAAAGGA
* * * * * **
1527262 AACCATCATGTCAAAGGAAAGTGAAACAAGTTTGACTAGGATAGAACCATCACATCAAA-AGAAA
1 AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGACTAGGGCAGAACCATCACATCAAACA-AAA
* *
1527326 GTGAAAGGAGTTTGACCAGGGCAG
65 GCGAAAAGAGTTTGACCAGGGCAG
**
1527350 AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGA-TCAGGGCAGAACCATCATGTCAAACGAAA
1 AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGACT-AGGGCAGAACCATCACATCAAAC-AAA
* *
1527414 A-CAAAAAGAGTTTGACCAGGGTAG
64 AGCGAAAAGAGTTTGACCAGGGCAG
** * * * * * **
1527438 AACCATCACGTAAAACAAAAGTGAAAAGAGTTTGACCAGAGTAGAACCATCATGTCAAACAAAAG
1 AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGACTAGGGCAGAACCATCACATCAAACAAAAG
*
1527503 CGAAAAGAGTTTGACTC-GGGTAG
66 CGAAAAGAGTTTGAC-CAGGGCAG
* * * ** * * *
1527526 AACCATCACATTAAA-CAAAGCGAAATGAGTTTAACTAAGGCAAAACCATCACATCAAACAAAAG
1 AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGACTAGGGCAGAACCATCACATCAAACAAAAG
* * *
1527590 TGAAAGGAGTTTGACCAGGACAG
66 CGAAAAGAGTTTGACCAGGGCAG
* * * * *
1527613 AACCATCATGTCAAATGAATGTGAAATGAAGTTTGACGTAGG
1 AACCATCACGTAAAATGAAAGCGAAA-AAAGTTTGAC-TAGG
1527655 TCTAAAGATT
Statistics
Matches: 247, Mismatches: 48, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
86 1 0.00
87 72 0.29
88 159 0.64
89 11 0.04
90 4 0.02
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (88 bp):
AACCATCACGTAAAATGAAAGCGAAAAAAGTTTGACTAGGGCAGAACCATCACATCAAACAAAAG
CGAAAAGAGTTTGACCAGGGCAG
Found at i:1527503 original size:132 final size:131
Alignment explanation
Indices: 1527262--1527627 Score: 407
Period size: 132 Copynumber: 2.8 Consensus size: 131
1527252 AGTGAAAGGA
* ** * * *
1527262 AACCATCATGTCAAAGGAAAGTGAAACA-AGTTTGACTAGGATAGAACCATCACATCAAAA-GAA
1 AACCATCATGTCAAACGAAA-ACAAAAAGAGTTTGACTAGGGTAGAACCATCACAT-AAAACAAA
* * **
1527325 AGTGAAAGGAGTTTGACCAGGGCAGAACCATCACGTAAAATGAAAGCGAAAAAAGTTTGA-TCAG
64 AGTGAAAGGAGTTTGACCA-GGCAGAACCATCATGTCAAACAAAAGCGAAAAAAGTTTGACTC-G
1527389 GGCAG
127 GGCAG
* *
1527394 AACCATCATGTCAAACGAAAACAAAAAGAGTTTGACCAGGGTAGAACCATCACGTAAAACAAAAG
1 AACCATCATGTCAAACGAAAACAAAAAGAGTTTGACTAGGGTAGAACCATCACATAAAACAAAAG
* * * *
1527459 TGAAAAGAGTTTGACCAGAGTAGAACCATCATGTCAAACAAAAGCGAAAAGAGTTTGACTCGGGT
66 TGAAAGGAGTTTGACCAG-GCAGAACCATCATGTCAAACAAAAGCGAAAAAAGTTTGACTCGGGC
1527524 AG
130 AG
** * * * * * * * * *
1527526 AACCATCACATTAAAC-AAAGCGAAATGAGTTTAACTAAGGCAAAACCATCACATCAAACAAAAG
1 AACCATCATGTCAAACGAAAACAAAAAGAGTTTGACTAGGGTAGAACCATCACATAAAACAAAAG
1527590 TGAAAGGAGTTTGACCAGGACAGAACCATCATGTCAAA
66 TGAAAGGAGTTTGACCAGG-CAGAACCATCATGTCAAA
1527628 TGAATGTGAA
Statistics
Matches: 198, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
130 1 0.01
131 81 0.41
132 114 0.58
133 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (131 bp):
AACCATCATGTCAAACGAAAACAAAAAGAGTTTGACTAGGGTAGAACCATCACATAAAACAAAAG
TGAAAGGAGTTTGACCAGGCAGAACCATCATGTCAAACAAAAGCGAAAAAAGTTTGACTCGGGCA
G
Found at i:1528442 original size:180 final size:181
Alignment explanation
Indices: 1528211--1528722 Score: 552
Period size: 180 Copynumber: 2.8 Consensus size: 181
1528201 TGTGGTTATC
* * ** * *
1528211 TGATGCATCAATACCATTTAGTGGCTAAAAGAAAGGGATATGATTAGGAATGAGTGGTTAGGATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTAGGAATGA-TGGTCAGGATA
* * *
1528276 TCCTTGCCCCAAGAAAATCAGGATTTGTGATACATCAATACCATCTAGTGGTTGGATGAAAAGGA
65 TCCTTGCCCTAAG-AAATCAGGATTTGTGATGCATCAATACCATCTAGTGGTTGGAT-AAAGGGA
* * *
1528341 TATGATTGGGAATGTATGGTC-TG-CAT-C-TTCTCTAAGGAAATCAAGCTTTA
128 TATGATTGGGAATGTATGGTCAAGACATCCTTTCCCCAAGGAAATCAAGCTTTA
* * * *
1528391 TGATGCATCAATACCATCTAGTGGTTGGTTGAAGGGGATATTATTAGGAATGTATGGTCGGGATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTAGGAATG-ATGGTCAGGATA
** * *
1528456 TCCTTGCTTTAACGAAATCAGGCTTTGTGATGCATTAATACCATCTAGTGGTTGGATAAAGGGAT
65 TCCTTGCCCTAA-GAAATCAGGATTTGTGATGCATCAATACCATCTAGTGGTTGGATAAAGGGAT
* * * * * *
1528521 ATGATTGGGAATGTGTGGTCAAGATATCCTTTCCCCAAGGAAGTTAGGCTTTG
129 ATGATTGGGAATGTATGGTCAAGACATCCTTTCCCCAAGGAAATCAAGCTTTA
* * * *
1528574 TGATGCATCAAAACCATCTTGTGGTTGGATGAAAGGGATATGATT-GGGATGAATGGTCAGAATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTAGGAATG-ATGGTCAGGATA
* * * * * * *
1528638 TCCTTGCCCTAAGGAATTCA-GACCTTATGATGTATCAATAACATCTAGCGGTTGAATAAAGGGG
65 TCCTTGCCCTAA-GAAATCAGGA-TTTGTGATGCATCAATACCATCTAGTGGTTGGATAAA-GGG
1528702 ATATGATTGGGAA-GATATGGT
127 ATATGATTGGGAATG-TATGGT
1528723 TTGGACCCTC
Statistics
Matches: 275, Mismatches: 48, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
179 26 0.09
180 103 0.37
181 5 0.02
182 63 0.23
183 78 0.28
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (181 bp):
TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTAGGAATGATGGTCAGGATAT
CCTTGCCCTAAGAAATCAGGATTTGTGATGCATCAATACCATCTAGTGGTTGGATAAAGGGATAT
GATTGGGAATGTATGGTCAAGACATCCTTTCCCCAAGGAAATCAAGCTTTA
Found at i:1528573 original size:91 final size:91
Alignment explanation
Indices: 1528211--1528722 Score: 527
Period size: 91 Copynumber: 5.6 Consensus size: 91
1528201 TGTGGTTATC
* * ** * * *
1528211 TGATGCATCAATACCATTTAGTGGCTAAAAGAAAGGGATATGATTAGGAATG-AGTGGTTAGGAT
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTA-TGGTCA-GAT
* * *
1528275 ATCCTTGCCCCAAGAAAATCAGGATTTG
64 ATCCTTGCCCTAAGGAAATCAGGCTTTG
* * * *
1528303 TGATACATCAATACCATCTAGTGGTTGGATGAAAAGGATATGATTGGGAATGTATGGTCTG-CAT
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTATGGTCAGATAT
* * *
1528367 -CTT-CTCTAAGGAAATCAAGCTTTA
66 CCTTGCCCTAAGGAAATCAGGCTTTG
* * * * *
1528391 TGATGCATCAATACCATCTAGTGGTTGGTTGAAGGGGATATTATTAGGAATGTATGGTCGGGATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTATGGTC-AGATA
** *
1528456 TCCTTGCTTTAACGAAATCAGGCTTTG
65 TCCTTGCCCTAAGGAAATCAGGCTTTG
* *
1528483 TGATGCATTAATACCATCTAGTGGTTGGAT-AAAGGGATATGATTGGGAATGTGTGGTCAAGATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTATGGTC-AGATA
* * * *
1528547 TCCTTTCCCCAAGGAAGTTAGGCTTTG
65 TCCTTGCCCTAAGGAAATCAGGCTTTG
* * *
1528574 TGATGCATCAAAACCATCTTGTGGTTGGATGAAAGGGATATGATTGGG-ATGAATGGTCAGAATA
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTATGGTCAG-ATA
* * * *
1528638 TCCTTGCCCTAAGGAATTCAGACCTTA
65 TCCTTGCCCTAAGGAAATCAGGCTTTG
* * * *
1528665 TGATGTATCAATAACATCTAGCGGTTGAAT-AAAGGGGATATGATTGGGAA-GATATGGT
1 TGATGCATCAATACCATCTAGTGGTTGGATGAAA-GGGATATGATTGGGAATG-TATGGT
1528723 TTGGACCCTC
Statistics
Matches: 347, Mismatches: 63, Indels: 20
0.81 0.15 0.05
Matches are distributed among these distances:
88 68 0.20
89 4 0.01
90 9 0.03
91 149 0.43
92 116 0.33
93 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (91 bp):
TGATGCATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTGGGAATGTATGGTCAGATAT
CCTTGCCCTAAGGAAATCAGGCTTTG
Found at i:1542910 original size:79 final size:78
Alignment explanation
Indices: 1542815--1543037 Score: 249
Period size: 78 Copynumber: 2.8 Consensus size: 78
1542805 TCAAAAGGGG
*
1542815 TACTCCAACC-CTATTTTTACTTCTAAAACACTAAATTTTTCATCTTTGGGATACTCCAACCCCA
1 TACTCCAACCTC-ATTTTTACTTCTAAAACACTACATTTTTCATCTTTGGGATACTCCAACCCCA
1542879 TC-ATCTCT-AAGGGAA
65 TCTATCTCTGAA---AA
* * * *
1542894 TACTCCAACCTCATTTTTACTTCTAAAACACTACATTTATAATCTTTGGGAATATTCCAACCCTA
1 TACTCCAACCTCATTTTTACTTCTAAAACACTACATTTTTCATCTTTGGG-ATACTCCAACCCCA
1542959 -CTATCTCTGAAAA
65 TCTATCTCTGAAAA
* * ** * *
1542972 TACTCTAACCTCGTTTTTACTTCTAAAA-TGTCGCATTCTTCATCTTTAGGGATACTCCAACCCC
1 TACTCCAACCTCATTTTTACTTCTAAAACACT-ACATTTTTCATCTTT-GGGATACTCCAACCCC
1543036 AT
64 AT
1543038 TTTTACTTCC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
77 1 0.01
78 51 0.42
79 49 0.40
80 19 0.16
81 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (78 bp):
TACTCCAACCTCATTTTTACTTCTAAAACACTACATTTTTCATCTTTGGGATACTCCAACCCCAT
CTATCTCTGAAAA
Found at i:1550957 original size:116 final size:116
Alignment explanation
Indices: 1550753--1550968 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 116
1550743 TAGTGCAGTT
* * * ** *
1550753 GCCAAGTTGTCACAATGTGGCTCGAATACGAATCCTAACCAAGCCTGATTTAAATGGCCCACAAT
1 GCCAAGCTGTCACAATGTGACCCGAATACGAATCCTAACCAAGCCCAACTTAAATGGCCCACAAT
1550818 ATTATATTCATTAATGCATCACTTTTTTTAATTCTCTTATTTTATAAGGTG
66 ATTATATTCATTAATGCATCACTTTTTTTAATTCTCTTATTTTATAAGGTG
* * **
1550869 GCCAAGCTGTCGCAATGTGACCCGAATACGAATCTTGTCCAAGCCCAACTTAAATGGCCCACAAT
1 GCCAAGCTGTCACAATGTGACCCGAATACGAATCCTAACCAAGCCCAACTTAAATGGCCCACAAT
*
1550934 CTTATATTCATTAATGCATCACTTTTTTTAATTCT
66 ATTATATTCATTAATGCATCACTTTTTTTAATTCT
1550969 ATGGTTTTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (116 bp):
GCCAAGCTGTCACAATGTGACCCGAATACGAATCCTAACCAAGCCCAACTTAAATGGCCCACAAT
ATTATATTCATTAATGCATCACTTTTTTTAATTCTCTTATTTTATAAGGTG
Found at i:1553631 original size:79 final size:78
Alignment explanation
Indices: 1553330--1553634 Score: 285
Period size: 79 Copynumber: 3.9 Consensus size: 78
1553320 TGGAGATAAC
* * * * ** *
1553330 AACGGGGCT-GAGTATCCCCGATTATGGAAAACTGGTGTTCCAGAAATAAAATCGTGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCTATTATGAAAAAATGGTGTTTTAGAAATAAAATCGGGGTTGGAGT
1553394 ATCACCTCGGAAAT
66 ATC-CCTCGGAAAT
* * * * * * *
1553408 AACAGGGTTGTAATAT-CCCTGATTAT-AAAAATTGGTATTTTAAAAATGAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCT-ATTATGAAAAAATGGTGTTTTAGAAATAAAATCGGGGTTGGAG
*
1553471 TATCCCCTCGAAAAT
65 TAT-CCCTCGGAAAT
* * * * * ** *
1553486 AACGGGGTTGGAGTATCTCCAATTGTG-AAAAATCGATGATTTAGAAATAAGGTCGGGGTTGAAG
1 AACGGGGTTGGAGTATCCCCTATTATGAAAAAAT-GGTGTTTTAGAAATAAAATCGGGGTTGGAG
*
1553550 TATCCTCTTGGAAAT
65 TATCC-CTCGGAAAT
* * * *
1553565 AACGGGGTTGGAGTATCCCCTATTGTGAAAAAATGGTGTTTTGGAAATAAAATCAGAGTTGGAGT
1 AACGGGGTTGGAGTATCCCCTATTATGAAAAAATGGTGTTTTAGAAATAAAATCGGGGTTGGAGT
1553630 ATCCC
66 ATCCC
1553635 CCATTGTGGA
Statistics
Matches: 178, Mismatches: 41, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
78 76 0.43
79 96 0.54
80 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCTATTATGAAAAAATGGTGTTTTAGAAATAAAATCGGGGTTGGAGT
ATCCCTCGGAAAT
Found at i:1556095 original size:33 final size:33
Alignment explanation
Indices: 1556035--1556098 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1556025 TGATACATTG
*
1556035 TAAAATGTATCGATACAATGAGCAATGTATCCA
1 TAAAATGTATCGATACAATGAGAAATGTATCCA
*
1556068 TAAAATGTATCGGTACAATGCA-AAATGTATC
1 TAAAATGTATCGATACAATG-AGAAATGTATC
1556099 AATACATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TAAAATGTATCGATACAATGAGAAATGTATCCA
Found at i:1556782 original size:51 final size:51
Alignment explanation
Indices: 1556614--1556794 Score: 213
Period size: 51 Copynumber: 3.6 Consensus size: 51
1556604 TCTAGAAAGA
* * * * ** *
1556614 AAATGTATTGATACATTTTTTATTGTATTGATACATTCTAGG-AATGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTGACCC
* * *
1556664 AAATGTATCGATA-AATTTTCATTGTATCGATACATTTTGGGTTTTTGACCT
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGG-TTTTGACCC
* * *
1556715 AAATATATCAATACATTATTCATTGTATCGATACATTCTGGGTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTGACCC
*
1556766 AAATGTATCGATACATTTTTCAATGTATC
1 AAATGTATCGATACATTTTTCATTGTATC
1556795 AATAAATCTA
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 23 0.21
50 12 0.11
51 48 0.44
52 25 0.23
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTGACCC
Found at i:1559106 original size:97 final size:96
Alignment explanation
Indices: 1558950--1559173 Score: 270
Period size: 97 Copynumber: 2.3 Consensus size: 96
1558940 TTTATTCATT
* * * *
1558950 GGGATACTCCAACCCCATTCATCGAGGGGATACTTCAACCTCGTTTTTAAACTTATCAAGATCTA
1 GGGATACTCCAACCCCATTCATCGAGGGGATACTCCAACCCCATTTCTAAACTTATCAAGATCTA
* *
1559015 AACCTT-ATTCTTACTCAAATTGTCATCATCG
66 AACCTTAATT-TCACCCAAATTGTCATCATCG
* * * *
1559046 GGGATACTCCAACCCCATTCTTTTGAGGGGATACTCCAACCCCATTTCTAAACTTGTCAAGATTT
1 GGGATACTCCAACCCCATTC-ATCGAGGGGATACTCCAACCCCATTTCTAAACTTATCAAGATCT
* * *
1559111 AAATCTTAATTTCACCCAAATTGTCCTCTTCG
65 AAACCTTAATTTCACCCAAATTGTCATCATCG
* * *
1559143 AGGACACTCCAACCCCATTCCTCCGAGGGGA
1 GGGATACTCCAACCCCATTCAT-CGAGGGGA
1559174 CACTTCATCC
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
96 21 0.19
97 84 0.78
98 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (96 bp):
GGGATACTCCAACCCCATTCATCGAGGGGATACTCCAACCCCATTTCTAAACTTATCAAGATCTA
AACCTTAATTTCACCCAAATTGTCATCATCG
Found at i:1563342 original size:13 final size:13
Alignment explanation
Indices: 1563324--1563349 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1563314 TACACCAAGT
1563324 ATGTATCGATACA
1 ATGTATCGATACA
1563337 ATGTATCGATACA
1 ATGTATCGATACA
1563350 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1563347 original size:32 final size:33
Alignment explanation
Indices: 1563306--1563369 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1563296 TAGCCAAACT
* **
1563306 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1563338 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1563370 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1565096 original size:17 final size:18
Alignment explanation
Indices: 1565064--1565097 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1565054 ATCTTTGCTC
*
1565064 AAAGGAGAATAGAGCAAA
1 AAAGGACAATAGAGCAAA
1565082 AAAGGACAA-AGAGCAA
1 AAAGGACAATAGAGCAA
1565098 GTAATATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.09, G:0.26, T:0.03
Consensus pattern (18 bp):
AAAGGACAATAGAGCAAA
Found at i:1565593 original size:21 final size:21
Alignment explanation
Indices: 1565560--1565604 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1565550 TTGCAAGTTG
*
1565560 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1565582 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1565602 AAA
1 AAA
1565605 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1567675 original size:20 final size:20
Alignment explanation
Indices: 1567650--1567701 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1567640 TACAAACCAA
** *
1567650 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
1567670 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
1567689 TGTATCGATACAA
1 TGTATCGATACAA
1567702 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:1567707 original size:19 final size:18
Alignment explanation
Indices: 1567650--1567707 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
1567640 TACAAACCAA
*
1567650 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
1567670 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1567689 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1567708 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1570676 original size:13 final size:13
Alignment explanation
Indices: 1570658--1570683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1570648 ACATTTTTCT
1570658 TTGTATCGATACA
1 TTGTATCGATACA
1570671 TTGTATCGATACA
1 TTGTATCGATACA
1570684 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1570847 original size:20 final size:20
Alignment explanation
Indices: 1570804--1570849 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1570794 AAATCTTTTG
1570804 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1570825 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1570845 CAAAA
1 CAAAA
1570850 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1572543 original size:40 final size:40
Alignment explanation
Indices: 1572499--1572629 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 40
1572489 ATTAATAAAC
1572499 GGGGGAGATAAAGGAGAGAATGCGTGAATTACCTTATTAA
1 GGGGGAGATAAAGGAGAGAATGCGTGAATTACCTTATTAA
** *** * * * * *
1572539 GGGGGAGAATGTACTTGATTAAGGGGGAGAATTA--TTAATAAA
1 GGGGGAG-ATAAAGGAGA-GAA-TGCGTGAATTACCTT-ATTAA
1572581 CGGGGGAGATAAAGGAGAGAATGCGTGAATTACCTTATTAA
1 -GGGGGAGATAAAGGAGAGAATGCGTGAATTACCTTATTAA
1572622 GGGGGAGA
1 GGGGGAGA
1572630 ATGTACAAAT
Statistics
Matches: 64, Mismatches: 20, Indels: 14
0.65 0.20 0.14
Matches are distributed among these distances:
40 23 0.36
41 13 0.20
42 13 0.20
43 15 0.23
ACGTcount: A:0.37, C:0.06, G:0.35, T:0.22
Consensus pattern (40 bp):
GGGGGAGATAAAGGAGAGAATGCGTGAATTACCTTATTAA
Found at i:1572571 original size:83 final size:83
Alignment explanation
Indices: 1572463--1572635 Score: 339
Period size: 83 Copynumber: 2.1 Consensus size: 83
1572453 TTTTTGATAT
1572463 GAAT-TACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTGAA
1 GAATGTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTGAA
1572527 TTACCTTATTAAGGGGGA
66 TTACCTTATTAAGGGGGA
1572545 GAATGTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTGAA
1 GAATGTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTGAA
1572610 TTACCTTATTAAGGGGGA
66 TTACCTTATTAAGGGGGA
1572628 GAATGTAC
1 GAATGTAC
1572636 AAATTTGTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 4 0.04
83 86 0.96
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.24
Consensus pattern (83 bp):
GAATGTACTTGATTAAGGGGGAGAATTATTAATAAACGGGGGAGATAAAGGAGAGAATGCGTGAA
TTACCTTATTAAGGGGGA
Found at i:1572587 original size:21 final size:22
Alignment explanation
Indices: 1572537--1572589 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1572527 TTACCTTATT
* *
1572537 AAGGGGGAGAATGTACTTGATT
1 AAGGGGGAGAATGTACTTAATA
1572559 AAGGGGGAGAAT-TA-TTAATA
1 AAGGGGGAGAATGTACTTAATA
1572579 AACGGGGGAGA
1 AA-GGGGGAGA
1572590 TAAAGGAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 10 0.36
22 12 0.43
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.21
Consensus pattern (22 bp):
AAGGGGGAGAATGTACTTAATA
Found at i:1573305 original size:13 final size:13
Alignment explanation
Indices: 1573287--1573312 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1573277 TACACCAAGT
1573287 ATGTATCGATACA
1 ATGTATCGATACA
1573300 ATGTATCGATACA
1 ATGTATCGATACA
1573313 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1573310 original size:32 final size:33
Alignment explanation
Indices: 1573269--1573332 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1573259 TAGCCAAACT
* **
1573269 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1573301 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1573333 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1578214 original size:38 final size:38
Alignment explanation
Indices: 1578152--1578229 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
1578142 TTTATTCAAT
* *
1578152 ATAAAATATAATAATAAGTAGAAATCGAAAATTAAAAAA
1 ATAAAATATAATAATAAGTAGAAAT-AAAAAATAAAAAA
*
1578191 ATAATAATA-AATATTAA-TAGAAATAAAAAATAAAAAA
1 ATAA-AATATAATAATAAGTAGAAATAAAAAATAAAAAA
1578228 AT
1 AT
1578230 CATGAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 13 0.37
38 7 0.20
39 11 0.31
40 4 0.11
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.24
Consensus pattern (38 bp):
ATAAAATATAATAATAAGTAGAAATAAAAAATAAAAAA
Found at i:1578314 original size:31 final size:31
Alignment explanation
Indices: 1578276--1578341 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1578266 TGCATGTAAG
*
1578276 GCAATGTAGCATGCAATCATGGGAGACACAT
1 GCAATGTAGCATGCAATCATGGGAGACACAA
*
1578307 GCAATGTAGCATGCAATCATGGGGGACACAA
1 GCAATGTAGCATGCAATCATGGGAGACACAA
1578338 GCAA
1 GCAA
1578342 ATGGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (31 bp):
GCAATGTAGCATGCAATCATGGGAGACACAA
Found at i:1578922 original size:31 final size:31
Alignment explanation
Indices: 1578887--1578974 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
1578877 CGAAACCAAT
* * * *
1578887 AGCTCGAGCTTCATCCAGCTTTCA-TGCTAGC
1 AGCTCGAGCCTCTTCCAGCTTCCACGGC-AGC
* *
1578918 AGCTCAAGCCTCTTCCAGCTTCCACGGCGGC
1 AGCTCGAGCCTCTTCCAGCTTCCACGGCAGC
1578949 AGCTCGAGCCTCTTCCAGCTTCCACG
1 AGCTCGAGCCTCTTCCAGCTTCCACG
1578975 AACACAGCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
31 47 0.96
32 2 0.04
ACGTcount: A:0.17, C:0.39, G:0.20, T:0.24
Consensus pattern (31 bp):
AGCTCGAGCCTCTTCCAGCTTCCACGGCAGC
Found at i:1579028 original size:24 final size:21
Alignment explanation
Indices: 1578964--1579046 Score: 103
Period size: 21 Copynumber: 3.8 Consensus size: 21
1578954 GAGCCTCTTC
*
1578964 CAGCTTCCACGAACACAGCAG
1 CAGCATCCACGAACACAGCAG
*
1578985 CAGCATCCATGAACACAGCAG
1 CAGCATCCACGAACACAGCAG
1579006 CAGCATCCACGAACACGGTAGCAG
1 CAGCATCCACGAACAC---AGCAG
* *
1579030 TAGCATCCATGAACACA
1 CAGCATCCACGAACACA
1579047 ATAGCAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 35 0.65
24 19 0.35
ACGTcount: A:0.36, C:0.34, G:0.19, T:0.11
Consensus pattern (21 bp):
CAGCATCCACGAACACAGCAG
Found at i:1579041 original size:45 final size:42
Alignment explanation
Indices: 1578964--1579046 Score: 121
Period size: 45 Copynumber: 1.9 Consensus size: 42
1578954 GAGCCTCTTC
*
1578964 CAGCTTCCACGAACACAGCAGCAGCATCCATGAACACAGCAG
1 CAGCATCCACGAACACAGCAGCAGCATCCATGAACACAGCAG
*
1579006 CAGCATCCACGAACACGGTAGCAGTAGCATCCATGAACACA
1 CAGCATCCACGAACAC---AGCAGCAGCATCCATGAACACA
1579047 ATAGCAGCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 15 0.42
45 21 0.58
ACGTcount: A:0.36, C:0.34, G:0.19, T:0.11
Consensus pattern (42 bp):
CAGCATCCACGAACACAGCAGCAGCATCCATGAACACAGCAG
Found at i:1585295 original size:13 final size:14
Alignment explanation
Indices: 1585272--1585300 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1585262 AAGGTGGTAT
1585272 AATGACCTTTCTGC
1 AATGACCTTTCTGC
1585286 AATG-CCTTTCTGC
1 AATGACCTTTCTGC
1585299 AA
1 AA
1585301 CAATATAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (14 bp):
AATGACCTTTCTGC
Found at i:1592747 original size:42 final size:42
Alignment explanation
Indices: 1592720--1593649 Score: 716
Period size: 42 Copynumber: 22.4 Consensus size: 42
1592710 TTTGATTCAA
*
1592720 CCTGTCAGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
** *
1592762 CC-GTTGGCTTTGACCTTAGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * *
1592803 CTTGTCAACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * *
1592845 CTTGTCGGCTTTGACCCTGGAGACTTTCTTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * *
1592887 CCTTTCAGCTTTGACCCTAAAGACTTTCCTTCCCATAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
*
1592929 CTTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* ** * *
1592971 -CTTTTTGACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * *
1593013 CCTATCGGCTTTGACCCTAAAGACTTTCATTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * *
1593055 CTTGTC-GACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * *
1593097 CTTGTC-GACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTG
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
*
1593139 CCTGTCGGCTTTGACCCTAGAGACTTTCCTT--C---GTCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * *
1593176 CCTATC-GACTTTGACCCTCGAGACATTACTACCCTTAGTCTG
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * *
1593218 CCTTTC-GACTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTA
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * *
1593260 CCTATCGGCTTTGACCCT-GAAAACCTTCCTTCCCTTAGTCTG
1 CCTGTCAGCTTTGACCCTAG-AGACTTTCCTTCCCTTAGTCTG
* * * *
1593302 CCAT-T-AGCTTTGACCATGGAGAC-TTCCTACCCTCAGTCTG
1 CC-TGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * *
1593342 CTTGTC-GACTTTGACCTTGGAGACTTT-CTTACCCTTAGACTA
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTT-CCCTTAGTCTG
* * * * ** *
1593384 CCTATC-GGTTTGACCTTGGAGACTTTCCAACCCTTAGTTTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * ** * *
1593425 CCTGTC-GACTTTGACCCTGGAGACTTTCCTACCCCCAGTTTA
1 CCTGTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
** * * *
1593467 CCTGTTGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTC-G
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * * *
1593508 GCTCGTC-GAC-TTGACCTTGGAGAATTTTCTACCCTTAGTCTG
1 CCT-GTCAG-CTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * ** * *
1593550 CCTGTCGGCTTTAACCCTGGAGACTTTTCAACCTTTAGCCTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* * * * * * * * *
1593592 CCTATCGGCCTTGACTCTGGAAACTTTTCTACCCTTAGTTTG
1 CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
* *
1593634 CCTCTCGGCTTTGACC
1 CCTGTCAGCTTTGACC
1593650 TTGAAGACTG
Statistics
Matches: 738, Mismatches: 122, Indels: 56
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.00
37 29 0.04
39 2 0.00
40 19 0.03
41 136 0.18
42 543 0.74
43 8 0.01
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.37
Consensus pattern (42 bp):
CCTGTCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTG
Found at i:1592899 original size:84 final size:84
Alignment explanation
Indices: 1592724--1593658 Score: 880
Period size: 84 Copynumber: 11.2 Consensus size: 84
1592714 ATTCAACCTG
* * * *
1592724 TCAGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCC-GTTGGCTTTGACCTTAGAGACTTT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
1592788 CCTTCCCTTAGTCTG-CTT
66 CCTTCCCTTAGTCTGCCTT
* *
1592806 GTCAACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGACTT
1 -TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
*
1592871 TCTTTCCCTTAGTCTGCCTT
65 TCCTTCCCTTAGTCTGCCTT
* ** * * * *
1592891 TCAGCTTTGACCCTAAAGACTTTCCTTCCCATAGTCTGCTTGTCAGCTTTGACCCTAGAGACTTT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
1592956 CCTTCCCTTAGTCTG-CTT
66 CCTTCCCTTAGTCTGCCTT
** * **
1592974 TTTGACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTT
1 TCAG-CTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
*
1593039 TCATTCCCTTAGTCTG-CTT
65 TCCTTCCCTTAGTCTGCCTT
* * *
1593058 GTC-GACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCTTGTCGACTTTGACCTTGGAGACT
1 -TCAG-CTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
*
1593122 TTCCTTCCCTTAGTCTGCCTG
64 TTCCTTCCCTTAGTCTGCCTT
* * * * * * *
1593143 TCGGCTTTGACCCTAGAGACTTTCCTT--C---GTCTGCCTATCGACTTTGACCCTCGAGACATT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
* *
1593203 ACTACCCTTAGTCTGCCTT
66 CCTTCCCTTAGTCTGCCTT
* * * * * *
1593222 TC-GACTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTACCTATCGGCTTTGACCCTGAAAACCT
1 TCAG-CTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
*
1593286 TCCTTCCCTTAGTCTGCCAT
65 TCCTTCCCTTAGTCTGCCTT
* * * * * *
1593306 T-AGCTTTGACCATGGAGAC-TTCCTACCCTCAGTCTGCTTGTCGACTTTGACCTTGGAGACTTT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
* * *
1593369 -CTTACCCTTAGACTACCTA
66 CCTT-CCCTTAGTCTGCCTT
* ** * *
1593388 TC-GGTTTGACCTTGGAGACTTTCCAACCCTTAGTTTGCCTGTCGACTTTGACCCTGGAGACTTT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
* ** * *
1593452 CCTACCCCCAGTTTACCTGT
66 CCTTCCCTTAGTCTGCCT-T
* * * * * * * *
1593472 T-GGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTC-GGCTCGTCGAC-TTGACCTTGGAGAATT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCT-GTCGGCTTTGACCCTGGAGACTT
* * *
1593534 TTCTACCCTTAGTCTGCCTG
65 TCCTTCCCTTAGTCTGCCTT
* * * * ** * * * * * *
1593554 TCGGCTTTAACCCTGGAGACTTTTCAACCTTTAGCCTGCCTATCGGCCTTGACTCTGGAAACTTT
1 TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
* * * *
1593619 TCTACCCTTAGTTTGCCTC
66 CCTTCCCTTAGTCTGCCTT
* *
1593638 TCGGCTTTGACCTTGAAGACT
1 TCAGCTTTGACCTTGGAGACT
1593659 GCCTCATTTA
Statistics
Matches: 709, Mismatches: 120, Indels: 45
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.00
79 65 0.09
81 4 0.01
82 62 0.09
83 169 0.24
84 401 0.57
85 7 0.01
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (84 bp):
TCAGCTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
CCTTCCCTTAGTCTGCCTT
Found at i:1592952 original size:126 final size:126
Alignment explanation
Indices: 1592728--1593658 Score: 937
Period size: 126 Copynumber: 7.5 Consensus size: 126
1592718 AACCTGTCAG
* * * *
1592728 CTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCGT-T-GGCTTTGACCTTAGAGACTTTCCT
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCC-TATCGGCTTTGACCCTAAAGACTTTCCT
* * * *
1592791 TCCCTTAGTCTGCTTGTCAACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCTTGTCGG
65 TCCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* * *
1592853 CTTTGACCCTGGAGACTTTCTTTCCCTTAGTCTGCCTTTCAGCTTTGACCCTAAAGACTTTCCTT
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCCTT
* * * * *
1592918 CCCATAGTCTGCTTGTC-AGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCTGCTTTTTGA
66 CCCTTAGTCTGCTTGTCGA-CTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* *
1592979 CTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCATT
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCCTT
* *
1593044 CCCTTAGTCTGCTTGTCGACTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCTTGTCGA
66 CCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* * *
1593105 CTTTGACCTTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTT
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCCTT
* * * * *
1593170 --C---GTCTGCCTATCGACTTTGACCCTCGAGACATTACTACCCTTAGTCTGCCTT-TCGA
66 CCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTG-CTTGTCGA
* *
1593226 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTACCTATCGGCTTTGACCCTGAAA-ACCTTCCT
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCT-AAAGACTTTCCT
* * * *
1593290 TCCCTTAGTCTGCCAT-TAG-CTTTGACCATGGAGAC-TTCCTACCCTCAGTCTGCTTGTCGA
65 TCCCTTAGTCTG-CTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* * * * ** **
1593350 CTTTGACCTTGGAGACTTTCTTACCCTTAGACTACCTATCGG-TTTGACCTTGGAGACTTTCCAA
1 CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCCTT
* * ** * * * * *
1593414 CCCTTAGTTTGCCTGTCGACTTTGACCCTGGAGACTTTCCTACCCCCAGTTTACCTGTTGG
66 CCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* * * * * * ** * *
1593475 CTTTGACCCTGGAGACTTT-TCTTCCCTCAGTC-GGCTCGTCGAC-TTGACCTTGGAGAATTTTC
1 CTTTGACCTTGGAGACTTTCT-TTCCCTTAGTCTGCCT-ATCGGCTTTGACCCTAAAGACTTTCC
* * * * * * * * * * *
1593537 TACCCTTAGTCTGCCTGTCGGCTTTAACCCTGGAGACTTTTCAACCTTTAGCCTGCCTATCGG
64 TTCCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
* * * * * * *
1593600 CCTTGA-CTCTGGAAACTTT-TCTACCCTTAGTTTGCCTCTCGGCTTTGACCTTGAAGACT
1 CTTTGACCT-TGGAGACTTTCT-TTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACT
1593659 GCCTCATTTA
Statistics
Matches: 689, Mismatches: 94, Indels: 45
0.83 0.11 0.05
Matches are distributed among these distances:
121 101 0.15
122 8 0.01
123 30 0.04
124 80 0.12
125 193 0.28
126 274 0.40
127 3 0.00
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (126 bp):
CTTTGACCTTGGAGACTTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAAAGACTTTCCTT
CCCTTAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCTTGTCGA
Found at i:1593606 original size:125 final size:125
Alignment explanation
Indices: 1593393--1593626 Score: 288
Period size: 125 Copynumber: 1.9 Consensus size: 125
1593383 ACCTATCGGT
* * * *
1593393 TTGACCTTGGAGACTTTCCAACCCTTAGTTTGCCTGTCGACTTTGACCCTGGAGACTTTCCTACC
1 TTGACCTTGGAGAATTTCCAACCCTTAGTCTGCCTGTCGACTTTAACCCTGGAGACTTTCCAACC
** * * * * *
1593458 CCCAGTTTACCTGTTGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCGGCTCGTCGAC
66 CCCAGCCTACCTATCGGCCTTGACCCTGGAAACTTTTCTACCCTCAGTCGGCTCGTCGAC
* * * *
1593518 TTGACCTTGGAGAATTTTCTACCCTTAGTCTGCCTGTCGGCTTTAACCCTGGAGACTTTTCAACC
1 TTGACCTTGGAGAATTTCCAACCCTTAGTCTGCCTGTCGACTTTAACCCTGGAGACTTTCCAACC
*** * *
1593583 TTTAGCCTGCCTATCGGCCTTGACTCTGGAAACTTTTCTACCCT
66 CCCAGCCTACCTATCGGCCTTGACCCTGGAAACTTTTCTACCCT
1593627 TAGTTTGCCT
Statistics
Matches: 89, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
125 89 1.00
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.35
Consensus pattern (125 bp):
TTGACCTTGGAGAATTTCCAACCCTTAGTCTGCCTGTCGACTTTAACCCTGGAGACTTTCCAACC
CCCAGCCTACCTATCGGCCTTGACCCTGGAAACTTTTCTACCCTCAGTCGGCTCGTCGAC
Found at i:1594294 original size:31 final size:31
Alignment explanation
Indices: 1594252--1594317 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1594242 TGCATGCAAG
* *
1594252 GCAATGTAGCATGCAATCATGGGAGACACAT
1 GCAATGCAGCATGCAATCATGGGAGACACAA
* *
1594283 GCAATGCAGCATGTAATCATGGGGGACACAA
1 GCAATGCAGCATGCAATCATGGGAGACACAA
1594314 GCAA
1 GCAA
1594318 ATGGAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (31 bp):
GCAATGCAGCATGCAATCATGGGAGACACAA
Found at i:1600929 original size:13 final size:13
Alignment explanation
Indices: 1600913--1600945 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1600903 ACAATTCATC
1600913 ATGTATCGATACA
1 ATGTATCGATACA
1600926 ATGTATCGATACA
1 ATGTATCGATACA
*
1600939 TTGTATC
1 ATGTATC
1600946 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1600931 original size:33 final size:33
Alignment explanation
Indices: 1600893--1600959 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1600883 ATTACAAGCT
1600893 ATGTATCAATACAATT-CATCATGTATCGATACA
1 ATGTATCAATAC-ATTGCATCATGTATCGATACA
* *
1600926 ATGTATCGATACATTGTATCATGTATCGATACA
1 ATGTATCAATACATTGCATCATGTATCGATACA
1600959 A
1 A
1600960 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
ATGTATCAATACATTGCATCATGTATCGATACA
Found at i:1601013 original size:20 final size:20
Alignment explanation
Indices: 1600988--1601042 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1600978 CTGCCAATCT
**
1600988 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1601008 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
1601027 AATGTATCGATACAAT
1 CATGTATCGATACAAT
1601043 GTATTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1601660 original size:21 final size:21
Alignment explanation
Indices: 1601596--1601666 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
1601586 AGTTTTCATT
*
1601596 TTTCTCCCCCTTAATTAAAGAA
1 TTTCT-CCCCTTAATCAAAGAA
*
1601618 TTTCT-CCTTTAATCAAA-AA
1 TTTCTCCCCTTAATCAAAGAA
*
1601637 TTTCTCCCCTTAATCAAAGCA
1 TTTCTCCCCTTAATCAAAGAA
1601658 TTTCTCCCC
1 TTTCTCCCC
1601667 CTTTTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 7 0.16
20 21 0.49
21 10 0.23
22 5 0.12
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTCTCCCCTTAATCAAAGAA
Found at i:1603600 original size:13 final size:13
Alignment explanation
Indices: 1603568--1603609 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1603558 AAATAGTACC
*
1603568 CAATGTATCTATA
1 CAATGTATCGATA
* *
1603581 TAGTGTATCGATA
1 CAATGTATCGATA
1603594 CAATGTATCGATA
1 CAATGTATCGATA
1603607 CAA
1 CAA
1603610 GGAATATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1603810 original size:28 final size:28
Alignment explanation
Indices: 1603757--1603810 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1603747 AACATGCATA
* * *
1603757 ATTCATTCACAACATAATAAACATCAAC
1 ATTCATACACAACAAAACAAACATCAAC
1603785 ATTCATACAACAACAAAACAAA-ATCA
1 ATTCATAC-ACAACAAAACAAACATCA
1603811 TCAAAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (28 bp):
ATTCATACACAACAAAACAAACATCAAC
Found at i:1604836 original size:87 final size:86
Alignment explanation
Indices: 1604691--1604864 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 86
1604681 AAGGTTACCT
* *
1604691 CCTTCATCTTTCTCAAGCTTTGTTGAAGTACTCATCGGAGTTTCACATGGTTTGACTTGATCCAT
1 CCTTCATCCTTCTCAAGCTTTCTTGAAGTACTCATCGGAGTTTCACATGGTTTGACTTGATCCAT
1604756 TTGAAATCTTTTGAGTAGCTC
66 TTGAAATCTTTTGAGTAGCTC
1604777 CCTTCATCCTTCTCAAGCTTTTCTTGAAGTACTCATCGGAGTTTCACATGGTTTGACTTGATCCA
1 CCTTCATCCTTCTCAAGC-TTTCTTGAAGTACTCATCGGAGTTTCACATGGTTTGACTTGATCCA
1604842 TTTGAAATCTTTTGAGTAGCTC
65 TTTGAAATCTTTTGAGTAGCTC
1604864 C
1 C
1604865 TTTGTATATT
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 17 0.20
87 68 0.80
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (86 bp):
CCTTCATCCTTCTCAAGCTTTCTTGAAGTACTCATCGGAGTTTCACATGGTTTGACTTGATCCAT
TTGAAATCTTTTGAGTAGCTC
Found at i:1606087 original size:21 final size:21
Alignment explanation
Indices: 1606061--1606117 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1606051 AAATTATCCA
1606061 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1606082 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1606103 AATGTATCGATACAT
1 AATGTATCGATACAT
1606118 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1606266 original size:13 final size:13
Alignment explanation
Indices: 1606248--1606273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1606238 CATTTTTCTA
1606248 TGTATCGATACAT
1 TGTATCGATACAT
1606261 TGTATCGATACAT
1 TGTATCGATACAT
1606274 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1606270 original size:33 final size:33
Alignment explanation
Indices: 1606228--1606294 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1606218 GCCAAGGAAA
***
1606228 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
1606261 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
1606294 T
1 T
1606295 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:1607537 original size:55 final size:55
Alignment explanation
Indices: 1607452--1608127 Score: 1051
Period size: 55 Copynumber: 12.3 Consensus size: 55
1607442 TCCGCTTTTT
*
1607452 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * **
1607507 GGTCCTCAAAGAGCAGGACACCGCTT-AAAGCCCACACAAGTTGGTGGCACCCTT-C
1 AGTCCTCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
1607562 AGTCCCCGAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1607617 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1607672 AGTCCTCATAGAGCAGGACACCTTTCAAAGCCCTCACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1607727 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
1607782 AGTCCTCAAAAAGTAGGCCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1607837 AGTCCTCAAAAAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1607892 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1607947 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1608002 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * *
1608057 AGTCCTCAAAGAGAAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1608112 AGTCCTCAAAGAGCAG
1 AGTCCTCAAAGAGCAG
1608128 AATACACTTT
Statistics
Matches: 581, Mismatches: 34, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
54 6 0.01
55 570 0.98
56 5 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1607642 original size:27 final size:27
Alignment explanation
Indices: 1607612--1607754 Score: 69
Period size: 27 Copynumber: 5.2 Consensus size: 27
1607602 TTGGTGGCAT
*
1607612 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCAAGTCCTCAAAGAGCAGGACACC
* * * ** *
1607639 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-AAGTCCTCA-AAG-AGCAGGACACC
* *
1607667 TTTCTAGTCCTCATAGAGCAGGACACC
1 TTTCAAGTCCTCAAAGAGCAGGACACC
* * ** *
1607694 TTTCAAAGCCCTCACAAGTTGGTGG-CA-T
1 TTTC-AAGTCCTCA-AAG-AGCAGGACACC
*
1607722 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCAAGTCCTCAAAGAGCAGGACACC
1607749 TTTCAA
1 TTTCAA
1607755 AGCCCACACA
Statistics
Matches: 77, Mismatches: 29, Indels: 20
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 9 0.12
27 26 0.34
28 21 0.27
29 9 0.12
30 6 0.08
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (27 bp):
TTTCAAGTCCTCAAAGAGCAGGACACC
Found at i:1618658 original size:9 final size:9
Alignment explanation
Indices: 1618644--1618727 Score: 64
Period size: 9 Copynumber: 8.9 Consensus size: 9
1618634 TCTCTTCAAA
1618644 AAAAAAAAG
1 AAAAAAAAG
1618653 AAAAAAAAG
1 AAAAAAAAG
1618662 AGCAAAAAAA-
1 A--AAAAAAAG
1618672 AAGAAAAAA-
1 AA-AAAAAAG
*
1618681 AAAACAAAAC
1 AAAA-AAAAG
*
1618691 AAAAAAAAC
1 AAAAAAAAG
*
1618700 AAAACAAAG
1 AAAAAAAAG
*
1618709 AAAAAGAGAG
1 AAAAA-AAAG
1618719 AAAAGAAAA
1 AAAA-AAAA
1618728 AGAACCTGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
8 3 0.05
9 38 0.60
10 14 0.22
11 8 0.13
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1618728 original size:1 final size:1
Alignment explanation
Indices: 1618641--1618713 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
1618631 CCTTCTCTTC
* * ** * * * * *
1618641 AAAAAAAAAAAGAAAAAAAAGAGCAAAAAAAAAGAAAAAAAAAACAAAACAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1618706 AAGAAAAA
1 AAAAAAAA
1618714 GAGAGAAAAG
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1619748 original size:29 final size:29
Alignment explanation
Indices: 1619715--1619802 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
1619705 AAGAGCAGGA
1619715 CACCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
* * * * **
1619744 CACC-TTT-CAGTCCTCA-AAG-AGCAGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
*
1619769 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
1619799 CACC
1 CACC
1619803 CTTCAGTCCC
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
25 3 0.07
26 7 0.17
27 8 0.20
28 9 0.22
29 11 0.27
30 3 0.07
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1619781 original size:55 final size:55
Alignment explanation
Indices: 1619697--1620482 Score: 1269
Period size: 55 Copynumber: 14.3 Consensus size: 55
1619687 TCCGCTTTTT
* *
1619697 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
**
1619752 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCCTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
1619807 AGTCCCCGAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1619862 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1619917 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1619972 AGTCCGCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
1620027 AGTCCTCAAAAAGCAGGCCACCTTTCAAAGCCCTCACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1620082 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
1620137 AGTCCTCAAAAAGTAGGCCACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1620192 AGTCCTCAAAAAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1620247 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1620302 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1620357 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
1620412 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1620467 AGTCCTCAAAGAGCAG
1 AGTCCTCAAAGAGCAG
1620483 AATACACTTT
Statistics
Matches: 689, Mismatches: 36, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
54 6 0.01
55 676 0.98
56 7 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1621306 original size:19 final size:19
Alignment explanation
Indices: 1621282--1621349 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1621272 AATTCAACAA
1621282 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1621301 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1621316 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1621333 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1621350 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1621321 original size:13 final size:13
Alignment explanation
Indices: 1621303--1621327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1621293 ACATAAGTTT
1621303 TGTATCGATACAA
1 TGTATCGATACAA
1621316 TGTATCGATACA
1 TGTATCGATACA
1621328 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1621325 original size:32 final size:32
Alignment explanation
Indices: 1621284--1621346 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1621274 TTCAACAATT
*
1621284 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1621316 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1621347 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1621407 original size:13 final size:13
Alignment explanation
Indices: 1621389--1621414 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1621379 CATTTTTCTG
1621389 TGTATCGATACAT
1 TGTATCGATACAT
1621402 TGTATCGATACAT
1 TGTATCGATACAT
1621415 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1621411 original size:33 final size:33
Alignment explanation
Indices: 1621369--1621435 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1621359 GCCAAGGAAA
***
1621369 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1621402 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1621435 T
1 T
1621436 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1623855 original size:28 final size:27
Alignment explanation
Indices: 1623788--1623860 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1623778 TTCTAAAATC
*
1623788 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1623815 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
*
1623843 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
1623861 GTTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1623918 original size:52 final size:53
Alignment explanation
Indices: 1623843--1623960 Score: 127
Period size: 52 Copynumber: 2.3 Consensus size: 53
1623833 TTATTTCTGA
* * **
1623843 GGGGATACTCCAA-TCCCGGTTTTATTT-TCAAAACT-CCAATTTTCCTTTAATC
1 GGGGATACTCCAACTCCCGATTTTATTTCT-AAAAATACCAATTTTCC-ACAATC
* *
1623895 GGGGATACTCCAACT-CTGATTTTATTTCTAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACTCCCGATTTTATTTCTAAAAATACCAATTTTCCACAATC
*
1623947 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1623961 CTCGTTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
52 45 0.80
53 11 0.20
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (53 bp):
GGGGATACTCCAACTCCCGATTTTATTTCTAAAAATACCAATTTTCCACAATC
Found at i:1623980 original size:28 final size:28
Alignment explanation
Indices: 1623944--1624015 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
1623934 ATTTTTCACA
* *
1623944 ATCGAGGATACTCCAA-CCTCGTTATTTC
1 ATCGGGGATACTCCAACCCT-GTTACTTC
1623972 ATCGGGGATACTCCAACCCTGTTACTTC
1 ATCGGGGATACTCCAACCCTGTTACTTC
***
1624000 CGAGGGGATACTCCAA
1 ATCGGGGATACTCCAA
1624016 TCCCGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTGTTACTTC
Found at i:1624012 original size:160 final size:158
Alignment explanation
Indices: 1623733--1624031 Score: 431
Period size: 160 Copynumber: 1.9 Consensus size: 158
1623723 AATTCTCCAC
* * * *
1623733 AATCGGGGATATTCCAACTCCTATTTTATTTTTAAAACACTAATTTTCTAAAATCGGGGATACTC
1 AATCGGGGATACTCCAACTCCTATTTTATTTTAAAAACACCAATTTTCTAAAATCGAGGATACTC
* * *
1623798 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGGT
66 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAATCCCGAT
1623863 TTTATTTTCAAAACTCCAATTTTCCTTT
131 TTTATTTTCAAAACTCCAATTTTCCTTT
* *
1623891 AATCGGGGATACTCCAACT-CTGATTTTATTTCTAAAAATACCAATTTT-TCACAATCGAGGATA
1 AATCGGGGATACTCCAACTCCT-ATTTTATTT-TAAAAACACCAATTTTCT-AAAATCGAGGATA
* * *
1623954 CTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCTGTTACTTCCGAGGGGATACTCCAATCC
63 CTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAATCC
*
1624019 CGATTTTTTTTTC
127 CGATTTTATTTTC
1624032 TTCTGATCAT
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
157 2 0.02
158 28 0.23
159 37 0.30
160 57 0.46
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (158 bp):
AATCGGGGATACTCCAACTCCTATTTTATTTTAAAAACACCAATTTTCTAAAATCGAGGATACTC
CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAATCCCGAT
TTTATTTTCAAAACTCCAATTTTCCTTT
Found at i:1628504 original size:20 final size:21
Alignment explanation
Indices: 1628479--1628532 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
1628469 GTTACAAGCT
1628479 ATGTATCGATACAATT-CATC
1 ATGTATCGATACAATTGCATC
*
1628499 ATGTATCGATAC-ATTGTATC
1 ATGTATCGATACAATTGCATC
1628519 ATGTATCGATACAA
1 ATGTATCGATACAA
1628533 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 3 0.10
20 27 0.87
21 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGCATC
Found at i:1628606 original size:19 final size:20
Alignment explanation
Indices: 1628582--1628633 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1628572 ACAATTGTCC
* *
1628582 ATGTATCAATACAATGAAT-
1 ATGTATCGATACAAAGAATA
*
1628601 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGAATA
1628621 ATGTATCGATACA
1 ATGTATCGATACA
1628634 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:1629704 original size:13 final size:13
Alignment explanation
Indices: 1629683--1629713 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1629673 TCGATACATT
*
1629683 ATACCTTGTATCG
1 ATACATTGTATCG
1629696 ATACATTGTATCG
1 ATACATTGTATCG
1629709 ATACA
1 ATACA
1629714 CGGACAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (13 bp):
ATACATTGTATCG
Found at i:1635917 original size:19 final size:21
Alignment explanation
Indices: 1635893--1635944 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1635883 GGCGATACAT
1635893 TGTATCGATACA-CTACT-TA
1 TGTATCGATACATCTACTGTA
* *
1635912 TGTATCGATACATTTACTGTT
1 TGTATCGATACATCTACTGTA
1635933 TGTATCGATACA
1 TGTATCGATACA
1635945 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTACTGTA
Found at i:1636782 original size:52 final size:49
Alignment explanation
Indices: 1636726--1637001 Score: 174
Period size: 52 Copynumber: 5.4 Consensus size: 49
1636716 TATGCTAAGA
* * *
1636726 CAAGGCCAATGACATTGGGCTTAGGAATGTTAAAGATGCCAATACGCTGATT
1 CAAGGCCAATGACATTGGACTTA--AA-GCTAAAGATGCCAATACACTGATT
* * **
1636778 CAAGGCCAATGATATTGGACTTAAAGCTGAAGATGCCAATGTACTGATT
1 CAAGGCCAATGACATTGGACTTAAAGCTAAAGATGCCAATACACTGATT
** * * * * ***
1636827 CAAGGCCAGCGACAGTGGTCTTAAAGATGACGAAGCTGCCAATATGTTGATT
1 CAAGGCCAATGACATTGGACTTAAAGCT-A--AAGATGCCAATACACTGATT
** * * * * **
1636879 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTACTGATT
1 CAAGGCCAATGACATTGGACTTAAAGCTAAAGATGCCAATACACTGATT
** * * **
1636928 CAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATT
1 CAAGGCCAATGACATTGGACTTAAAGCT---AAAGATGCCAATACACTGATT
** *
1636980 CAAGGCCAGCGATATTGGACTT
1 CAAGGCCAATGACATTGGACTT
1637002 GTGCCAATGT
Statistics
Matches: 187, Mismatches: 31, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
49 84 0.45
50 2 0.01
52 101 0.54
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
CAAGGCCAATGACATTGGACTTAAAGCTAAAGATGCCAATACACTGATT
Found at i:1636867 original size:101 final size:100
Alignment explanation
Indices: 1636757--1637594 Score: 529
Period size: 87 Copynumber: 9.0 Consensus size: 100
1636747 TAGGAATGTT
* * ** *
1636757 AAAGATGCCAATACGCTGATTCAAGGCCAATGATATTGGACTTAAAGCTGAAGATGCCAATGTAC
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCT-AAGGTGCCAATGTAC
* *
1636822 TGATTCAAGGCCAGCGACAGTGGTCTTAAAGATGAC
65 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * *
1636858 GAAGCTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTAC
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCT-AAGGTGCCAATGTAC
1636923 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
65 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* *
1636959 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---GTGCCAATGTGCT
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCTAAGGTGCCAATGTACT
*
1637015 GATTCAAGGCCAGCGACATTAGACTTAAAGATGAC
66 GATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * * * *
1637050 AAAGGC-GACAATATGCTGATTCAAGGCCAACGATATTGGTCTTAAAGAC-AAGGTGCCAATATG
1 AAA-GCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-CTAAGGTGCCAATGTA
* *
1637113 CTGATTCAAGGCCAGCGATATTGGTCTT-AA-A-GAC
64 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * *
1637147 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG-------GCT--TGTGCCAATGTGCT
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCTAAGGTGCCAATGTACT
*
1637202 GATTCAAGGCTAGCG--A-T--AC-T----A-GAC
66 GATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
** * * * * * * * *
1637226 -TTG-TGCTAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGAC-AAGGTGCCAATATGC
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-CTAAGGTGCCAATGTAC
* * *
1637288 TGATTTAAGGCCAGCGATATTGGGCTT---G-TG-C
65 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * * * *
1637319 AAA--TG------TGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGAC-AAGGTGCCAATATGC
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-CTAAGGTGCCAATGTAC
* *
1637375 TGATTCAAGGCCAGCGATATTGGGC-T-----T---
65 TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * * * *
1637402 ---G-TGCCAATGTGTTGATTCAAGGCCAGCGACATT-GATCATT-AAGAC-AAGGTGCCACTAT
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-C-TTAAAG-CTAAGGTGCCAATGT
* * * **
1637460 GCTGATTCAAGGCCAGCGATATTGGAC-TCAAGATGGT
63 ACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
* * * * *
1637497 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGAATTAAAGATGAAGGTGCCAATGTGC
1 AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCT-AAGGTGCCAATGTAC
* *
1637562 TAATTCGAA-GCCAACGACATTGGACTTAGAAGA
65 TGATTC-AAGGCCAGCGACATTGGACTTA-AAGA
1637595 AGACGCCACC
Statistics
Matches: 613, Mismatches: 64, Indels: 119
0.77 0.08 0.15
Matches are distributed among these distances:
78 29 0.05
79 5 0.01
81 3 0.00
82 1 0.00
84 1 0.00
85 3 0.00
86 3 0.00
87 190 0.31
88 3 0.00
89 2 0.00
90 1 0.00
91 81 0.13
92 4 0.01
93 4 0.01
94 1 0.00
95 2 0.00
96 33 0.05
97 3 0.00
98 4 0.01
99 34 0.06
100 70 0.11
101 132 0.22
102 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (100 bp):
AAAGCTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCTAAGGTGCCAATGTACT
GATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
Found at i:1637017 original size:39 final size:39
Alignment explanation
Indices: 1636963--1637040 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
1636953 GATGACAAAG
* *
1636963 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTT
*
1637002 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTT
1637041 AAAGATGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTT
Found at i:1637066 original size:91 final size:91
Alignment explanation
Indices: 1636911--1637227 Score: 399
Period size: 91 Copynumber: 3.4 Consensus size: 91
1636901 AAAGATGAAG
* *
1636911 GTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGCCAATATGCT
1636976 GATTCAAGGCCAGCGATATTGGACTT
66 GATTCAAGGCCAGCGATATTGGACTT
* *
1637002 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGCGACAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGCCAATATGCT
* *
1637067 GATTCAAGGCCAACGATATTGGTCTT
66 GATTCAAGGCCAGCGATATTGGACTT
* * * *
1637093 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA-A-GAC-AAGGTGC
1 ---------GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGC
*
1637154 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
57 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1637189 GTGCCAATGTGCTGATTCAAGGCTAGCGATACTAGACTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTT
1637228 GTGCTAATGT
Statistics
Matches: 198, Mismatches: 19, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
87 34 0.17
91 85 0.43
96 38 0.19
97 3 0.02
98 1 0.01
99 2 0.01
100 35 0.18
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (91 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTT
Found at i:1637132 original size:48 final size:48
Alignment explanation
Indices: 1637002--1637594 Score: 445
Period size: 48 Copynumber: 12.9 Consensus size: 48
1636992 TATTGGACTT
* * * *
1637002 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA-A-GAC-AAG
* * *
1637054 GCGACAATATGCTGATTCAAGGCCAACGATATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
1637102 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
*
1637150 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT---------
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
* * **
1637189 GTGCCAATGTGCTGATTCAAGGCTAGCGATA-----C-T--AGAC-TT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
* * * * *
1637228 GTGCTAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
* *
1637276 GTGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTT---------
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
* * * *
1637315 GTGCAAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
*
1637363 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT---------
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
* * * *
1637402 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGATCATT-AAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTC-TTAAAGACAAG
* * *
1637450 GTGCCACTATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA-A--G-ACAAG
* ** *
1637501 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGAATTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGA-CAAG
* * * * *
1637550 GTGCCAATGTGCTAATTCGAA-GCCAACGACATTGGACTTAGAAGA
1 GTGCCAATATGCTGATTC-AAGGCCAGCGATATTGGTCTTA-AAGA
1637595 AGACGCCACC
Statistics
Matches: 439, Mismatches: 60, Indels: 86
0.75 0.10 0.15
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
39 120 0.27
40 2 0.00
44 1 0.00
45 1 0.00
47 6 0.01
48 185 0.42
49 38 0.09
50 8 0.02
51 43 0.10
52 33 0.08
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (48 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGACAAG
Found at i:1637204 original size:39 final size:39
Alignment explanation
Indices: 1637150--1637435 Score: 239
Period size: 39 Copynumber: 6.9 Consensus size: 39
1637140 TAAAGACAAG
*
1637150 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * *
1637189 GTGCCAATGTGCTGATTCAAGGCTAGCGATACTAGACTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * * *
1637228 GTGCTAATGTGTTGATTCAAGGCCAACGACATTGGTCTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* *
1637267 AAAGACAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * *
1637315 GTGCAAATGTGCTGATTCAAGGCCAGTGACATTGGTCTT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
*
1637354 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
* *
1637402 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTG
1637436 ATCATTAAGA
Statistics
Matches: 195, Mismatches: 34, Indels: 36
0.74 0.13 0.14
Matches are distributed among these distances:
39 129 0.66
48 66 0.34
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (39 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
Found at i:1637677 original size:28 final size:29
Alignment explanation
Indices: 1637646--1637702 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
1637636 AACTTTTATG
*
1637646 CTTTTG-AAGGTTGCCACTGACTTGTGGC
1 CTTTTGAAAGGGTGCCACTGACTTGTGGC
1637674 CTTTTGAAAAGGGTGCCACTGACTTGTGG
1 CTTTTG-AAAGGGTGCCACTGACTTGTGG
1637703 GCTTAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
30 20 0.77
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (29 bp):
CTTTTGAAAGGGTGCCACTGACTTGTGGC
Found at i:1637758 original size:27 final size:27
Alignment explanation
Indices: 1637728--1637831 Score: 86
Period size: 34 Copynumber: 3.7 Consensus size: 27
1637718 GATGCTAAGG
*
1637728 AGTTGTGGACTTAAAAGGGTGCCACGA
1 AGTTATGGACTTAAAAGGGTGCCACGA
*
1637755 AGTTATGGACTTAAAAGGAAAAAGAATGCCACGG
1 AGTTATGGACTTAAAAGG-----G--TGCCACGA
* * *
1637789 AGTTGTGGAGTTAAAAGGGT--CACAA
1 AGTTATGGACTTAAAAGGGTGCCACGA
1637814 AGTTATGGACTTAAAAGG
1 AGTTATGGACTTAAAAGG
1637832 AAAAATAGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
25 19 0.31
27 18 0.29
29 1 0.02
32 1 0.02
34 23 0.37
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.22
Consensus pattern (27 bp):
AGTTATGGACTTAAAAGGGTGCCACGA
Found at i:1637768 original size:60 final size:61
Alignment explanation
Indices: 1637680--1637854 Score: 214
Period size: 59 Copynumber: 2.9 Consensus size: 61
1637670 TGGCCTTTTG
* * * * *
1637680 AAAAGGGTGCCACTG-ACTTGTGGGCTTAAAAGGAGAAAG-ATGCTAAGGAGTTGTGGACTT
1 AAAAGGGTGCCAC-GAAGTTATGGACTTAAAAGGAAAAAGAATGCCAAGGAGTTGTGGACTT
* *
1637740 AAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGAGTT
1 AAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAATGCCAAGGAGTTGTGGACTT
* * * *
1637801 AAAAGGGT--CACAAAGTTATGGACTTAAAAGGAAAAATAGTGCCATGGAGTTGTG
1 AAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAATGCCAAGGAGTTGTG
1637855 CGCTTTAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
59 43 0.42
60 33 0.32
61 26 0.25
ACGTcount: A:0.37, C:0.11, G:0.31, T:0.22
Consensus pattern (61 bp):
AAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAATGCCAAGGAGTTGTGGACTT
Found at i:1637904 original size:61 final size:63
Alignment explanation
Indices: 1637839--1637960 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 63
1637829 AGGAAAAATA
* * *
1637839 GTGCCATGGAGTTGTGCG-CTTTAAAAAGAAAAAG-GTGCCACAGCGTTGTGGAC-TTAAAAGG
1 GTGCCACGGAGTTGTG-GACATTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTAAAAGG
* *
1637900 GTGCCACGGAGTTGTGGACATTGAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA
1 GTGCCACGGAGTTGTGGACATTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTAAAA
1637961 AGAAAAATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 1 0.02
61 29 0.55
62 17 0.32
63 6 0.11
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (63 bp):
GTGCCACGGAGTTGTGGACATTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGACTTTAAAAGG
Found at i:1637905 original size:27 final size:27
Alignment explanation
Indices: 1637867--1638022 Score: 114
Period size: 27 Copynumber: 5.2 Consensus size: 27
1637857 CTTTAAAAAG
* *
1637867 AAAAAGGTGCCACAGCGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
*
1637894 AAAAGGGTGCCACGGAGTTGTGGACATT
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT
*
1637922 GAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 -AAAAG-----G-GTGCCACAGAGTTGTGGAC-TT
* * *
1637957 AAAAAGAAAAATGTGCCCCGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACAGAGTTGTGGACTT
1637990 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
1638017 AAAAGG
1 AAAAGG
1638023 AAAATGAGTG
Statistics
Matches: 107, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
27 47 0.44
28 2 0.02
29 5 0.05
32 5 0.05
33 2 0.02
34 17 0.16
35 29 0.27
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGACTT
Found at i:1637956 original size:96 final size:95
Alignment explanation
Indices: 1637740--1638075 Score: 414
Period size: 96 Copynumber: 3.6 Consensus size: 95
1637730 TTGTGGACTT
* * * * * *
1637740 AAAAGGGTGCCACGAAGTTATGGAC-TTAAAAGGAAAAAGAATGCCACGGAGTTGTGGAGTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-ATGCCACGGAGTTGTGGACTTAAA
* *
1637804 AGGGT--CACAAAGTTATGGACTTAAAAGGA
65 AGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * * * *
1637833 AAAATAGTGCCATGGAGTTGTGCGCTTTAAAAAGAAAAAGGTGCCACAGCGTTGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGATGCCACGGAGTTGTGGACTTAAAA
*
1637898 GGGTGCCACGGAGTTGTGGACATTGAAAA-GA
66 GGGTGCCACAGAGTTGTGGAC-TT-AAAAGGA
* *
1637929 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAATG-TGCCCCGGAGTTGTGGACTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GATGCCACGGAGTTGTGGACTTAAA
1637993 AGGGTGCCACAGAGTTGTGGACTTAAAAGGA
65 AGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * *
1638024 AAATGAGTGCCACGGAGTTGTGGGCTTTAAAGA-AAAAAGATGCCACTGAGTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGATGCCACGGAGTT
1638076 ATAGACTTGG
Statistics
Matches: 207, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
93 44 0.21
94 32 0.15
95 46 0.22
96 80 0.39
97 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (95 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGATGCCACGGAGTTGTGGACTTAAAA
GGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1637981 original size:34 final size:34
Alignment explanation
Indices: 1637894--1638145 Score: 160
Period size: 34 Copynumber: 7.8 Consensus size: 34
1637884 TTGTGGACTT
* *
1637894 AAAAGGGTGCCACGGAGTTGTGGACATTGAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAAGA
* *
1637929 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAAGA
* *
1637964 AAAA-TGTGCCCCGGAGTTGTGGACTT-AAAAG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
1637995 ----G-GTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGA
* * *
1638024 AAATGAGTGCCACGGAGTTGTGGGCTT-TAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGA
* * * **
1638057 AAAA-AGATGCCACTGAGTTATAGACTT-GGAAGA
1 AAAAGAG-TGCCACGGAGTTGTGGACTTAAAAAGA
* ** *
1638090 AAAGGA-TGCCACTAAGTCGTGGACTT----AG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGA
*
1638118 AAAAGAGATGCCACTGAGTTGTGGACTT
1 AAAAGAG-TGCCACGGAGTTGTGGACTT
1638146 TGAAAAGAGA
Statistics
Matches: 174, Mismatches: 31, Indels: 29
0.74 0.13 0.12
Matches are distributed among these distances:
27 19 0.11
28 9 0.05
29 2 0.01
30 18 0.10
32 23 0.13
33 33 0.19
34 36 0.21
35 34 0.20
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGA
Found at i:1638005 original size:61 final size:60
Alignment explanation
Indices: 1637929--1638056 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 60
1637919 ATTGAAAAGA
* *
1637929 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAT-GTGCCCCGGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGAC-TT-AAAAGAAAAATAGTGCCACGGAGTTGTGGACTT
* * *
1637990 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAATGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGAAAAAT-AGTGCCACGGAGTTGTGGACTT
*
1638051 TAAAGA
1 AAAAGA
1638057 AAAAAGATGC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 10 0.17
60 2 0.03
61 46 0.79
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (60 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGAAAAATAGTGCCACGGAGTTGTGGACTT
Found at i:1638130 original size:30 final size:31
Alignment explanation
Indices: 1638022--1638584 Score: 528
Period size: 31 Copynumber: 18.0 Consensus size: 31
1638012 GACTTAAAAG
* * *
1638022 GAAAATGAG-TGCCACGGAGTTGTGGGCTTTAAA
1 GAAAA-GAGATGCCACTGAGTCGTGGACTTT--A
* ** * *
1638055 GAAAAAAGATGCCACTGAGTTATAGACTTGGAA
1 GAAAAGAGATGCCACTGAGTCGTGGACTT--TA
*
1638088 GAAAAG-GATGCCACTAAGTCGTGGAC-TTA
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
*
1638117 GAAAAGAGATGCCACTGAGTTGTGGACTTT-
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
1638147 GAAAAGAGATTGCCACTGAGTCGTGGACTTTGGA
1 GAAAAGAGA-TGCCACTGAGTCGTGGACTTT--A
* * *
1638181 GAAAA-A-ATG-CAGTGAGTGGTGGACTTTG
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
* * *
1638209 GGACA-AGATGCCACTGAGTCGTGGGCTTT-
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
* *
1638238 GAGAAGAGATTGCCACTGAGTCATGGACTTTGAA
1 GAAAAGAGA-TGCCACTGAGTCGTGGACTTT--A
*
1638272 GAAAAAAGATGCCACTGAGTCGTGGACTTT-
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
* *
1638302 GAGAAGGGATTGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGAGA-TGCCACTGAGTCGTGGACTTT--A
*
1638336 GAAAAAAGATGCCACTGAGTCGTGGACTTTGA
1 GAAAAGAGATGCCACTGAGTCGTGGACTTT-A
*
1638368 GAAAAGAGATGCCACTGTGTCGTGGACTTTA
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
*
1638399 -AAAAGAGATGCCACTGAGTTGTGGACTTT-
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
1638428 GAAAAGAGATTGCCACTGAGTCGTGGACTTT-
1 GAAAAGAGA-TGCCACTGAGTCGTGGACTTTA
* * * *
1638459 GAAAAAAAAATGCCACTGAGTCATGGACTTTGG
1 G-AAAAGAGATGCCACTGAGTCGTGGACTTT-A
* * *
1638492 GACAA-A-ATGCCACTGAGTTGTGGGCTTT-
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
*
1638520 GAGAAGAGATTGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGAGA-TGCCACTGAGTCGTGGACTTT--A
*
1638554 GAAAAAAGATGCCACTGAGTCGTGGACTTTA
1 GAAAAGAGATGCCACTGAGTCGTGGACTTTA
1638585 AGAAGATATT
Statistics
Matches: 444, Mismatches: 55, Indels: 64
0.79 0.10 0.11
Matches are distributed among these distances:
28 8 0.02
29 13 0.03
30 122 0.27
31 128 0.29
32 57 0.13
33 91 0.20
34 25 0.06
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (31 bp):
GAAAAGAGATGCCACTGAGTCGTGGACTTTA
Found at i:1638292 original size:64 final size:63
Alignment explanation
Indices: 1638061--1638588 Score: 552
Period size: 61 Copynumber: 8.5 Consensus size: 63
1638051 TAAAGAAAAA
** * * * * * *
1638061 AGATGCCACTGAGTTATAGACTTGGAAG-AAAAGGATGCCACTAAGTCGTGGACTTAGAAAAG
1 AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
* * *
1638123 AGATGCCACTGAGTTGTGGACTTT---GAAAAGAGATTGCCACTGAGTCGTGGACTTTGGAGAAA
1 AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA-TGCCACTGAGTCGTGGACTTT-GAGAAG
* * * * * *
1638185 AAATG-CAGTGAGTGGTGGACTTTG--G-GACAAGATGCCACTGAGTCGTGGGCTTTGAGAAG
1 AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
*
1638244 AGATTGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
1 AGA-TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
*
1638308 GGATTGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAA
1 AGA-TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAG--AA
1638373 G
63 G
* * * *
1638374 AGATGCCACTGTGTCGTGGACTTT--A-AAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAG
1 AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
* *
1638434 AGATTGCCACTGAGTCGTGGACTTTGAA-AAAAAA-ATGCCACTGAGTCATGGACTTTGGGACA-
1 AGA-TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGA-AG
* * * *
1638496 AAATGCCACTGAGTTGTGGGCTTTG-AG--AAGAGATTGCCACTGAGTCGTGGACTTTGAAGAAA
1 AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA-TGCCACTGAGTCGTGGACTTTG-AG--A
*
1638558 AA
62 AG
1638560 AGATGCCACTGAGTCGTGGACTTT-AAGAA
1 AGATGCCACTGAGTCGTGGACTTTGAAGAA
1638589 GATATTTAAA
Statistics
Matches: 395, Mismatches: 46, Indels: 46
0.81 0.09 0.09
Matches are distributed among these distances:
59 11 0.03
60 35 0.09
61 116 0.29
62 84 0.21
63 10 0.03
64 114 0.29
65 20 0.05
66 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (63 bp):
AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAG
Found at i:1638451 original size:281 final size:282
Alignment explanation
Indices: 1638031--1638589 Score: 908
Period size: 281 Copynumber: 2.0 Consensus size: 282
1638021 GGAAAATGAG
* * *
1638031 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAAGATGCCACTGAGTTATAGACTTGGAAGAAAAGGA
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAAGATGCCACTGAGTCATAGACTTGGAAGAAAAGGA
1638096 TGCCACTAAGTCGTGGACTTAGAAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAGAGATTGCC
66 TGCCACTAAGTCGTGGACTTAGAAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAGAGATTGCC
* * * ** *
1638161 ACTGAGTCGTGGACTTTGGAGAAAAAATG-CAGTGAGTGGTGGACTTTGGGACAAGATGCCACTG
131 ACTGAGTCGTGGACTTTGAAAAAAAAATGCCACTGAGTCATGGACTTTGGGACAAAATGCCACTG
1638225 AGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGA
196 AGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGA
*
1638290 GTCGTGGACTTTGAGAAGGGAT
261 GTCGTGGACTTTAAGAAGGGAT
* * * * *
1638312 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAAAGAG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAAGATGCCACTGAGTCATAGACTTGGAAGAAAAG-G
**
1638376 ATGCCACTGTGTCGTGGACTTTA-AAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAGAGATTG
65 ATGCCACTAAGTCGTGGAC-TTAGAAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAGAGATTG
1638440 CCACTGAGTCGTGGACTTTGAAAAAAAAATGCCACTGAGTCATGGACTTTGGGACAAAATGCCAC
129 CCACTGAGTCGTGGACTTTGAAAAAAAAATGCCACTGAGTCATGGACTTTGGGACAAAATGCCAC
* *
1638505 TGAGTTGTGGGCTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACT
194 TGAGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACT
1638570 GAGTCGTGGACTTTAAGAAG
259 GAGTCGTGGACTTTAAGAAG
1638590 ATATTTAAAG
Statistics
Matches: 256, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
280 7 0.03
281 135 0.53
282 114 0.45
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (282 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAAGATGCCACTGAGTCATAGACTTGGAAGAAAAGGA
TGCCACTAAGTCGTGGACTTAGAAAAGAGATGCCACTGAGTTGTGGACTTTGAAAAGAGATTGCC
ACTGAGTCGTGGACTTTGAAAAAAAAATGCCACTGAGTCATGGACTTTGGGACAAAATGCCACTG
AGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGA
GTCGTGGACTTTAAGAAGGGAT
Done.