Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold828
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: 49648
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Found at i:3389 original size:38 final size:39
Alignment explanation
Indices: 3345--3436 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
3335 GTTGCGGTGT
3345 CCGAGGCTCCCGCACATCCGCACCAAGGTG-CAATGCT-C
1 CCGAGGCTCCCGCACAT-CGCACCAAGGTGCCAATGCTGC
* *
3383 CTGAGGCTCCCGCACATCGCACCAAGGTGCCGATGCTGC
1 CCGAGGCTCCCGCACATCGCACCAAGGTGCCAATGCTGC
3422 CCGAGGCTCCCGCAC
1 CCGAGGCTCCCGCAC
3437 GACCAAGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 12 0.24
38 22 0.45
39 15 0.31
ACGTcount: A:0.18, C:0.42, G:0.26, T:0.13
Consensus pattern (39 bp):
CCGAGGCTCCCGCACATCGCACCAAGGTGCCAATGCTGC
Found at i:3650 original size:40 final size:41
Alignment explanation
Indices: 3471--4016 Score: 554
Period size: 39 Copynumber: 13.6 Consensus size: 41
3461 CTCCGCAGCG
* * **
3471 TAGGT-CCGCTGGTGTCGCAGGCTCCCGCAC-ATCCAAGCAACC
1 TAGGTGCCGATGGTGCCG-AGGCTCCCGCACGA-CCAAG-GGCC
* *
3513 AAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAATGGCC
1 TAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCC
* *
3554 TAGGT-TCGATGGTGTCCCAGGCTCCCG--C-ACCAA--GCC
1 TAGGTGCCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCC
* *
3590 AAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCT
1 TAGGTGCCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCC
*
3632 TAGGTGCCGATGGT-CCGAGGCTCTCGCACGACC-AGGGCC
1 TAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCC
*
3671 TAGGTG-CGATGGTGCCGAGGCT-CCGCACGACCAGGGGCC
1 TAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCC
*
3710 TAGGTGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAGGGGCC
1 TA-G-GTGCCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCC
3754 TAGGTTGCCGATGGTGCCGAGGCTCCCGCACTGACC-AGGGCC
1 TAGG-TGCCGATGGTGCCGAGGCTCCCGCAC-GACCAAGGGCC
* *
3796 TAGGTGTCCGA-GGTGGTCGAGG-TCCCCCACGACCAAGGG--
1 TAGGTG-CCGATGGT-GCCGAGGCTCCCGCACGACCAAGGGCC
* * *
3835 TAGGTACCGGTGGTGCCGA-GCT-TCGCAACGA-CAAGGGCC
1 TAGGTGCCGATGGTGCCGAGGCTCCCGC-ACGACCAAGGGCC
*
3874 TAGTTGCCGATGGTGCCCGAGGCT-CCGCACGA--AAGGGCC
1 TAGGTGCCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCC
* *
3913 TTGGTTCCGATGGTGCCCGAGGCT-CCGCACGACCAAGGGCC
1 TAGGTGCCGATGGTG-CCGAGGCTCCCGCACGACCAAGGGCC
*
3954 TAGGTTCCGATGGTGCCGAGGCTCCCGCACGA-CAAGGGCC
1 TAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCC
3994 TAGGTTG-CGATGGT--CGAGGCTCC
1 TAGG-TGCCGATGGTGCCGAGGCTCC
4017 GCAATCAAGC
Statistics
Matches: 436, Mismatches: 36, Indels: 68
0.81 0.07 0.13
Matches are distributed among these distances:
36 7 0.02
37 28 0.06
38 42 0.10
39 84 0.19
40 71 0.16
41 72 0.17
42 78 0.18
43 35 0.08
44 19 0.04
ACGTcount: A:0.17, C:0.32, G:0.35, T:0.16
Consensus pattern (41 bp):
TAGGTGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCC
Found at i:3966 original size:242 final size:240
Alignment explanation
Indices: 3517--4016 Score: 632
Period size: 242 Copynumber: 2.1 Consensus size: 240
3507 GCAACCAAGG
* * *
3517 TGCCGATGGTGCCGAGGCTCCCGCACGACCAATGGCCTAGGTTCGATGGTGTCCCAGGCTCCCGC
1 TGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTCGATGGTGTCCCAGGCCCCCAC
* *
3582 ACCAAGCCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGGTGCCGATGGTC
66 ACCAAGCCAAGGTACCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGCCGATGGTC
* * *
3647 CGAGGCTCTCGCACGACCAGGGCCTAGGTGCGATGGTGCCGAGGCTCCGCACGACCAGGGGCCTA
131 CGAGGCTCTCGCACGACAAGGGCCTAGGTCCGATGGTGCCGAGGCTCCGCACGACCAAGGGCCTA
*
3712 GGTGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAGGGGCCTAGGT
196 GGTGTGCCGATGGTG-CCGAGGCTCCCGCACGA-CAAGGGCCTAGGT
*
3759 TGCCGATGGTGCCGAGGCTCCCGCACTGACC-AGGGCCTAGGTGTCCGA-GGTGGT-CGAGGTCC
1 TGCCGATGGTGCCGAGGCTCCCGCAC-GACCAAGGGCCTAGGT-T-CGATGGT-GTCCCAGG-CC
*** * * *
3821 CCCACGACCAAGGGTAGGTACCGGTGGTG-CCGA-GCT-TCGCAACGA-CAAGGGCCTAGTTGCC
61 CCCAC-ACCAAGCCAAGGTACCGATGGTGCCCGAGGCTCCCGC-ACGACCAAGGGCCTAGGTGCC
*
3882 GATGGTGCCCGAGGCTC-CGCACGA-AAGGGCCTTGGTTCCGATGGTGCCCGAGGCTCCGCACGA
124 GATGGT--CCGAGGCTCTCGCACGACAAGGGCCTAGG-TCCGATGGTG-CCGAGGCTCCGCACGA
3945 CCAAGGGCCTAGGT-T-CCGATGGTGCCGAGGCTCCCGCACGACAAGGGCCTAGGT
185 CCAAGGGCCTAGGTGTGCCGATGGTGCCGAGGCTCCCGCACGACAAGGGCCTAGGT
3999 TG-CGATGGT--CGAGGCTCC
1 TGCCGATGGTGCCGAGGCTCC
4017 GCAATCAAGC
Statistics
Matches: 230, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
237 9 0.04
239 7 0.03
240 14 0.06
241 17 0.07
242 77 0.33
243 36 0.16
244 52 0.23
245 18 0.08
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (240 bp):
TGCCGATGGTGCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTCGATGGTGTCCCAGGCCCCCAC
ACCAAGCCAAGGTACCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGCCGATGGTC
CGAGGCTCTCGCACGACAAGGGCCTAGGTCCGATGGTGCCGAGGCTCCGCACGACCAAGGGCCTA
GGTGTGCCGATGGTGCCGAGGCTCCCGCACGACAAGGGCCTAGGT
Found at i:4222 original size:22 final size:24
Alignment explanation
Indices: 4194--4237 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
4184 CCGGAGGTCT
4194 TGTTCAAAGGGG-AGGG-CCGGGA
1 TGTTCAAAGGGGAAGGGACCGGGA
4216 TGTTCAAAGGGGAAGGGACCGG
1 TGTTCAAAGGGGAAGGGACCGG
4238 AGACTTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.25, C:0.14, G:0.48, T:0.14
Consensus pattern (24 bp):
TGTTCAAAGGGGAAGGGACCGGGA
Found at i:19360 original size:58 final size:59
Alignment explanation
Indices: 19269--19389 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 59
19259 CCCTCCCCAA
* *
19269 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTTCGGTACCCAATAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
* *
19328 TCCC-AAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCCAACAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
19386 TCCC
1 TCCC
19390 TGTCCCTCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 54 0.93
59 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (59 bp):
TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
Found at i:19804 original size:24 final size:24
Alignment explanation
Indices: 19777--19827 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
19767 CCGGTTAGGT
19777 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
19801 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
19825 TCC
1 TCC
19828 TGGAATATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.43, G:0.35, T:0.14
Consensus pattern (24 bp):
TCCCGGCGGTGCTCCGGCGAGCCA
Found at i:20120 original size:42 final size:42
Alignment explanation
Indices: 20017--20999 Score: 878
Period size: 42 Copynumber: 23.5 Consensus size: 42
20007 CACATTGCTG
* * * * * *
20017 CTTGGACGTGCTGGAGCCTTGGACGCCATCGGCAACCTAGGAC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* * * * * * **
20060 GTTTG-TCGTGCGAGAGCCTCGAGCACCACCGGCACCTTGGTG
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
*
20102 CTTGGATGTGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* ** * * *
20145 CCTGGCCGCGCGGGAGCCTC-GGTACCCT-GGCAACCTAGGCC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20186 CTTGG-TCGTGCGAGAGCCTCGGGCACCATCGGAACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* *
20228 C-T-G-TCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCG
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
20269 CTTGG-TCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* * * *
20311 CCTGGTCATGT--AGGAGCTTCGGCCACCATCGGCAACCTAGGCC
1 CTTGG--ATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
20354 CTTGG-TCGTGCGAGAGCCTC--G-------GGCACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* **
20387 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTG
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
*
20429 CTTGGATGTGCGGGAGCCTTGGGCACCATCGGCAACCTAGGCC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
20472 CCTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20515 CTTGG-TCGTGCGAGAGCCTCGGG-ACCATTGGCACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
*
20556 CTTGG-TCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
20598 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
20641 C-TGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG-C
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20682 CTT-GATCGTGCGAGAACCTCGGGCACCATCGGCAACCTAGG-C
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* * * **
20724 CTT-GATCGTGCGAGAACCTCGGGCACCATCGGCACCTTGGTG
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
** *
20766 CTTGGATGTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20809 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGC
1 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-CC
* * * * **
20852 CTTGGATGTGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTG
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* * * * * **
20894 CTTGGATGTGCGGGAGCCTCGAGAAGCATTGGCACCTTGGTG
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* *
20936 CTTGGATGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGAC
1 CTTGGATGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20979 GTTGGATGTGCGGGTGCCTCG
1 CTTGGATGTGCGGGAGCCTCG
21000 AGCAGCAGGG
Statistics
Matches: 803, Mismatches: 96, Indels: 82
0.82 0.10 0.08
Matches are distributed among these distances:
33 28 0.03
34 3 0.00
35 1 0.00
40 27 0.03
41 80 0.10
42 388 0.48
43 272 0.34
44 3 0.00
45 1 0.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.18
Consensus pattern (42 bp):
CTTGGATGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
Found at i:20162 original size:85 final size:84
Alignment explanation
Indices: 20001--21035 Score: 1008
Period size: 85 Copynumber: 12.4 Consensus size: 84
19991 GGTGCGGGAG
* * * * * * * * *
20001 CATCGGCACATTGCTGCTTGGACGTGCTGGAGCCTTGGACGCCATCGGCAACCTAGGACGTTTGT
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGT
* *
20066 CGTGCGAGAGCCTCGAGCAC
65 CGTGCGGGAGCCTCGGGCAC
* * *
20086 CACCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCCCCTGGC
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGT
* *
20151 CGCGCGGGAGCCTC-GGTAC
65 CGTGCGGGAGCCTCGGGCAC
* * ** *
20170 CCT-GGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTCGGGCACCATCGG-AACCTAGGCCC-T-
1 CATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTG
*
20230 GTCGTGCGGGAGCCTCGGCCAC
63 GTCGTGCGGGAGCCTCGGGCAC
* * *
20252 CATCGGCAACCTAGGCGCTTGG-TCGTGCGGGAGCCTCGGCCACCATCGGC-ACCTAGGCCCCTG
1 CATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTG
* ** * *
20315 GTCATGTAGGAGCTTCGGCCAC
63 GTCGTGCGGGAGCCTCGGGCAC
* ** *
20337 CATCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTC-G-------GGC-ACCTAGGCCCTTGG
1 CATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGG
20392 TCGTGCGGGAGCCTCGGGCAC
64 TCGTGCGGGAGCCTCGGGCAC
* *
20413 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTTGGGCACCATCGGCAACCTAGGCCCCTGGT
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCC-TCGGCACCATCGGCAACCTAGGCCCTTGGT
20478 CGTGCGGGAGCCTCGGGCAC
65 CGTGCGGGAGCCTCGGGCAC
* ** * * *
20498 CATCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTCGGGACCATTGGC-ACCTAGGCCCTTGG
1 CATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGG
*
20561 TCGTGCGGGAGCCTCGGCCAC
64 TCGTGCGGGAGCCTCGGGCAC
* **
20582 CATCGGCACCTAGGCCCTTGGATGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCC-TGGT
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGT
20646 CGTGCGGGAGCCTCGGGCAC
65 CGTGCGGGAGCCTCGGGCAC
* * * *
20666 CATCGGCAACCTAGG-CCTT-GATCGTGCGAGAACCTCGGGCACCATCGGCAACCTAGG-CCTTG
1 CATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTG
* * *
20728 ATCGTGCGAGAACCTCGGGCAC
63 GTCGTGCGGGAGCCTCGGGCAC
* *
20750 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCCCTTGGT
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCG-GCACCATCGGCAACCTAGGCCCTTGGT
20815 CGTGCGGGAGCCTCGGGCAC
65 CGTGCGGGAGCCTCGGGCAC
* * * **
20835 CATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCCTCGAGCAGCATTGGC-ACCTTGGTGCTTGG
1 CATCGGCACCTTGGTG-CTTGGATGTGCGGGAGCCTCG-GCACCATCGGCAACCTAGGCCCTTGG
* * *
20899 AT-GTGCGGGAGCCTCGAGAAG
64 -TCGTGCGGGAGCCTCGGGCAC
* * *
20920 CATTGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGGACACCATCGGCAACCTAGGACGTTGGA
1 CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGG-
* * *
20985 T-GTGCGGGTGCCTCGAGCAG
64 TCGTGCGGGAGCCTCGGGCAC
** * *
21005 CAGGGGCACCCTGGTGGCTCGGATGTGCGGG
1 CATCGGCACCTTGGT-GCTTGGATGTGCGGG
21036 CTAAAGAAAA
Statistics
Matches: 816, Mismatches: 97, Indels: 73
0.83 0.10 0.07
Matches are distributed among these distances:
75 21 0.03
76 41 0.05
77 1 0.00
81 14 0.02
82 8 0.01
83 104 0.13
84 248 0.30
85 311 0.38
86 68 0.08
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.18
Consensus pattern (84 bp):
CATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTC
GTGCGGGAGCCTCGGGCAC
Found at i:20194 original size:126 final size:128
Alignment explanation
Indices: 20017--20999 Score: 974
Period size: 126 Copynumber: 7.8 Consensus size: 128
20007 CACATTGCTG
* * * * * * * *
20017 CTTGGACGTGCTGGAGCCTTGGACGCCATCGGCAACCTAGGACGTTTGTCGTGCGAGAGCCTCGA
1 CTTGGTCGTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGG
* * ** *
20082 GCACCACCGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTCAGGCACCATCGGCAACCTAGGCC
65 GCACCATCGGCACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* * * * *
20145 CCTGGCCGCGCGGGAGCCTCGGTACCCT-GGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG
1 CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG
* * *
20209 CACCATCGGAACCTAGGCCC-T-G-TCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCG
66 CACCATCGGCACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* * * *
20269 CTTGGTCGTGCGGGAGCCTCGGCCACCATCGGC-ACCTAGGCCCCTGGTCATG-TAGGAGCTTCG
1 CTTGGTCGTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTTGGTCGTGCGA-GAGCCTCG
* *
20332 GCCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTC--G-------GGC-ACCTAGGC
64 GGCACCATCGGC-ACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
20386 C
128 C
* ** * *
20387 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTTG
1 CTTGGTCGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTCG
*
20450 GGCACCATCGGCAACCTAGGCCCCTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
64 GGCACCATCGGC-ACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
20514 C
128 C
* * * * *
20515 CTTGGTCGTGCGAGAGCCTCGGGACCATTGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGC
1 CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG
20579 CACCATCGGCACCTAGGCCCTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
66 CACCATCGGCACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* *
20641 C-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG-CCTTGATCGTGCGAGAACCTCGG
1 CTTGGTCGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGG
* * * **
20704 GCACCATCGGCAACCTAGG-CCTT-GATCGTGCGAGAACCTCGGGCACCATCGGC-ACCTTGGTG
65 GCACCATCGGC-ACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
* * *
20766 CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCCCTTGGTCGTGCGGGAGCCTCG
1 CTTGG-TCGTGCGGGAGCCTCG-GCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCG
* * * * * * *
20830 GGCACCATCGGCACCTTGGTGCCTTGGAT-GTGCGGGAGCCTCGAGCAGCATTGGC-ACCTTGGT
64 GGCACCATCGGCACCTAGG-CCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
*
20893 G
128 C
* * * * ** *
20894 CTTGGAT-GTGCGGGAGCCTCGAGAAGCATTGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTC
1 CTTGG-TCGTGCGGGAGCCTCG-GCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGCCTC
* * * *
20956 GGACACCATCGGCAACCTAGGACGTTGGAT-GTGCGGGTGCCTCG
63 GGGCACCATCGGC-ACCTAGGCCCTTGGATCGTGCGGGAGCCTCG
21000 AGCAGCAGGG
Statistics
Matches: 730, Mismatches: 90, Indels: 71
0.82 0.10 0.08
Matches are distributed among these distances:
118 95 0.13
119 6 0.01
120 1 0.00
123 1 0.00
124 54 0.07
125 67 0.09
126 218 0.30
127 155 0.21
128 130 0.18
129 3 0.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.18
Consensus pattern (128 bp):
CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG
CACCATCGGCACCTAGGCCCTTGGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
Found at i:20387 original size:33 final size:33
Alignment explanation
Indices: 20345--20427 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
20335 ACCATCGGCA
20345 ACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGC
1 ACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGC
*
20378 ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGC
1 ACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGC
*
20411 ACCATCGGCACCTTGGT
1 ACC-TAGGC-CCTTGGT
20428 GCTTGGATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 35 0.76
34 4 0.09
35 7 0.15
ACGTcount: A:0.12, C:0.34, G:0.35, T:0.19
Consensus pattern (33 bp):
ACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGC
Found at i:20699 original size:23 final size:23
Alignment explanation
Indices: 20673--20742 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
20663 CACCATCGGC
20673 AACCTAGGCCTTGATCGTGCGAG
1 AACCTAGGCCTTGATCGTGCGAG
* * ***
20696 AACCTCGGGCACCATCG-GC---
1 AACCTAGGCCTTGATCGTGCGAG
20715 AACCTAGGCCTTGATCGTGCGAG
1 AACCTAGGCCTTGATCGTGCGAG
20738 AACCT
1 AACCT
20743 CGGGCACCAT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 12 0.36
20 2 0.06
22 2 0.06
23 17 0.52
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
AACCTAGGCCTTGATCGTGCGAG
Found at i:20754 original size:23 final size:23
Alignment explanation
Indices: 20686--20754 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
20676 CTAGGCCTTG
20686 ATCGTGCGAGAACCTCGGGCACC
1 ATCGTGCGAGAACCTCGGGCACC
* * ***
20709 ATCG-GC---AACCTAGGCCTTG
1 ATCGTGCGAGAACCTCGGGCACC
20728 ATCGTGCGAGAACCTCGGGCACC
1 ATCGTGCGAGAACCTCGGGCACC
20751 ATCG
1 ATCG
20755 GCACCTTGGT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 12 0.38
20 2 0.06
22 2 0.06
23 16 0.50
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (23 bp):
ATCGTGCGAGAACCTCGGGCACC
Found at i:25863 original size:15 final size:15
Alignment explanation
Indices: 25839--25877 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
25829 GCATCAGGTG
* *
25839 TGGCATGGCATGGAA
1 TGGCACGGCACGGAA
*
25854 TGGCACGGCACGGCA
1 TGGCACGGCACGGAA
25869 TGGCACGGC
1 TGGCACGGC
25878 CAAGTGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.41, T:0.13
Consensus pattern (15 bp):
TGGCACGGCACGGAA
Found at i:28030 original size:22 final size:21
Alignment explanation
Indices: 28000--28058 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
27990 ATACAATCAT
*
28000 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
28022 AGATATGATTTTGTAAATCTTAG
1 AGATTTGA-TTTGT-AATCTTAG
28045 AGATTTGATTTGTA
1 AGATTTGATTTGTA
28059 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 12 0.38
24 7 0.22
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:35129 original size:47 final size:47
Alignment explanation
Indices: 35071--35614 Score: 782
Period size: 47 Copynumber: 11.4 Consensus size: 47
35061 CAGCCAAGAG
*
35071 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
35118 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
35165 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
35216 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
35267 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
35314 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
35361 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
35408 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
35455 AGTGTCTATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
35502 AGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * *
35549 AGTGTATATATGTGACAAGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
35596 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
35615 TCCCGAAAGG
Statistics
Matches: 467, Mismatches: 26, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 371 0.79
49 2 0.00
51 94 0.20
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:35789 original size:37 final size:37
Alignment explanation
Indices: 35733--35811 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
35723 CCGAGCTCTA
* * *
35733 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
35770 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
35807 AAGAC
1 AAGAC
35812 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:37667 original size:22 final size:21
Alignment explanation
Indices: 37637--37694 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
37627 ATACAATCAT
*
37637 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
37659 AGATATGATTTGTAAATCTTAG
1 AGATTTGATTTGT-AATCTTAG
37681 AGATTTGATTTGTA
1 AGATTTGATTTGTA
37695 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 24 0.75
23 7 0.22
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:38193 original size:5 final size:5
Alignment explanation
Indices: 38180--38215 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
38170 TTCAATTTTC
* *
38180 TGCCG TGCCA TGCCG TGCCA TGCCA TGCCA TGCCA T
1 TGCCA TGCCA TGCCA TGCCA TGCCA TGCCA TGCCA T
38216 ACTTCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.14, C:0.39, G:0.25, T:0.22
Consensus pattern (5 bp):
TGCCA
Found at i:38828 original size:24 final size:24
Alignment explanation
Indices: 38789--38842 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
38779 CCGGTTAGGT
* * *
38789 TCCCGGCGGTGCTCCGACGATCCA
1 TCCCGGCGATGATCCGACGAGCCA
*
38813 TCCCGGCGATGATCCGGCGAGCCA
1 TCCCGGCGATGATCCGACGAGCCA
38837 TCCCGG
1 TCCCGG
38843 GATACACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.41, G:0.31, T:0.15
Consensus pattern (24 bp):
TCCCGGCGATGATCCGACGAGCCA
Found at i:38967 original size:58 final size:59
Alignment explanation
Indices: 38875--38996 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 59
38865 TCCCTCCCCA
* *
38875 ATCCCAAAAGGTAGAATTCGGATACCGTTACATGTTCGGTACCCAATAATGAATGAATC
1 ATCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATC
* *
38934 ATCCC-AAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCCAACAATGAATGAATC
1 ATCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATC
*
38992 GTCCC
1 ATCCC
38997 TGTCCCTCCC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 53 0.91
59 5 0.09
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (59 bp):
ATCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATC
Found at i:39423 original size:24 final size:24
Alignment explanation
Indices: 39396--39442 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
39386 TTAGGTTCCC
39396 GGCGGTGCTCCGGCGAGCCATCCT
1 GGCGGTGCTCCGGCGAGCCATCCT
39420 GGCGGTGCTCCGGCGAGCCATCC
1 GGCGGTGCTCCGGCGAGCCATCC
39443 CGGAATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.38, G:0.38, T:0.15
Consensus pattern (24 bp):
GGCGGTGCTCCGGCGAGCCATCCT
Found at i:39735 original size:42 final size:42
Alignment explanation
Indices: 39657--40581 Score: 978
Period size: 42 Copynumber: 21.9 Consensus size: 42
39647 GCCTTGGATG
* * *
39657 CCATCGGCAACCTAGGACGTTTGTCGTGCGGGAGCCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * **
39700 CCACCGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGGCA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
* * **
39742 CCATCGGCAACCTAGGCCCCTGGTCGCGCGGGAGCCTC-GATA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
*
39784 CCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * *
39827 CCATCGGAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCCA
1 CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* *
39869 CCATCGGCAACCTAGGCGCTTGGTCGTGCGGGAGCCTCGGCCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * ** * * *
39912 CCATCGGCACCTAGGCCCCTGGTCATGTAGGAGCTTTGGTCA
1 CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
*
39954 CCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
*
39997 CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCAGGCA
1 CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* ** *
40039 CCATCGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTTGGGCA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
*
40081 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
*
40124 CCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG-A
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* *
40166 CCATTGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCA
1 CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
40208 CCATCGGCACCTAGGCCCTTGGAT-GTGCGGGAGCCTCGGGCA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
*
40250 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * *
40293 CCATCGGCAACCTAGG-CCTTGATCGTGCGAGAACCTCGGGCA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * * ** *
40335 CCATCGGAAACCTCGG-CCTTGATCGTGCAAGAACCTCGGGCA
1 CCATCGG-CACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* ** **
40377 CCATCGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGAACA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
* * *
40419 CCATCGGCAACCTCGG-CCTTGGTCGTGAGGGAGCCTC-GGAA
1 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* ** * *
40460 CCATCGGCACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGAGAA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
* * * ** * *
40502 GCAT-TGCACCTTGGTGCTTGGAT-GTACGGGAGCCTCGGACA
1 CCATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
* * *
40543 CCATCGGCAACCTAGGACATTGGAT-GTGCGGGTGCCTCG
1 CCATCGGC-ACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
40582 AGCAGCAGGG
Statistics
Matches: 757, Mismatches: 102, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.01
41 98 0.13
42 394 0.52
43 259 0.34
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.18
Consensus pattern (42 bp):
CCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
Found at i:39773 original size:85 final size:85
Alignment explanation
Indices: 39657--40581 Score: 1024
Period size: 85 Copynumber: 11.0 Consensus size: 85
39647 GCCTTGGATG
* ** * * * *
39657 CCATCGGCAACCTAGGACGTTTGTCGTGCGGGAGCCTCGGGCACCACCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
39722 ATGTGCGGGAGCCTCGGGCA
66 ATGTGCGGGAGCCTCGGGCA
* ** *
39742 CCATCGGCAACCTAGGCCCCTGGTCGCGCGGGAGCCTC-GATACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCGCTTG
*
39806 G-TCGTGCGAGAGCCTCGGGCA
65 GAT-GTGCGGGAGCCTCGGGCA
*
39827 CCATCGG-AACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCGCTTG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCGCTTG
*
39891 G-TCGTGCGGGAGCCTCGGCCA
65 GAT-GTGCGGGAGCCTCGGGCA
* ** * * * *
39912 CCATCGGC-ACCTAGGCCCCTGGTCATGTAGGAGCTTTGGTCACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCGCTTG
*
39976 G-TCGTGCGAGAGCCTCGGGCA
65 GAT-GTGCGGGAGCCTCGGGCA
* * * *
39997 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCAGGCACCATCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
*
40061 ATGTGCGGGAGCCTTGGGCA
66 ATGTGCGGGAGCCTCGGGCA
*
40081 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCGCTTG
*
40146 G-TCGTGCGAGAGCCTCGGG-A
65 GAT-GTGCGGGAGCCTCGGGCA
* * * *
40166 CCATTGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCCCTTGG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
40230 ATGTGCGGGAGCCTCGGGCA
66 ATGTGCGGGAGCCTCGGGCA
40250 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC-CTT-
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCGCTTG
* *
40313 GATCGTGCGAGAACCTCGGGCA
65 GAT-GTGCGGGAGCCTCGGGCA
* * * * ** * * *
40335 CCATCGGAAACCTCGG-CCTTGATCGTGCAAGAACCTCGGGCACCATCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
**
40399 ATGTGCGGGAGCCTCGAACA
66 ATGTGCGGGAGCCTCGGGCA
* * * * * *
40419 CCATCGGCAACCTCGG-CCTTGGTCGTGAGGGAGCCTC-GGAACCATCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
* *
40482 ATGTGCGGGAGCCTCGAGAA
66 ATGTGCGGGAGCCTCGGGCA
* * * ** * * * *
40502 GCAT-TGC-ACCTTGGTGCTTGGAT-GTACGGGAGCCTCGGACACCATCGGCAACCTAGGAC-AT
1 CCATCGGCAACCTAGGCCCCTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGG-CGCT
*
40563 TGGATGTGCGGGTGCCTCG
63 TGGATGTGCGGGAGCCTCG
40582 AGCAGCAGGG
Statistics
Matches: 730, Mismatches: 90, Indels: 41
0.85 0.10 0.05
Matches are distributed among these distances:
81 6 0.01
82 18 0.02
83 92 0.13
84 228 0.31
85 353 0.48
86 33 0.05
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.18
Consensus pattern (85 bp):
CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCGCTTGG
ATGTGCGGGAGCCTCGGGCA
Found at i:39810 original size:127 final size:129
Alignment explanation
Indices: 39657--40581 Score: 1025
Period size: 127 Copynumber: 7.3 Consensus size: 129
39647 GCCTTGGATG
* * * * * **
39657 CCATCGGCAACCTAGGACGTTTGTCGTGCGGGAGCCTCGGGCACCACCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
* * **
39722 AT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGCGCGGGAGCCTC-GATA
66 ATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * *
39784 CCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGCACCATCGGAACCTAGGCCCCTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
* * *
39849 -TCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCGCTTGGTCGTGCGGGAGCCTCGGCCA
66 ATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * ** * * *
39912 CCATCGGC-ACCTAGGCCCCTGGTCATGTAGGAGCTTTGGTCACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTTG
* *
39976 G-TCGTGCGAGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCAGGCA
65 GATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* ** * *
40039 CCATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTTGGGCACCATCGGCAACCTAGGCCCCT
1 CCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTT
*
40102 GG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGG-
64 GGATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGC
40165 A
129 A
* *
40166 CCATTGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCCCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
*
40230 AT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCA
66 ATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
* * * * *
40293 CCATCGGCAACCTAGG-CCTTGATCGTGCGAGAACCTCGGGCACCATCGGAAACCTCGG-CCTT-
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGG-CACCTAGGCCCTTG
** * * ** **
40355 GATCGTGCAAGAACCTCGGGCACCATCGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGAAC
65 GATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGC
40418 A
129 A
* * * * **
40419 CCATCGGCAACCTCGG-CCTTGGTCGTGAGGGAGCCTC-GGAACCATCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
* * * * * ** * *
40482 AT-GTGCGGGAGCCTCGAGAAGCAT-TGC-ACCTTGGTGCTTGGAT-GTACGGGAGCCTCGGACA
66 ATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA
* * *
40543 CCATCGGCAACCTAGGACATTGGAT-GTGCGGGTGCCTCG
1 CCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG
40582 AGCAGCAGGG
Statistics
Matches: 690, Mismatches: 91, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
124 55 0.08
125 45 0.07
126 137 0.20
127 360 0.52
128 93 0.13
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.18
Consensus pattern (129 bp):
CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
ATCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCA
Found at i:40340 original size:23 final size:23
Alignment explanation
Indices: 40314--40382 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
40304 CTAGGCCTTG
40314 ATCGTGCGAGAACCTCGGGCACC
1 ATCGTGCGAGAACCTCGGGCACC
* ***
40337 ATC--G-GA-AACCTCGGCCTTG
1 ATCGTGCGAGAACCTCGGGCACC
*
40356 ATCGTGCAAGAACCTCGGGCACC
1 ATCGTGCGAGAACCTCGGGCACC
40379 ATCG
1 ATCG
40383 GCACCTTGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 12 0.36
20 2 0.06
21 2 0.06
22 1 0.03
23 16 0.48
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (23 bp):
ATCGTGCGAGAACCTCGGGCACC
Found at i:48530 original size:58 final size:57
Alignment explanation
Indices: 48436--48552 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 57
48426 CCTCCCCAAT
* *
48436 CCAAAGGTAGAATTCGGATACCGTTACATGTTCGGTACCCAATAATGAATGAATCGTC
1 CCAAAGGTAGAATTCGGATACCGTTACATGTCCGGTA-CCAACAATGAATGAATCGTC
* *
48494 CCAAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCAACAATGAATGAATCGTC
1 CCAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCAACAATGAATGAATCGTC
48551 CC
1 CC
48553 TGTCTCCTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
57 21 0.38
58 34 0.62
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (57 bp):
CCAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCAACAATGAATGAATCGTC
Done.