Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 11 of 253
Found at i:3254407 original size:15 final size:14
Alignment explanation
Indices: 3254377--3254403 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3254367 AAAATGTGTT
3254377 TTTTTTAATATTTA
1 TTTTTTAATATTTA
3254391 TTTTTTAATATTT
1 TTTTTTAATATTT
3254404 TATTATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:3254676 original size:39 final size:39
Alignment explanation
Indices: 3254629--3254706 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
3254619 AATGTAACTT
3254629 ATTTAATCACAAAAGGATATTTTTGTAATGTAACGCCTC
1 ATTTAATCACAAAAGGATATTTTTGTAATGTAACGCCTC
3254668 ATTTAATCACAAAAGGATATTTTTGTAATGTAACGCCTC
1 ATTTAATCACAAAAGGATATTTTTGTAATGTAACGCCTC
3254707 GAAATTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (39 bp):
ATTTAATCACAAAAGGATATTTTTGTAATGTAACGCCTC
Found at i:3257437 original size:19 final size:18
Alignment explanation
Indices: 3257415--3257458 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3257405 AAATAATTAT
3257415 TAAAAAAC-TAAAAGATATA
1 TAAAAAACTTAAAA-A-ATA
3257434 TAAAAAACTTAAAAAATA
1 TAAAAAACTTAAAAAATA
3257452 TAAAAAA
1 TAAAAAA
3257459 AAAACTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (18 bp):
TAAAAAACTTAAAAAATA
Found at i:3257459 original size:20 final size:19
Alignment explanation
Indices: 3257416--3257460 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3257406 AATAATTATT
* *
3257416 AAAAAACTAAAAGATATAT
1 AAAAAACTAAAAAATATAA
3257435 AAAAAACTTAAAAAATATAA
1 AAAAAAC-TAAAAAATATAA
3257455 AAAAAA
1 AAAAAA
3257461 AACTCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAACTAAAAAATATAA
Found at i:3259011 original size:14 final size:14
Alignment explanation
Indices: 3258992--3259039 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3258982 AAGTTAATTA
3258992 TTTATATTAAAAAT
1 TTTATATTAAAAAT
**
3259006 TTTATAAGTTAATTA-
1 TTTAT-A-TTAAAAAT
3259021 TTTATATTAAAAAT
1 TTTATATTAAAAAT
3259035 TTTAT
1 TTTAT
3259040 GCATATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 11 0.41
15 6 0.22
16 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TTTATATTAAAAAT
Found at i:3259014 original size:29 final size:29
Alignment explanation
Indices: 3258981--3259039 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3258971 GATTAAAGAG
3258981 TAAGTTAATTATTTATATTAAAAATTTTA
1 TAAGTTAATTATTTATATTAAAAATTTTA
3259010 TAAGTTAATTATTTATATTAAAAATTTTA
1 TAAGTTAATTATTTATATTAAAAATTTTA
3259039 T
1 T
3259040 GCATATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAGTTAATTATTTATATTAAAAATTTTA
Found at i:3260935 original size:49 final size:49
Alignment explanation
Indices: 3260871--3260967 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
3260861 TAAATTAGTT
*
3260871 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTGTTAAAAATTCAA
1 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCAA
3260920 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCA
1 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCA
3260968 TCTATTTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (49 bp):
CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCAA
Found at i:3261642 original size:14 final size:15
Alignment explanation
Indices: 3261625--3261654 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3261615 TAAATTTGAT
3261625 TAAATAAAA-TAAAA
1 TAAATAAAATTAAAA
3261639 TAAATAAAATTAAAA
1 TAAATAAAATTAAAA
3261654 T
1 T
3261655 TGAGTTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATAAAATTAAAA
Found at i:3263979 original size:3 final size:3
Alignment explanation
Indices: 3263971--3264000 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3263961 TAATTATTTC
3263971 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3264001 TTTGCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3264470 original size:28 final size:28
Alignment explanation
Indices: 3264439--3264494 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3264429 AACCCATGTA
* *
3264439 ATTTTTGTCCATTTTGGTAATTGTACTT
1 ATTTTGGTCCATTTTGGTAATTGAACTT
* *
3264467 ATTTTGGTCCGTTTTGGTACTTGAACTT
1 ATTTTGGTCCATTTTGGTAATTGAACTT
3264495 GACAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (28 bp):
ATTTTGGTCCATTTTGGTAATTGAACTT
Found at i:3275969 original size:38 final size:38
Alignment explanation
Indices: 3275918--3276108 Score: 256
Period size: 38 Copynumber: 5.0 Consensus size: 38
3275908 AGCACCCGAT
*
3275918 ATATATCCGGGTTAAGTCCTGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
*
3275956 ATATATCTGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
*
3275994 ATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* * * * *
3276032 ATATATCCAGGTTAAATCCCACATGCTTAGTGCTGGTA
1 ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
* * * *
3276070 TTATATCCGAGCTTAAAGTCCCACAGGCTTTGTGCTGGT
1 ATATATCCG-GGTT-AAGTCCCGCAGGCTTCGTGCTGGT
3276109 GACTGGATTC
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
38 113 0.82
39 3 0.02
40 21 0.15
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
ATATATCCGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
Found at i:3295402 original size:39 final size:39
Alignment explanation
Indices: 3295357--3295476 Score: 222
Period size: 39 Copynumber: 3.1 Consensus size: 39
3295347 TGTAAGACAT
*
3295357 TGGAAATGTATCCAGGCTAAAGTCCCGCAGGCTTCGTGC
1 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
3295396 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
1 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
*
3295435 TAGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
1 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
3295474 TGG
1 TGG
3295477 TAATATAATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGC
Found at i:3300301 original size:39 final size:39
Alignment explanation
Indices: 3300256--3300337 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
3300246 ATGCAAGACA
3300256 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
3300295 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
3300334 CTGG
1 CTGG
3300338 TAATATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:3304804 original size:15 final size:14
Alignment explanation
Indices: 3304771--3304811 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3304761 ACAGTTTTTG
3304771 ATTTGGGGAAAAAA
1 ATTTGGGGAAAAAA
*
3304785 GTTTGGGGAAAAAA
1 ATTTGGGGAAAAAA
*
3304799 TATTTGGAGAAAA
1 -ATTTGGGGAAAA
3304812 TGTTGGGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.24
Consensus pattern (14 bp):
ATTTGGGGAAAAAA
Found at i:3304844 original size:14 final size:15
Alignment explanation
Indices: 3304816--3304844 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3304806 AGAAAATGTT
3304816 GGGGATTTCGGGGAA
1 GGGGATTTCGGGGAA
3304831 GGGGATTT-GGGGAA
1 GGGGATTTCGGGGAA
3304845 AATAAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.03, G:0.55, T:0.21
Consensus pattern (15 bp):
GGGGATTTCGGGGAA
Found at i:3305360 original size:125 final size:123
Alignment explanation
Indices: 3305102--3305507 Score: 417
Period size: 125 Copynumber: 3.3 Consensus size: 123
3305092 TGCACCTAGC
** ** * ** * * **
3305102 GCCGCTAAAGCTTGACCTATTGCGATGTTTTTAACCTAGCATCGCTAATGCCA-TAAAAATTCCA
1 GCCGCTATTGCTT-ACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCA
* * * **
3305166 TTAAAAACGACGCCGTTTTGTTTAAAGGAAAACGATTTTTATG-GCATTTTTATGAAAAAT
65 CTAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTT-TGCGCATTTTTAT-AAAAAT
* * * *
3305226 GCCTCTATTG--TAGTCTTTTTGCGGAC-TTTTTCACCTAGCGCCACTAATGCCATTATAAACAC
1 GCCGCTATTGCTTA--CCTATTGCGG-CGTTTTTCACCTAGCGCCACTAATGCCACTATAAACAC
* *
3305288 CACTAAAAACGGCGCCATTTTGTTTAAAGTAAAATTATTTTTTGCAGCGTTTTTATCAAAAAT
63 CACTAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGC-GCATTTTTAT-AAAAAT
* *
3305351 GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCGCTAATGCCACTATAAACGCCAC
1 GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCAC
** *
3305416 TAAAAACGACGTTATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTTGATAAAAAC
66 TAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGC-GCATTTTT-ATAAAAAT
* * *
3305476 ACCGCTATTGCTTACCTTTTGTGGCGTTTTTC
1 GCCGCTATTGCTTACCTATTGCGGCGTTTTTC
3305508 TCATAAATGC
Statistics
Matches: 235, Mismatches: 37, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
121 1 0.00
122 1 0.00
123 31 0.13
124 50 0.21
125 148 0.63
126 2 0.01
127 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (123 bp):
GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCAC
TAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGCATTTTTATAAAAAT
Found at i:3306670 original size:21 final size:21
Alignment explanation
Indices: 3306640--3306680 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3306630 TAACAGAACC
*
3306640 GCTGATGTGGCAAATTAACTA
1 GCTGACGTGGCAAATTAACTA
* *
3306661 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCAAATTAACT
3306681 TGCCACGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCAAATTAACTA
Found at i:3306740 original size:3 final size:3
Alignment explanation
Indices: 3306732--3306805 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
3306722 CTTTTAACAG
* * * * *
3306732 AGA AGA AGA AGA A-A CAGC AGC AGC AGT AGA AGA AGA A-A AAA AGA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
3306776 AGA AGA AGA AGA AGA AGA AGC AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3306806 TTAAAGAGCT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.62, C:0.07, G:0.30, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:3308001 original size:15 final size:15
Alignment explanation
Indices: 3307982--3308024 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
3307972 ACCCTTAAAC
3307982 ACTAAACCATAAAAT
1 ACTAAACCATAAAAT
*
3307997 CCTAAACCATAAAAT
1 ACTAAACCATAAAAT
3308012 ACTAAACCATAAA
1 ACTAAACCATAAA
3308025 CCATAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (15 bp):
ACTAAACCATAAAAT
Found at i:3308164 original size:7 final size:7
Alignment explanation
Indices: 3307984--3308150 Score: 78
Period size: 7 Copynumber: 23.4 Consensus size: 7
3307974 CCTTAAACAC
3307984 TAAACCA
1 TAAACCA
3307991 TAAAATCC-
1 T-AAA-CCA
3307999 TAAACCA
1 TAAACCA
**
3308006 TAAAATA
1 TAAACCA
3308013 CTAAACCA
1 -TAAACCA
3308021 TAAACCA
1 TAAACCA
3308028 TAAATCC-
1 TAAA-CCA
3308035 TAAA-CA
1 TAAACCA
3308041 CTAAACTC-
1 -TAAAC-CA
*
3308049 TAAAACA
1 TAAACCA
3308056 TAAATTCC-
1 TAAA--CCA
* *
3308064 -AACCCT
1 TAAACCA
*
3308070 TAAAACA
1 TAAACCA
*
3308077 TAAA-TA
1 TAAACCA
*
3308083 GTAAACCC
1 -TAAACCA
* *
3308091 TAAGCTA
1 TAAACCA
*
3308098 TAAACCG
1 TAAACCA
*
3308105 TAAAACA
1 TAAACCA
3308112 CTAAACCA
1 -TAAACCA
3308120 TAAACCA
1 TAAACCA
3308127 TAAACCA
1 TAAACCA
3308134 TAAACCA
1 TAAACCA
*
3308141 TAAACTA
1 TAAACCA
3308148 TAA
1 TAA
3308151 TGATAAACCC
Statistics
Matches: 120, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
5 3 0.03
6 4 0.03
7 92 0.77
8 17 0.14
9 4 0.03
ACGTcount: A:0.54, C:0.25, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:3327233 original size:55 final size:55
Alignment explanation
Indices: 3327101--3327268 Score: 214
Period size: 55 Copynumber: 3.1 Consensus size: 55
3327091 AAACATCCAG
* *
3327101 GAAAAGAATAGCCTGTGTGGCAAACTCCGAAAGGAAT-TCCTTTATGGAAAACTCT
1 GAAAAGAATAGCCTTTGTGGCAAACTCTGAAAGGAATGT-CTTTATGGAAAACTCT
*
3327156 GAAAAGAATAACCTTTGTGGCAAACT-TGAAAGGAATGTCTTTATGGAAAACTCT
1 GAAAAGAATAGCCTTTGTGGCAAACTCTGAAAGGAATGTCTTTATGGAAAACTCT
* * * * * * *
3327210 GAAAAAAATAGCCTTTTATGGCAAACTCTGAAAAGAATGCCTTTGTGGGAAAGTCT
1 GAAAAGAATAGCC-TTTGTGGCAAACTCTGAAAGGAATGTCTTTATGGAAAACTCT
3327266 GAA
1 GAA
3327269 TGGAATGCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 36 0.36
55 37 0.37
56 26 0.26
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (55 bp):
GAAAAGAATAGCCTTTGTGGCAAACTCTGAAAGGAATGTCTTTATGGAAAACTCT
Found at i:3327266 original size:27 final size:27
Alignment explanation
Indices: 3327101--3327279 Score: 162
Period size: 27 Copynumber: 6.5 Consensus size: 27
3327091 AAACATCCAG
* * *
3327101 GAAAAGAATAGCCTGTGTGGCAAACTCC
1 GAAAAGAAT-GCCTTTATGGCAAACTCT
* * *
3327129 GAAAGGAATTCCTTTATGGAAAACTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
* *
3327156 GAAAAGAATAACCTTTGTGGCAAACT-T
1 GAAAAGAAT-GCCTTTATGGCAAACTCT
* * *
3327183 GAAAGGAATGTCTTTATGGAAAACTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
*
3327210 GAAAAAAATAGCCTTTTATGGCAAACTCT
1 GAAAAGAAT-GCC-TTTATGGCAAACTCT
* * *
3327239 GAAAAGAATGCCTTTGTGGGAAAGTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
**
3327266 GAATGGAATGCCTT
1 GAAAAGAATGCCTT
3327280 GATGACACAT
Statistics
Matches: 122, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
26 12 0.10
27 62 0.51
28 26 0.21
29 22 0.18
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (27 bp):
GAAAAGAATGCCTTTATGGCAAACTCT
Found at i:3328655 original size:16 final size:17
Alignment explanation
Indices: 3328634--3328669 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3328624 ATATCATTAT
*
3328634 AAATAA-TATTTAAATA
1 AAATAATTATTAAAATA
3328650 AAATAATTATTAAAATA
1 AAATAATTATTAAAATA
3328667 AAA
1 AAA
3328670 AGAATCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAATTATTAAAATA
Found at i:3337411 original size:4 final size:4
Alignment explanation
Indices: 3337402--3337434 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
3337392 TTGCTACTAA
3337402 TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
3337435 TGTTGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3341787 original size:21 final size:21
Alignment explanation
Indices: 3341763--3341813 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3341753 AATTTAAATT
3341763 GCAATAAAATAAATGGCTAAA
1 GCAATAAAATAAATGGCTAAA
3341784 GCAATAAAATAAATGGCTAAA
1 GCAATAAAATAAATGGCTAAA
**
3341805 TTAATAAAA
1 GCAATAAAA
3341814 ATTAAGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.22
Consensus pattern (21 bp):
GCAATAAAATAAATGGCTAAA
Found at i:3343332 original size:19 final size:19
Alignment explanation
Indices: 3343308--3343347 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3343298 TCAGAATAGT
3343308 TAGCAGGATTACCAGACTA
1 TAGCAGGATTACCAGACTA
*
3343327 TAGCAGGATTACTAGACTA
1 TAGCAGGATTACCAGACTA
3343346 TA
1 TA
3343348 CCTCTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGCAGGATTACCAGACTA
Found at i:3346594 original size:18 final size:18
Alignment explanation
Indices: 3346571--3346606 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3346561 GTTGGTTGGG
3346571 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3346589 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3346607 AACGAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TTTAGGGGAAACTCAAGA
Found at i:3347396 original size:20 final size:20
Alignment explanation
Indices: 3347371--3347408 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3347361 TGATGGGGAG
3347371 CAAGAATATC-AAGTTGGATT
1 CAAGAA-ATCGAAGTTGGATT
3347391 CAAGAAATCGAAGTTGGA
1 CAAGAAATCGAAGTTGGA
3347409 GGAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
CAAGAAATCGAAGTTGGATT
Found at i:3349308 original size:46 final size:46
Alignment explanation
Indices: 3349253--3349572 Score: 500
Period size: 46 Copynumber: 7.0 Consensus size: 46
3349243 AGTGTGCTCT
* *
3349253 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3349299 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3349345 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3349391 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3349437 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3349483 GTGATATGAAATGAAG-AAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATG-TGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3349529 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3349573 TCATGTCAAA
Statistics
Matches: 258, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
45 3 0.01
46 254 0.98
47 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3351625 original size:18 final size:18
Alignment explanation
Indices: 3351602--3351636 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3351592 ATGCAAATGT
3351602 ATAAAAACAAAAAATAAC
1 ATAAAAACAAAAAATAAC
* *
3351620 ATAAAAATAACAAATAA
1 ATAAAAACAAAAAATAA
3351637 TTTACGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (18 bp):
ATAAAAACAAAAAATAAC
Found at i:3352114 original size:39 final size:40
Alignment explanation
Indices: 3352025--3352115 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 40
3352015 GATATATAAA
*
3352025 TAATACAATAAATAATAAAAATAATATAATATGTAATAATT
1 TAATA-AATAAATAATAAAAATAATATAATATATAATAATT
3352066 TACAT--ATAAAT-ATAAAAATAA-ATAATATATAA-AGTATT
1 TA-ATAAATAAATAATAAAAATAATATAATATATAATA--ATT
3352104 TAATAAATAAAT
1 TAATAAATAAAT
3352116 TATGCAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
36 1 0.02
37 12 0.27
38 15 0.34
39 12 0.27
41 2 0.05
42 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (40 bp):
TAATAAATAAATAATAAAAATAATATAATATATAATAATT
Found at i:3353417 original size:14 final size:14
Alignment explanation
Indices: 3353400--3353427 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3353390 AGAGATGCCA
3353400 AATTTGCTATCTTC
1 AATTTGCTATCTTC
3353414 AATTTGCTATCTTC
1 AATTTGCTATCTTC
3353428 CAATACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
AATTTGCTATCTTC
Found at i:3353434 original size:44 final size:44
Alignment explanation
Indices: 3353384--3353846 Score: 579
Period size: 44 Copynumber: 10.5 Consensus size: 44
3353374 TGCACCCCGC
* * * * * **
3353384 CAATACAGAGATGCCAAATTTGCTATCTTCAATTTGCTATCTTC
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* * *
3353428 CAATACAGAGACGCCAAATTTGCTATCTTTGATCTGCTTTCTGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* * *
3353472 CAATACAGAGACACTAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* * * * * *
3353516 CAATATAGAGACACCAAATCTGTTATCTTCAATCTGCTATCTGT
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* *
3353560 CAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* *
3353604 CAATATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGG
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* * * *
3353648 CAATATAGAGACACCAAATCTTCTATCTTCAATCTGCTCTCTGGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCT-GA
* *
3353693 -AATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* * * *
3353736 CAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTATTTGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
* *
3353780 CAATACAGAGACGCCAAATCTGCTGTGTTCGATCTGCTCTCTGGA
1 CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCT-GA
3353825 -AATACAGAGACGCCAAATCTGC
1 CAATACAGAGACGCCAAATCTGC
3353847 CACCGGTGAT
Statistics
Matches: 370, Mismatches: 46, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
43 2 0.01
44 365 0.99
45 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
CAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGA
Found at i:3353564 original size:132 final size:132
Alignment explanation
Indices: 3353397--3353845 Score: 637
Period size: 132 Copynumber: 3.4 Consensus size: 132
3353387 TACAGAGATG
* * *** * * *
3353397 CCAAATTTGCTATCTTCAATTTGCTATCTTCCAATACAGAGACGCCAAATTTGCTATCTTTGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGAAATACAGAGACGCCAAATCTGTTATCTTCGATC
* * * *
3353462 TGCTTTCTGACAATACAGAGACACTAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
3353527 CA
131 CA
* ** *
3353529 CCAAATCTGTTATCTTCAATCTGCTATCTGTCAATACAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGAAATACAGAGACGCCAAATCTGTTATCTTCGATC
* *
3353594 TGCTCTCTGACAATATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGGCAATATAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
3353659 CA
131 CA
* * *
3353661 CCAAATCTTCTATCTTCAATCTGCTCTCTGGAAATACAGAGACACCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGAAATACAGAGACGCCAAATCTGTTATCTTCGATC
* * *
3353726 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTATTTGACAATACAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
*
3353791 CG
131 CA
* * * *
3353793 CCAAATCTGCTGTGTTCGATCTGCTCTCTGGAAATACAGAGACGCCAAATCTG
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGAAATACAGAGACGCCAAATCTG
3353846 CCACCGGTGA
Statistics
Matches: 284, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 284 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (132 bp):
CCAAATCTGCTATCTTCAATCTGCTATCTGGAAATACAGAGACGCCAAATCTGTTATCTTCGATC
TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
CA
Found at i:3365921 original size:11 final size:12
Alignment explanation
Indices: 3365900--3365951 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
3365890 ATAAATAGTT
*
3365900 TATAATAAAATGA
1 TATAAT-AAATAA
3365913 TAT-ATAAATAA
1 TATAATAAATAA
3365924 TATAATAAAT-A
1 TATAATAAATAA
3365935 -ATAA-AAATAA
1 TATAATAAATAA
3365945 TATAATA
1 TATAATA
3365952 TGTAATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 13 0.38
12 9 0.26
13 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:3365942 original size:21 final size:23
Alignment explanation
Indices: 3365900--3365951 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
3365890 ATAAATAGTT
*
3365900 TATAATAAAATGATATATAAATAA
1 TATAAT-AAATGATATAAAAATAA
3365924 TATAATAAAT-A-ATAAAAATAA
1 TATAATAAATGATATAAAAATAA
3365945 TATAATA
1 TATAATA
3365952 TGTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.59
22 1 0.04
23 4 0.15
24 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TATAATAAATGATATAAAAATAA
Found at i:3366010 original size:39 final size:40
Alignment explanation
Indices: 3365921--3366011 Score: 93
Period size: 39 Copynumber: 2.3 Consensus size: 40
3365911 GATATATAAA
* *
3365921 TAATATAATAAATAATAAAAATAATATAATATGTAATAATT
1 TAATA-AATAAATAATAAAAATAATAAAATATGAAATAATT
3365962 TACAT--ATAAAT-ATAAAAATAAATAAAATAT-AAAGT-ATT
1 TA-ATAAATAAATAATAAAAAT-AATAAAATATGAAA-TAATT
3366000 TAATAAATAAAT
1 TAATAAATAAAT
3366012 TATGCAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
37 2 0.05
38 15 0.35
39 22 0.51
41 2 0.05
42 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (40 bp):
TAATAAATAAATAATAAAAATAATAAAATATGAAATAATT
Found at i:3372123 original size:24 final size:24
Alignment explanation
Indices: 3372096--3372151 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
3372086 ATCACAAACA
3372096 TGCCAAAAGACCATACATTTCAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3372120 TGCCAAAAGACCATACATTTGAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3372144 TACCAAAA
1 TGCCAAAA
3372152 AGCGGTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (24 bp):
TGCCAAAAGACCATACATTTCAAT
Found at i:3377432 original size:46 final size:46
Alignment explanation
Indices: 3377382--3377551 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
3377372 TGGTTGAGCA
* * *
3377382 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
* * * * *
3377428 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAA--A--CG
* * *
3377475 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
* *
3377521 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
3377552 CTAGGGGCGG
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 57 0.58
47 28 0.28
48 3 0.03
50 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
Found at i:3377493 original size:93 final size:93
Alignment explanation
Indices: 3377379--3377549 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
3377369 GGATGGTTGA
* * * * * *
3377379 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACAAACGCCCGAACTCGTTGAGT
3377444 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
3377472 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACAAACGCCCGAACTCGTTGAGT
3377537 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3377550 ACCTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:3386817 original size:24 final size:24
Alignment explanation
Indices: 3386790--3386846 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
3386780 ATCACAAACA
3386790 TGCCAAAAGACCATACATTTCAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3386814 TGCCAAAAGACCATACATTTGAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3386838 TACCAAAAG
1 TGCCAAAAG
3386847 GCGGTCAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (24 bp):
TGCCAAAAGACCATACATTTCAAT
Found at i:3392231 original size:93 final size:92
Alignment explanation
Indices: 3392073--3392242 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 92
3392063 GGATGGTTGA
* * * * *
3392073 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCATTGAGTTGAGTCGAGTTCACTCATGGATACGAACGCCCGAACTCGTTGAGTT
3392138 GAGTCCGAGTTCGTGAAATGTAACTAG
66 GAGTCCGAGTTCGTGAAATGTAACTAG
*
3392165 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGT-CGAGTTCACTCATGGATACGAACGCCCGAACTCGTTGAGT
3392230 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
3392243 ACCTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 23 0.32
93 48 0.68
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCATTGAGTTGAGTCGAGTTCACTCATGGATACGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:3392242 original size:46 final size:46
Alignment explanation
Indices: 3392077--3392244 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 46
3392067 GGTTGAGCAT
* * * *
3392077 CCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGATACGAACGC
* * * *
3392122 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-AC-TAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--AATGGATACGAACGC
* *
3392167 ATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATACGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGATACGAACGC
*
3392215 CCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC
3392245 CTAGGGGCGG
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
45 23 0.23
46 40 0.40
47 33 0.33
48 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGATACGAACGC
Found at i:3515330 original size:18 final size:19
Alignment explanation
Indices: 3515307--3515356 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
3515297 GACATATTTC
*
3515307 ATTTAATTTTAATAGA-TA
1 ATTTAATTTTAATAAATTA
*
3515325 ATTTAATTATAATAAATTA
1 ATTTAATTTTAATAAATTA
*
3515344 A-ATAATTTTAATA
1 ATTTAATTTTAATA
3515357 TATCTTAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTAATTTTAATAAATTA
Found at i:3518598 original size:15 final size:14
Alignment explanation
Indices: 3518575--3518612 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3518565 ATTTGTCAGT
3518575 AAAAT-ATTTTCCGA
1 AAAATGATTTT-CGA
*
3518589 AAAATGATTTTTGA
1 AAAATGATTTTCGA
3518603 AAAATGATTT
1 AAAATGATTT
3518613 ACTTTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (14 bp):
AAAATGATTTTCGA
Found at i:3518724 original size:16 final size:16
Alignment explanation
Indices: 3518703--3518743 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3518693 CTGTATTTAC
*
3518703 ATATATTGATAAATAT
1 ATATATTAATAAATAT
*
3518719 ATATATTAATAAATTT
1 ATATATTAATAAATAT
*
3518735 ATATTTTAA
1 ATATATTAA
3518744 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTAATAAATAT
Found at i:3520345 original size:25 final size:25
Alignment explanation
Indices: 3520294--3520346 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3520284 TTGATCACTC
**
3520294 AAACTCATCTTTTGAGTTGGAATAA
1 AAACTCATCTTTTGAGAGGGAATAA
*
3520319 AAACTCATCTTTTTAGAAGGGAA-AA
1 AAACTCATCTTTTGAG-AGGGAATAA
3520344 AAA
1 AAA
3520347 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (25 bp):
AAACTCATCTTTTGAGAGGGAATAA
Found at i:3521348 original size:17 final size:17
Alignment explanation
Indices: 3521326--3521360 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3521316 TCAATCAAAT
3521326 CCAAGAAAAAGTCGTCA
1 CCAAGAAAAAGTCGTCA
3521343 CCAAGAAAAAGTCGTCA
1 CCAAGAAAAAGTCGTCA
3521360 C
1 C
3521361 AATCACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (17 bp):
CCAAGAAAAAGTCGTCA
Found at i:3521713 original size:5 final size:6
Alignment explanation
Indices: 3521697--3521722 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3521687 CCCAAGAGGA
3521697 AGGGGG AGGGGG AGGGGG AGGGGG AG
1 AGGGGG AGGGGG AGGGGG AGGGGG AG
3521723 AGGAAGCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:3522473 original size:16 final size:19
Alignment explanation
Indices: 3522448--3522512 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 19
3522438 TAAAATTGAA
3522448 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
3522467 A-A-TAATAAATTATATTAATT
1 ATATTAAT-AATT-TATTAA-T
3522487 ATATTAATAATTTATT-AT
1 ATATTAATAATTTATTAAT
3522505 ATAATTAA
1 AT-ATTAA
3522513 ATATAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.08
17 5 0.13
18 10 0.26
19 7 0.18
20 5 0.13
21 5 0.13
22 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:3522518 original size:22 final size:23
Alignment explanation
Indices: 3522462--3522518 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
3522452 TAAATAATTT
3522462 ATTAAA-ATAATAAATTATATTA
1 ATTAAATATAATAAATTATATTA
* *
3522484 ATTATAT-TAATAATTTATTATATA
1 ATTAAATATAATAAATTA-TAT-TA
3522508 ATTAAATATAA
1 ATTAAATATAA
3522519 ATAATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 14 0.50
23 3 0.11
24 8 0.29
25 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTAAATATAATAAATTATATTA
Found at i:3522524 original size:38 final size:39
Alignment explanation
Indices: 3522448--3522525 Score: 99
Period size: 38 Copynumber: 2.0 Consensus size: 39
3522438 TAAAATTGAA
*
3522448 ATATTAAATAATTTATTAAAATAATAAATTATATTAATT
1 ATATTAAATAATTTATTAAAATAATAAATTATAATAATT
*
3522487 ATATT-AATAATTTATT-ATATAATTAAA-TATAAATAATT
1 ATATTAAATAATTTATTAAAATAA-TAAATTAT-AATAATT
3522525 A
1 A
3522526 AATATGTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 8 0.23
38 22 0.63
39 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
ATATTAAATAATTTATTAAAATAATAAATTATAATAATT
Found at i:3522583 original size:21 final size:21
Alignment explanation
Indices: 3522543--3522584 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3522533 ATGTTTAATA
*
3522543 ATATTAAAAATATAATATTTT
1 ATATTAAAAATATAAAATTTT
* *
3522564 ATATTAAAATTTTAAAATTTT
1 ATATTAAAAATATAAAATTTT
3522585 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTAAAAATATAAAATTTT
Found at i:3526583 original size:14 final size:14
Alignment explanation
Indices: 3526564--3526591 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3526554 AAATTTAAAA
3526564 CATATTTTGAAATT
1 CATATTTTGAAATT
3526578 CATATTTTGAAATT
1 CATATTTTGAAATT
3526592 ATTTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
CATATTTTGAAATT
Found at i:3533849 original size:13 final size:13
Alignment explanation
Indices: 3533831--3533858 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3533821 ATAAATATAC
3533831 CTATATTTTTAAA
1 CTATATTTTTAAA
3533844 CTATATTTTTAAA
1 CTATATTTTTAAA
3533857 CT
1 CT
3533859 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (13 bp):
CTATATTTTTAAA
Found at i:3541367 original size:10 final size:10
Alignment explanation
Indices: 3541337--3541479 Score: 59
Period size: 10 Copynumber: 14.9 Consensus size: 10
3541327 TTAAATGATT
3541337 TTTTTTAT-A
1 TTTTTTATAA
3541346 TTTTTTAT-A
1 TTTTTTATAA
*
3541355 TTTTTAATAA
1 TTTTTTATAA
* *
3541365 TTTATCATAA
1 TTTTTTATAA
3541375 TTTTTTATAA
1 TTTTTTATAA
* ** **
3541385 CTAATTAGGA
1 TTTTTTATAA
* *
3541395 TATTTTGA-AT
1 T-TTTTTATAA
3541405 TTTTTTATAA
1 TTTTTTATAA
** *
3541415 AATTTTA-AT
1 TTTTTTATAA
3541424 TTTTTTATTAA
1 TTTTTTA-TAA
3541435 --TTTTAT-A
1 TTTTTTATAA
3541442 -TTTTTATAA
1 TTTTTTATAA
*
3541451 TTTATTATAA
1 TTTTTTATAA
** *
3541461 GCTTTTATGA
1 TTTTTTATAA
3541471 TTTTTTATA
1 TTTTTTATA
3541480 TAAATTATTT
Statistics
Matches: 94, Mismatches: 32, Indels: 15
0.67 0.23 0.11
Matches are distributed among these distances:
7 1 0.01
8 7 0.07
9 33 0.35
10 49 0.52
11 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3541426 original size:19 final size:19
Alignment explanation
Indices: 3541396--3541450 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3541386 TAATTAGGAT
3541396 ATTTTGAATTTTTTTATAAA
1 ATTTT-AATTTTTTTATAAA
*
3541416 ATTTTAATTTTTTTAT-TA
1 ATTTTAATTTTTTTATAAA
*
3541434 ATTTT-ATATTTTTATAA
1 ATTTTAATTTTTTTATAA
3541451 TTTATTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 11 0.35
20 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTAATTTTTTTATAAA
Found at i:3545513 original size:131 final size:129
Alignment explanation
Indices: 3545348--3545819 Score: 402
Period size: 130 Copynumber: 3.6 Consensus size: 129
3545338 AATCAAGACC
* * * * ** * * *
3545348 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGCAACCCA-CACGTTAGGGCACGATTC
* * *
3545413 C-CGAATTGTCAAACACC-GAGTATTGCCCTCATTTTAAAGGATTTTTAAAAGAGC-CGAGTGAA
65 CACGAATTGCCAAACACCAGA-TATCGCCCTCATTTT-AAGGA-TTTTAAAAGA-CACGAGCGAA
3545475 ATTT
126 ATTT
* * * * *
3545479 TGAAGGGATATTTGATTATTTTAAACAATCGAGAAATTGCTACCCCACACGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGC-AACCCACACGTTAGGGCACGATTC
* * *
3545544 CACGAATTGCCAAATACCAGATATCGCCTTCATTTTAGGGATTTTAAAAGACACGAGCGAAATTT
65 CACGAATTGCCAAACACCAGATATCGCCCTCATTTTAAGGATTTTAAAAGACACGAGCGAAATTT
* * *
3545609 TAAAGTGATATTCGATTATTTTGAGCAGAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATT
1 TAAAGGGATATTCGATTATTTTGAACA-ATCGAGAAATTGCAACCC-ACACGTTAGGGCACGATT
* * * * * * * * ** *
3545673 CCGCGAATTGCCAAACATCA-A-ATCTCATCTTAGTTTAAGGGATTTTAAAAGATATGAATGGAA
64 CCACGAATTGCCAAACACCAGATATCGC-CCTCATTTTAA-GGATTTTAAAAGACACGAGCGAAA
3545736 TTT
127 TTT
** * * *
3545739 CGAAGGGAAATTCAATTATTTTGAGCAAAT--ACGAAATTGCAACCCAACACGTTAGGGCACGAT
1 TAAAGGGATATTCGATTATTTTGAAC-AATCGA-GAAATTGCAACCC-ACACGTTAGGGCACGAT
* *
3545802 TCCGCGAATTGCCGAACA
63 TCCACGAATTGCCAAACA
3545820 TCAAATTTCG
Statistics
Matches: 282, Mismatches: 49, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
128 4 0.01
129 12 0.04
130 179 0.63
131 53 0.19
132 32 0.11
133 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (129 bp):
TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGCAACCCACACGTTAGGGCACGATTCC
ACGAATTGCCAAACACCAGATATCGCCCTCATTTTAAGGATTTTAAAAGACACGAGCGAAATTT
Found at i:3549524 original size:32 final size:34
Alignment explanation
Indices: 3549480--3549542 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
3549470 ATTTCTTTTT
*
3549480 TTGGTCATTCAATTATGAATTT-TTT-TTTTAAA
1 TTGGTCACTCAATTATGAATTTGTTTCTTTTAAA
3549512 TTGGTCACTCAATTATGAATTTGTTTCTTTT
1 TTGGTCACTCAATTATGAATTTGTTTCTTTT
3549543 TTGGTGACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 21 0.75
33 3 0.11
34 4 0.14
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.56
Consensus pattern (34 bp):
TTGGTCACTCAATTATGAATTTGTTTCTTTTAAA
Found at i:3549556 original size:31 final size:30
Alignment explanation
Indices: 3549471--3549560 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
3549461 CTATGGGCCA
*
3549471 TTTCTTTTTTTGGTCATTCAATTATGAATTT
1 TTTC-TTTTTTGGTCACTCAATTATGAATTT
3549502 TTT-TTTTAAATTGGTCACTCAATTATGAATTT
1 TTTCTTTT---TTGGTCACTCAATTATGAATTT
* *
3549534 GTTTCTTTTTTGGTGACCCAATTATGA
1 -TTTCTTTTTTGGTCACTCAATTATGA
3549561 TGTTTGGCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
29 4 0.08
31 19 0.37
32 21 0.41
33 3 0.06
34 4 0.08
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.54
Consensus pattern (30 bp):
TTTCTTTTTTGGTCACTCAATTATGAATTT
Found at i:3556632 original size:27 final size:27
Alignment explanation
Indices: 3556587--3556691 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
3556577 GCGAGGCTAC
* *
3556587 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
* *
3556614 CAGATATTGTGGCAGAGTCATCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* *
3556640 CAGATGTATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
3556667 CAGATAATTGAGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
3556692 GACAGGACGC
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 7 0.11
27 55 0.86
28 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:3558319 original size:26 final size:26
Alignment explanation
Indices: 3558289--3558344 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3558279 TGAAATTCCC
*
3558289 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
3558315 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
3558341 ATCA
1 ATCA
3558345 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:3564557 original size:27 final size:27
Alignment explanation
Indices: 3564512--3564669 Score: 155
Period size: 27 Copynumber: 5.9 Consensus size: 27
3564502 GCGAGGCTGC
* *
3564512 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
3564539 CAGATATTGTGGCAGAGTCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* * *
3564565 TAGATCTATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
3564592 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
3564619 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
3564646 CAGATAATTGTGGCATAGCCACCA
1 CAGAT-ATTGTGGCAGAGCCACCA
3564670 AGACGCTTCC
Statistics
Matches: 110, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.07
27 98 0.89
28 4 0.04
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:3564629 original size:54 final size:54
Alignment explanation
Indices: 3564530--3564669 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 54
3564520 GTGACGAAGT
* * * *
3564530 CACCAGATACAGAT-ATTGTGGCAGAGTCACCAGAATAGATCTATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
3564584 CACTAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
3564638 CACCAGATCAGATAATTGTGGCATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
3564670 AGACGCTTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.06
54 73 0.94
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:3585756 original size:23 final size:21
Alignment explanation
Indices: 3585730--3585785 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
3585720 CTTGCTTTTA
3585730 TATTATATATTGTAAGATTATTT
1 TATTATATATT-TAAGATTA-TT
*
3585753 TATTATATATATTAATATTATT
1 TATTATATAT-TTAAGATTATT
*
3585775 TATTATCTATT
1 TATTATATATT
3585786 ACTTTTCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 11 0.37
23 17 0.57
24 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTATATATTTAAGATTATT
Found at i:3585845 original size:16 final size:15
Alignment explanation
Indices: 3585799--3585846 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
3585789 TTTCACAAAT
3585799 TATTATTATTATTTTA
1 TATTATTATT-TTTTA
* *
3585815 CATCATTATTTTTTTA
1 TATTATTA-TTTTTTA
3585831 TATTATTATATTTTTA
1 TATTATTAT-TTTTTA
3585847 CTTGTATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.88
17 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATTTTTTA
Found at i:3586540 original size:33 final size:33
Alignment explanation
Indices: 3586495--3586569 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
3586485 TTGATATTGT
3586495 ATTACT-CTTTTTTGTATATCATGCATTATTTA
1 ATTACTACTTTTTTGTATATCATGCATTATTTA
*
3586527 ATTATTACTTTTTTGTATATCATGCATTATTTA
1 ATTACTACTTTTTTGTATATCATGCATTATTTA
3586560 ATTACTACTT
1 ATTACTACTT
3586570 CGTATGTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 5 0.12
33 35 0.88
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (33 bp):
ATTACTACTTTTTTGTATATCATGCATTATTTA
Found at i:3594189 original size:17 final size:19
Alignment explanation
Indices: 3594174--3594327 Score: 133
Period size: 17 Copynumber: 8.9 Consensus size: 19
3594164 AATTATATCT
3594174 TCTAAGATTGTATATCATA
1 TCTAAGATTGTATATCATA
*
3594193 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGTATATCATA
*
3594211 TTTAAGATTG--TATCATA
1 TCTAAGATTGTATATCATA
3594228 TCTAAGATTG-----CA-A
1 TCTAAGATTGTATATCATA
3594241 TC--AGATTG--TATCATA
1 TCTAAGATTGTATATCATA
* *
3594256 TCCAAGATTGCA-ATCATA
1 TCTAAGATTGTATATCATA
3594274 TCTAAGATTGTA-A-CATA
1 TCTAAGATTGTATATCATA
* *
3594291 TCTAAGATTGCATATCACA
1 TCTAAGATTGTATATCATA
*
3594310 TCTAAGATTGCATATCAT
1 TCTAAGATTGTATATCAT
3594328 TGAAGATTAT
Statistics
Matches: 116, Mismatches: 8, Indels: 22
0.79 0.05 0.15
Matches are distributed among these distances:
11 6 0.05
13 3 0.03
14 4 0.03
15 3 0.03
17 36 0.31
18 33 0.28
19 31 0.27
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGTATATCATA
Found at i:3594231 original size:35 final size:35
Alignment explanation
Indices: 3594174--3594319 Score: 180
Period size: 35 Copynumber: 4.3 Consensus size: 35
3594164 AATTATATCT
3594174 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
*
3594211 TTTAAGATTGTATCATATCTAAGATTG----CA-A
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
3594241 TC--AGATTGTATCATATCCAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
3594274 TCTAAGATTGTAACATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
3594310 TCTAAGATTG
1 TCTAAGATTG
3594320 CATATCATTG
Statistics
Matches: 95, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
28 22 0.23
30 2 0.02
31 2 0.02
32 2 0.02
33 3 0.03
35 40 0.42
36 15 0.16
37 9 0.09
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:3594255 original size:28 final size:28
Alignment explanation
Indices: 3594215--3594271 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3594205 ATCATATTTA
*
3594215 AGATTGTATCATATCTAAGATTGCAATC
1 AGATTGTATCATATCCAAGATTGCAATC
3594243 AGATTGTATCATATCCAAGATTGCAATC
1 AGATTGTATCATATCCAAGATTGCAATC
3594271 A
1 A
3594272 TATCTAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (28 bp):
AGATTGTATCATATCCAAGATTGCAATC
Found at i:3594257 original size:63 final size:64
Alignment explanation
Indices: 3594186--3594307 Score: 210
Period size: 63 Copynumber: 1.9 Consensus size: 64
3594176 TAAGATTGTA
* * *
3594186 TATCATATCTAAGATTGCAATCATATTTAAGATTGTATCATATCTAAGATTGCA-ATCAGATTG
1 TATCATATCCAAGATTGCAATCATATCTAAGATTGTAACATATCTAAGATTGCATATCAGATTG
3594249 TATCATATCCAAGATTGCAATCATATCTAAGATTGTAACATATCTAAGATTGCATATCA
1 TATCATATCCAAGATTGCAATCATATCTAAGATTGTAACATATCTAAGATTGCATATCA
3594308 CATCTAAGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 51 0.93
64 4 0.07
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (64 bp):
TATCATATCCAAGATTGCAATCATATCTAAGATTGTAACATATCTAAGATTGCATATCAGATTG
Found at i:3594335 original size:17 final size:18
Alignment explanation
Indices: 3594259--3594324 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
3594249 TATCATATCC
*
3594259 AAGATTGCA-ATCATATCT
1 AAGATTGCATAT-ACATCT
* * *
3594277 AAGATTGTA-ACATATCT
1 AAGATTGCATATACATCT
3594294 AAGATTGCATATCACATCT
1 AAGATTGCATAT-ACATCT
3594313 AAGATTGCATAT
1 AAGATTGCATAT
3594325 CATTGAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.34
18 10 0.24
19 17 0.41
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
AAGATTGCATATACATCT
Found at i:3595188 original size:207 final size:207
Alignment explanation
Indices: 3594722--3595845 Score: 1962
Period size: 207 Copynumber: 5.4 Consensus size: 207
3594712 AAATCTGCTT
* * * *
3594722 CTTCAATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* * ** * *
3594787 GCGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTCATAAGCACAATGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * ** * * *
3594852 GGATC-TGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTGTCCTCTGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3594916 GGAGACGCCAAA
196 GGAGACGCCAAA
*
3594928 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
3594993 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
3595058 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTGTCTGCCCGCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
*
3595123 AGAGACGCCAAA
196 GGAGACGCCAAA
3595135 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* *
3595200 GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
3595265 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTTGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3595330 GGAGACGCCAAA
196 GGAGACGCCAAA
3595342 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
3595407 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
*
3595472 GGATCTTGCTTCAGTATAAACATCTGAAGGCCATATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3595537 GGAGACGCCAAA
196 GGAGACGCCAAA
*
3595549 CTTCGATTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* *
3595614 GTGAAAACCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
3595679 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
3595744 GGAGACGCCAAA
196 GGAGACGCCAAA
* *
3595756 CTTCGATTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGACTTACTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
*
3595821 GTGAATGCCAAATCAGCTATGTCTT
66 GTGAAAGCCAAATCAGCTATGTCTT
3595846 GGTCTATTAC
Statistics
Matches: 880, Mismatches: 37, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
206 126 0.14
207 754 0.86
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
GGAGACGCCAAA
Found at i:3596126 original size:85 final size:85
Alignment explanation
Indices: 3595852--3596213 Score: 481
Period size: 85 Copynumber: 4.3 Consensus size: 85
3595842 TCTTGGTCTA
* * * * * *
3595852 TTACCTTACTGCTTAGGGG-TTAAGGTGCATTGTCTTAGATCTGCTCCGCTATTGCTTAGGGA-A
1 TTACCCTACTGCTTAGGGGATTAAGGCG-A--GTCTTCGATCTGCTCCACTACTACTTAGGGAGA
3595915 ATAAGATCTGCAAATTTAACCTG
63 ATAAGATCTGCAAATTTAACCTG
* * *
3595938 TTACCCTACTGCTTAGGGGATTAAGACGAGTCGTCATCGATCTGCTCCGCTACTGCTTAGGGAG-
1 TTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTACTTAGGGAGA
*
3596002 ATAAGATCTGC-----GAACCTG
63 ATAAGATCTGCAAATTTAACCTG
*
3596020 TTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTACTTAGGGGGAATA
1 TTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTACTTAGGGAGAATA
*
3596085 AGATCTACAAATTTAACCTG
66 AGATCTGCAAATTTAACCTG
* *
3596105 TTACCCTACTGCTTAGGGGATTAAGGCGGGTCTTCGATCTGCTCCACTACTACTTAAGGAGAATA
1 TTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTACTTAGGGAGAATA
3596170 AGATCTGCAAATTT-ACCTG
66 AGATCTGCAAATTTAACCTG
3596189 TTACCCTACTGCTTAGGGGATTAAG
1 TTACCCTACTGCTTAGGGGATTAAG
3596214 AGGCTGAATT
Statistics
Matches: 249, Mismatches: 16, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
79 25 0.10
80 10 0.04
81 1 0.00
82 37 0.15
84 33 0.13
85 82 0.33
86 19 0.08
87 42 0.17
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (85 bp):
TTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTACTTAGGGAGAATA
AGATCTGCAAATTTAACCTG
Found at i:3602927 original size:17 final size:18
Alignment explanation
Indices: 3602872--3603014 Score: 193
Period size: 17 Copynumber: 7.9 Consensus size: 18
3602862 AATCATATCT
*
3602872 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
3602891 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
3602909 TCTAAGATTG-TACCATA
1 TCTAAGATTGCTATCATA
*
3602926 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
3602944 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
3602961 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
3602978 TCTAAGATTGCATATCACA
1 TCTAAGATTGC-TATCATA
3602997 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
3603015 TGAAGATTAT
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
17 48 0.43
18 31 0.28
19 33 0.29
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:3602933 original size:35 final size:36
Alignment explanation
Indices: 3602872--3603014 Score: 211
Period size: 35 Copynumber: 4.0 Consensus size: 36
3602862 AATCATATCT
3602872 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATA
*
3602909 TCTAAGATTG-TACCATATCTAAGATTGCAATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATA
*
3602944 TCTAAGATTG-TATCATATCTAAGATTG-TATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATA
*
3602978 TCTAAGATTGCATATCACATCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCATATCTAAGATTGCA-ATCAT
3603015 TGAAGATTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
34 16 0.16
35 50 0.52
36 16 0.16
37 10 0.10
38 5 0.05
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (36 bp):
TCTAAGATTGATATCATATCTAAGATTGCAATCATA
Found at i:3602970 original size:52 final size:54
Alignment explanation
Indices: 3602872--3603014 Score: 227
Period size: 52 Copynumber: 2.7 Consensus size: 54
3602862 AATCATATCT
*
3602872 TCTAAGATTGTATATCATATCTAAGATTGCAATCATATCTAAGATTGTACCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTACCATA
* *
3602926 TCTAAGATTGCA-ATCATATCTAAGATTG-TATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTACCATA
*
3602978 TCTAAGATTGCATATCACATCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCAT
3603015 TGAAGATTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
52 34 0.42
53 31 0.38
54 11 0.14
55 5 0.06
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (54 bp):
TCTAAGATTGCATATCATATCTAAGATTGCAATCATATCTAAGATTGTACCATA
Found at i:3612009 original size:3 final size:3
Alignment explanation
Indices: 3612001--3612108 Score: 50
Period size: 3 Copynumber: 36.7 Consensus size: 3
3611991 TATTTATTTC
* * *
3612001 TAT TAT TA- TAT ATAT AAT T-T TAT TAT TAT TAT T-T GTTT TAT TTT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* ** * *
3612045 TAA CCT TAT TTT TA- TAT TAT ATAT TA- TAT AAT TAT T-T TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
3612087 TAT TAT TATT TAT TAT ATAT TA
1 TAT TAT TA-T TAT TAT -TAT TA
3612109 CTTTTCACAA
Statistics
Matches: 78, Mismatches: 15, Indels: 24
0.67 0.13 0.21
Matches are distributed among these distances:
2 13 0.17
3 52 0.67
4 13 0.17
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3612010 original size:20 final size:19
Alignment explanation
Indices: 3611987--3612107 Score: 85
Period size: 18 Copynumber: 6.4 Consensus size: 19
3611977 AATCTAACCC
3611987 TATATATTTATTTCTATTAT
1 TATATATTTATTT-TATTAT
*
3612007 TATATATATAATTTTATTAT
1 TATATAT-TTATTTTATTAT
*
3612027 TAT-TATTTGTTTTATT-T
1 TATATATTTATTTTATTAT
*
3612044 T-TA-ACCTTATTTT-TATAT
1 TATATA-TTTATTTTAT-TAT
* *
3612062 TATATA-TTATATAATTAT
1 TATATATTTATTTTATTAT
*
3612080 TTTATA-TTATTATTATTTAT
1 TATATATTTATT-TTA-TTAT
3612100 TATATATT
1 TATATATT
3612108 ACTTTTCACA
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
16 3 0.04
17 9 0.11
18 27 0.34
19 8 0.10
20 26 0.33
21 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (19 bp):
TATATATTTATTTTATTAT
Found at i:3612069 original size:7 final size:7
Alignment explanation
Indices: 3612057--3612108 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
3612047 ACCTTATTTT
3612057 TATATTA
1 TATATTA
3612064 TATATTA
1 TATATTA
3612071 TATA--A
1 TATATTA
*
3612076 T-TATTT
1 TATATTA
3612082 TATATTA
1 TATATTA
3612089 T-TATTA
1 TATATTA
*
3612095 TTTATTA
1 TATATTA
3612102 TATATTA
1 TATATTA
3612109 CTTTTCACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 7 0.18
7 27 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTA
Found at i:3612108 original size:20 final size:19
Alignment explanation
Indices: 3611991--3612108 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 19
3611981 TAACCCTATA
*
3611991 TATTTATTTCTATTATTAT
1 TATTTATTTATATTATTAT
*
3612010 ATATATAATTT-TATTATTAT
1 -TAT-TTATTTATATTATTAT
* *
3612030 TATTTGTTT-TATTTTTAACCT
1 TATTTATTTATATTATT-A--T
3612051 TATTT-TTATATTATATATTAT
1 TATTTATT-TA-TAT-TATTAT
*
3612072 ATAATTATTTTATATTATTAT
1 -TATTTA-TTTATATTATTAT
3612093 TATTTATTATATATTA
1 TATTTATT-TATATTA
3612109 CTTTTCACAA
Statistics
Matches: 79, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
18 10 0.13
19 6 0.08
20 26 0.33
21 19 0.24
22 7 0.09
23 6 0.08
24 5 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TATTTATTTATATTATTAT
Found at i:3612154 original size:14 final size:14
Alignment explanation
Indices: 3612120--3612157 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3612110 TTTTCACAAA
*
3612120 ATATTATTAT-TTT
1 ATATTATTATCTAT
*
3612133 ACATTATTATCTAT
1 ATATTATTATCTAT
3612147 ATATTATTATC
1 ATATTATTATC
3612158 ATTAAAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTATTATCTAT
Found at i:3612314 original size:21 final size:23
Alignment explanation
Indices: 3612289--3612347 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
3612279 ATCATTAATT
*
3612289 ACTTATTTTATAT-TATTCTA-A
1 ACTTATTTTATATATATTATATA
3612310 ACTTATATTTATATATATTATATA
1 ACTTAT-TTTATATATATTATATA
3612334 A-TTATTTTAT-TATA
1 ACTTATTTTATATATA
3612348 AATATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 10 0.29
22 12 0.35
23 10 0.29
24 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (23 bp):
ACTTATTTTATATATATTATATA
Found at i:3615331 original size:686 final size:682
Alignment explanation
Indices: 3613628--3615485 Score: 2067
Period size: 686 Copynumber: 2.6 Consensus size: 682
3613618 ATTACATTTT
* *
3613628 ACCTTTAAATTAATATTCTTAAAATTGCA--AAATATTTGAACAAGCATAGAGTTTTGATGGCTT
1 ACCTTTAAAATAATATTCTTAAAA--CCAGGAAATATTTGAACAAGCATAGAGTTTTGATGGCTT
* * * * *
3613691 AAAACGAGCCAAATAATCATGAAAATTCTAAAATATAAAACACAATTTTTTT-A-TTT-CTT-TT
64 AAAACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAATTTTTTTCATTTTATTTATT
*
3613752 TAGTATTATTGTTATCCAAATTATGTTTTATTAAATTAAGCATCATATTAAATTATTTTTCTAAA
129 TAATATTATTGTTATCCAAATTATGTTTTATTAAATT-A--AT--T-TTAAA--A------T---
* *
3613817 TTTTTTGTTGAATTTTTTATTTAAATATATTACAAAATTGTAGAATTATCACACATGTTAAGTTA
177 TTTTTTGTTGAATTTTTTATTTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTA
* * * * ** * *
3613882 CTCGATAAGTTT-TTCCACTATCGAAATGCCTTGGAATCGAAATCCCAAACTGAAACCAAATCAA
242 CTCG-TAA-TTTATTACACAATCGAAAT-CCTTTGAATCGAAACCCCAAACAAAAACCGAATCCA
* * *
3613946 AAACCCAAAACCAAAACT--A-AAAGTGAAAGCCCAAACTGACACCGAATCTAAAACTCCAAAGT
304 AACCCCAAAACCAAAACTAAATAAAGTGAAAGCCCAAACCGACACCGAATCTAAAACTCCAAACT
* * * * *
3614008 GAAAACTAAACTAAAACCAAAATCGAAAACCCAAACTTAAGGCTTTTAACATATTTGGTAACTAA
369 GAAAACTAAACTGAAACCTAAATTGAAAACCC-AACTTAAGGCTTTCAACATATTTGGTAACTAC
* * *
3614073 ATTTAAGGCTTTTTAAAATCATTTATTGTTTCTCATTCTAATCGAACTTTAAATGATTTCTACTG
433 ATTTAAGGCCTTTTAAAACCATCTATTGTTTCTCATTCTAATCGAACTTTAAATGATTTCTACTG
* *
3614138 TATGAAATGTGATCTTTCCGTTGGTCTGTTTTTCTAGCCAAATTGAATTATGTCTTAGATGAACT
498 TATGAAATGTAATCTTTCCATTGGTCTGTTTTTCTAGCCAAATTGAATTATGTCTTAGATGAACT
* * *
3614203 AAGCTCCCAAAGTAGCCTAATTGAAATAGGAAACCTAGAAATTCTGAGCAAATTGCGGCGATTTG
563 AAGCTACCAAAGTAGCC--------AT----AACCTAGAAATTCTGAGCAAATTGCGACCATTTG
*
3614268 TAATATTTTTAGCACCAAAATCTTAAGCTTTTAGTGATTGGTTTTCATAAAACAAAATTTCTAGT
616 TAATATTTTGAGCACCAAAATCTTAAGCTTTTAGTGATTGGTTTTCATAAAACAAAATTTC----
3614333 TTTAGAATCACATTTG
677 --T----T--CA--TG
*
3614349 ACCTTTAAAATAATATTCTTAAAACC-GGAAAATATTTGAACGAGCATAGAGTTTTGATGGCTTA
1 ACCTTTAAAATAATATTCTTAAAACCAGG-AAATATTTGAACAAGCATAGAGTTTTGATGGCTTA
3614413 AAACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAATTTTTTTTTCATTTTCATATT
65 AAACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAA--TTTTTTTCATTTT-AT-TT
* * * * **
3614478 ATTGTTATCCAAATTATGTTTTAT-TAAATTAAAAGTCATATTAAATTAATTTTCAAAA-TTTTT
126 A-T-TTA---ATATTAT-TGTTATCCAAATT--ATGTTTTATTAAATTAATTTT-AAAATTTTTT
* *
3614541 AGTTTAATTTTTTA-TTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTACTCGG
182 TGTTGAATTTTTTATTTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTACTC-G
** * * *
3614605 TAGGTTATCACACAATTGAAATGCTTTGGAATCGAAACCCCAAACAAAAACCGAATCCAAACCCC
246 TAATTTATTACACAATCGAAATCCTTT-GAATCGAAACCCCAAACAAAAACCGAATCCAAACCCC
* *
3614670 AAAACCGAAACTGAAAGTGAAAGTGAAAGCCCAAACCGACACCAAATCTAAAACTCCAAACTGAA
310 AAAACCAAAACT-AAA-T-AAAGTGAAAGCCCAAACCGACACCGAATCTAAAACTCCAAACTGAA
* *
3614735 AACTAAACTGAAACCTAAGTTGAAAACCCAAGTTAAGGGCTTTCAACATATTTGGGTAACTACAT
372 AACTAAACTGAAACCTAAATTGAAAACCCAACTTAA-GGCTTTCAACATATTT-GGTAACTACAT
** * **
3614800 TTAAGGCCTTTTAAAACCATCTATTGTTTCTCATTCTTGTCGAAGTTTAAATGATTTCTGTTGTA
435 TTAAGGCCTTTTAAAACCATCTATTGTTTCTCATTCTAATCGAACTTTAAATGATTTCTACTGT-
* * * *
3614865 ATGAAATGTAATCTTTCCATTGGTTTGTTTTTCTAGCTAAATTGAGTTTTGTCTTAGATGAACTA
499 ATGAAATGTAATCTTTCCATTGGTCTGTTTTTCTAGCCAAATTGAATTATGTCTTAGATGAACTA
* *
3614930 AGTTACCAAAGTAG-C-T-ACCTAGAAATTCTGAGCAAATTGTGACCATTTGTAATATTTTGAGC
564 AGCTACCAAAGTAGCCATAACCTAGAAATTCTGAGCAAATTGCGACCATTTGTAATATTTTGAGC
* * * *
3614992 CCCAAAATCTTAGGCTTTTGGTGATTGGTTTTCATAAAACGAAATTTC-T-A-G
629 ACCAAAATCTTAAGCTTTTAGTGATTGGTTTTCATAAAACAAAATTTCTTCATG
*
3615043 ACCTTTAAAATAATATTCTTAAAACCAGGAAATATTTGAACAAGCATAAAGTTTTGATGGCTT-A
1 ACCTTTAAAATAATATTCTTAAAACCAGGAAATATTTGAACAAGCATAGAGTTTTGATGGCTTAA
3615107 AACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAATTTTTTTCCATTTTATTTCATT
66 AACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAATTTTTTT-CATTTTATTT-ATT
3615172 TAATATTATTGTTATCCAAATTATGTTTTATTAAATTAATTTTAAAATTTTTTTGTTGAATTTTA
129 TAATATTATTGTTATCCAAATTATGTTTTATTAAATTAATTTTAAAATTTTTTTGTTGAATTTT-
* *
3615237 TTATTTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTATTCAGTAATTTATTGC
193 TTATTTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTACTC-GTAATTTATTAC
* * *
3615302 ACAATCAAAATACCTTTGAATCAAAACCCCAAACAAAAACCGAATCCAAACTCCAAAACCAAAAC
257 ACAATCGAAAT-CCTTTGAATCGAAACCCCAAACAAAAACCGAATCCAAACCCCAAAACCAAAAC
* * * * * *
3615367 TAAAATTAA---AAA-CCCAAATCGACACCGTATTTAAAACCCCAAACCT-AAAACTAAATTGAA
321 T-AAATAAAGTGAAAGCCCAAACCGACACCGAATCTAAAACTCCAAA-CTGAAAACTAAACTGAA
*
3615427 ACCTAAATTGAAAACCTAAACTTTTAAGGCTTTCAACATATTTAGGTAACTACATTTAA
384 ACCTAAATTGAAAACC-CAAC--TTAAGGCTTTCAACATATTT-GGTAACTACATTTAA
3615486 ACCATCTTAC
Statistics
Matches: 991, Mismatches: 102, Indels: 127
0.81 0.08 0.10
Matches are distributed among these distances:
680 54 0.05
681 7 0.01
682 31 0.03
683 8 0.01
684 34 0.03
685 9 0.01
686 124 0.13
687 4 0.00
689 3 0.00
690 3 0.00
691 10 0.01
692 6 0.01
693 44 0.04
694 59 0.06
695 2 0.00
697 1 0.00
700 1 0.00
711 86 0.09
716 1 0.00
717 5 0.01
718 101 0.10
719 19 0.02
721 98 0.10
723 13 0.01
724 84 0.08
725 70 0.07
726 71 0.07
728 2 0.00
729 1 0.00
730 3 0.00
731 7 0.01
733 2 0.00
734 10 0.01
735 6 0.01
736 12 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (682 bp):
ACCTTTAAAATAATATTCTTAAAACCAGGAAATATTTGAACAAGCATAGAGTTTTGATGGCTTAA
AACGAGCCAAAAAATAATGAAAATTCTGAAATATAAAATACAATTTTTTTCATTTTATTTATTTA
ATATTATTGTTATCCAAATTATGTTTTATTAAATTAATTTTAAAATTTTTTTGTTGAATTTTTTA
TTTATATATATTACAAAATTGTAAAATTATCACACATGTTAAGTTACTCGTAATTTATTACACAA
TCGAAATCCTTTGAATCGAAACCCCAAACAAAAACCGAATCCAAACCCCAAAACCAAAACTAAAT
AAAGTGAAAGCCCAAACCGACACCGAATCTAAAACTCCAAACTGAAAACTAAACTGAAACCTAAA
TTGAAAACCCAACTTAAGGCTTTCAACATATTTGGTAACTACATTTAAGGCCTTTTAAAACCATC
TATTGTTTCTCATTCTAATCGAACTTTAAATGATTTCTACTGTATGAAATGTAATCTTTCCATTG
GTCTGTTTTTCTAGCCAAATTGAATTATGTCTTAGATGAACTAAGCTACCAAAGTAGCCATAACC
TAGAAATTCTGAGCAAATTGCGACCATTTGTAATATTTTGAGCACCAAAATCTTAAGCTTTTAGT
GATTGGTTTTCATAAAACAAAATTTCTTCATG
Found at i:3615443 original size:13 final size:13
Alignment explanation
Indices: 3615413--3615446 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3615403 CCCCAAACCT
3615413 AAAA-CTAAATTG
1 AAAACCTAAATTG
3615425 -AAACCTAAATTG
1 AAAACCTAAATTG
3615437 AAAACCTAAA
1 AAAACCTAAA
3615447 CTTTTAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
13 9 0.45
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAACCTAAATTG
Found at i:3615952 original size:21 final size:21
Alignment explanation
Indices: 3615894--3615940 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3615884 CAAATTATTT
3615894 TTTATTGGATATATATAATTA
1 TTTATTGGATATATATAATTA
3615915 TTTATTGGATATATATAATTA
1 TTTATTGGATATATATAATTA
3615936 TTTAT
1 TTTAT
3615941 GTATGCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTATTGGATATATATAATTA
Found at i:3617193 original size:21 final size:22
Alignment explanation
Indices: 3617145--3617201 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3617135 CAAGGTCTAG
*
3617145 GATCTAAAGTCTAAGATTTTAA
1 GATCTAAAGTCTAAGATTTAAA
* *
3617167 GATCTAAAGTCTAGGGTTTAAA
1 GATCTAAAGTCTAAGATTTAAA
*
3617189 G-TCTAATGTCTAA
1 GATCTAAAGTCTAA
3617202 AGTTCAAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
GATCTAAAGTCTAAGATTTAAA
Found at i:3617340 original size:27 final size:27
Alignment explanation
Indices: 3617302--3617355 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3617292 GTAAGGGATA
3617302 GAAGAAGATGTGACGCATCTGTTTCAT
1 GAAGAAGATGTGACGCATCTGTTTCAT
*
3617329 GAAGAAGATGTGGCGCATCTGTTTCAT
1 GAAGAAGATGTGACGCATCTGTTTCAT
3617356 ACAATCCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GAAGAAGATGTGACGCATCTGTTTCAT
Found at i:3625741 original size:17 final size:18
Alignment explanation
Indices: 3625708--3625741 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3625698 ACTGAGGCAA
3625708 ATCAAACAAAATAAATAT
1 ATCAAACAAAATAAATAT
*
3625726 ATCAAA-AAAATTAATA
1 ATCAAACAAAATAAATA
3625742 ATAGTAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (18 bp):
ATCAAACAAAATAAATAT
Found at i:3631584 original size:16 final size:16
Alignment explanation
Indices: 3631565--3631595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3631555 GATTTAGGTC
*
3631565 TTTTAAATTTATAAAA
1 TTTTAAATTAATAAAA
3631581 TTTTAAATTAATAAA
1 TTTTAAATTAATAAA
3631596 GGTAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAATTAATAAAA
Found at i:3634061 original size:15 final size:16
Alignment explanation
Indices: 3634035--3634068 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3634025 TTTTTTGAAT
3634035 TATTTTTATTTAAAAA
1 TATTTTTATTTAAAAA
3634051 TATTTTT-TTTAAAAA
1 TATTTTTATTTAAAAA
3634066 TAT
1 TAT
3634069 AATACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTATTTAAAAA
Found at i:3634618 original size:54 final size:53
Alignment explanation
Indices: 3634531--3634687 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 53
3634521 TTTTATACAA
*
3634531 GCAAGTCCTTCAACTCAAGAACTCTTTCCATTCATCTTGTGATCACAGGCGCAG
1 GCAAGTCCTTCAACTC-AGAACTCTTTCCATTCATCTTGTGATCACAGGCACAG
* *
3634585 GCAACTCCTTCAACTCAGAAGCTCTTTCCATTCACCTTGTGATCACAGGCACAG
1 GCAAGTCCTTCAACTCAGAA-CTCTTTCCATTCATCTTGTGATCACAGGCACAG
* * *
3634639 GCAAGTCCTTCAAGTCAAAAACTCTTTCCATTCATCATGTGATCACAGG
1 GCAAGTCCTTCAACTC-AGAACTCTTTCCATTCATCTTGTGATCACAGG
3634688 ACAAGATAAC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
53 4 0.04
54 86 0.92
55 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (53 bp):
GCAAGTCCTTCAACTCAGAACTCTTTCCATTCATCTTGTGATCACAGGCACAG
Found at i:3636262 original size:24 final size:24
Alignment explanation
Indices: 3636200--3636271 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
3636190 AGAAAATTTT
3636200 TAAATTTTTAAATTTTTTT--ATA
1 TAAATTTTTAAATTTTTTTAAATA
3636222 T--ATTCTTTAGAATTTTTTTTAAATA
1 TAAATT-TTTA-AA-TTTTTTTAAATA
*
3636247 TAAATTTTTAAATTTTTATAAATA
1 TAAATTTTTAAATTTTTTTAAATA
3636271 T
1 T
3636272 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.07
21 4 0.10
22 3 0.07
23 7 0.17
24 12 0.29
25 6 0.14
26 4 0.10
27 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (24 bp):
TAAATTTTTAAATTTTTTTAAATA
Found at i:3636275 original size:20 final size:20
Alignment explanation
Indices: 3636203--3636285 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 20
3636193 AAATTTTTAA
* *
3636203 ATTTTTAAATTTTTTTATAT
1 ATTTTTAAATTTTTATAAAT
*
3636223 ATTCTTTAGAATTTTTTTTAAATAT
1 ATT-TTTA-AA-TTTTTAT-AA-AT
3636248 AAATTTTTAAATTTTTATAAAT
1 --ATTTTTAAATTTTTATAAAT
3636270 ATTTTTAAATTTTTAT
1 ATTTTTAAATTTTTAT
3636286 TGAGAGAGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
20 19 0.35
21 4 0.07
22 4 0.07
23 9 0.17
24 7 0.13
25 4 0.07
26 4 0.07
27 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (20 bp):
ATTTTTAAATTTTTATAAAT
Found at i:3639434 original size:53 final size:53
Alignment explanation
Indices: 3639365--3639472 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
3639355 CATTCGGGCA
3639365 TTGCTTTTATGAGCTCCTTGATGTGGTGGAGGAATCTTTGCGATATCTTACTG
1 TTGCTTTTATGAGCTCCTTGATGTGGTGGAGGAATCTTTGCGATATCTTACTG
*
3639418 TTGCTTTTATGAGCTCCTTGATGTGGTGGAGGAATCTTTGTGATATCTTACTG
1 TTGCTTTTATGAGCTCCTTGATGTGGTGGAGGAATCTTTGCGATATCTTACTG
3639471 TT
1 TT
3639473 TAGCACTTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.44
Consensus pattern (53 bp):
TTGCTTTTATGAGCTCCTTGATGTGGTGGAGGAATCTTTGCGATATCTTACTG
Found at i:3642205 original size:173 final size:172
Alignment explanation
Indices: 3641848--3642222 Score: 389
Period size: 173 Copynumber: 2.2 Consensus size: 172
3641838 TTAAAGGCAG
* * *
3641848 CCTAAACACCATTGACAACCAAACCAAAACATGAACTTAGTTGATCAAAGAGGCCTAGCAACAAC
1 CCTAAATACCATTGACAACCAAACCAAAACATGAACTTAGTTGATCAAAAAGGCCTAACAACAAC
* * * ** ** * *** *
3641913 CCGAATATGTTAAGCCAAACCCCATCAAATTCGGCTTTGTATAGCATATTGTTATCAAGAATAAG
66 CCAAACATGTTAAACCAAACCCCATCAAATTCAACTTCATATAACATATTACCAACAAGAATAAG
* *** * *
3641978 AATATTTTTTTCATTTAAACCAAAGAAACAATAAATAGGGCAG
131 AATA-TTATTTCACCAAAACCAAAGAAACAATAAATAGAGCAA
*
3642021 CCTAAATACCATTGACAACCAAACCAAAACATGAACTTAGTTGATCAAAAAGGTCTAACAACAAC
1 CCTAAATACCATTGACAACCAAACCAAAACATGAACTTAGTTGATCAAAAAGGCCTAACAACAAC
**
3642086 CCAAACATGTTAAACCAAACCCGCATCGGATTCAAACTTCATATAACATATTACCAACAAGAATT
66 CCAAACATGTTAAACCAAACCC-CATCAAATTC-AACTTCATATAACATATTACCAACAAGAA-T
* * *
3642151 CA-AATCA-TATTTCACCAAAATCGAAGAAACAA-AAATCA-AGCAA
128 AAGAAT-ATTATTTCACCAAAACCAAAGAAACAATAAAT-AGAGCAA
* * *
3642194 CCTAGATACCATTTGGCAATCAAACCAAA
1 CCTAAATACCA-TTGACAACCAAACCAAA
3642223 GCTGGCATCC
Statistics
Matches: 166, Mismatches: 30, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
173 97 0.58
174 43 0.26
175 23 0.14
176 3 0.02
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.22
Consensus pattern (172 bp):
CCTAAATACCATTGACAACCAAACCAAAACATGAACTTAGTTGATCAAAAAGGCCTAACAACAAC
CCAAACATGTTAAACCAAACCCCATCAAATTCAACTTCATATAACATATTACCAACAAGAATAAG
AATATTATTTCACCAAAACCAAAGAAACAATAAATAGAGCAA
Found at i:3643604 original size:17 final size:19
Alignment explanation
Indices: 3643572--3643606 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3643562 GAATTAAATA
3643572 ACTTAATTTCAACTAGTTT
1 ACTTAATTTCAACTAGTTT
3643591 ACTTAA-TT-AACTAGTT
1 ACTTAATTTCAACTAGTT
3643607 AAGCTCACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (19 bp):
ACTTAATTTCAACTAGTTT
Found at i:3645626 original size:21 final size:19
Alignment explanation
Indices: 3645569--3645627 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 19
3645559 TTTAAAAACA
*
3645569 TAATTGAGTGAAATATATGAT
1 TAATT-AGT-AAATATATTAT
3645590 TAATT-GTAAA-ACTATTAT
1 TAATTAGTAAATA-TATTAT
3645608 TGAATTAGTCAAATATATTA
1 T-AATTAGT-AAATATATTA
3645628 ATGTATTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 1 0.03
18 9 0.28
19 6 0.19
20 2 0.06
21 13 0.41
22 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (19 bp):
TAATTAGTAAATATATTAT
Found at i:3645851 original size:2 final size:2
Alignment explanation
Indices: 3645844--3645869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3645834 TCGACTACAA
3645844 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3645870 TAATCTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3650255 original size:16 final size:18
Alignment explanation
Indices: 3650234--3650272 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3650224 TGTTGATAAT
*
3650234 TTAAAAA-A-TATATGGA
1 TTAAAAATATTATATAGA
3650250 TTAAAAATATTATATAGA
1 TTAAAAATATTATATAGA
3650268 TTAAA
1 TTAAA
3650273 TTCATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (18 bp):
TTAAAAATATTATATAGA
Found at i:3662298 original size:18 final size:18
Alignment explanation
Indices: 3662275--3662313 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3662265 ACGGTATTGT
*
3662275 TAATTTTATCTCATCTAC
1 TAATTTCATCTCATCTAC
3662293 TAATTTCATCTCATCTAC
1 TAATTTCATCTCATCTAC
3662311 TAA
1 TAA
3662314 CGGCACGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTCATCTCATCTAC
Found at i:3662444 original size:18 final size:18
Alignment explanation
Indices: 3662418--3662455 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3662408 AGATTGAGTT
3662418 TTAAATATTAATTATATA
1 TTAAATATTAATTATATA
*
3662436 TTAATTATTAATTATATA
1 TTAAATATTAATTATATA
3662454 TT
1 TT
3662456 TATATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATATTAATTATATA
Found at i:3662566 original size:16 final size:17
Alignment explanation
Indices: 3662547--3662586 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3662537 TTTTTAATGT
*
3662547 ATTAATTTTTATA-AAA
1 ATTAATTTTTAAATAAA
3662563 ATTAA-TTTTAAATAAA
1 ATTAATTTTTAAATAAA
3662579 ATTAATTT
1 ATTAATTT
3662587 GAACAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATTTTTAAATAAA
Found at i:3662933 original size:18 final size:18
Alignment explanation
Indices: 3662910--3662945 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3662900 ATTTTGAGAG
3662910 TTAATTTTTTAAAATGAC
1 TTAATTTTTTAAAATGAC
3662928 TTAATTTTTTAAAATGAC
1 TTAATTTTTTAAAATGAC
3662946 AAATAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TTAATTTTTTAAAATGAC
Found at i:3667089 original size:18 final size:18
Alignment explanation
Indices: 3667066--3667113 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3667056 AAAATGTGAG
* *
3667066 AAATGATGTTCGCATTTT
1 AAATGATGTTCACATTTC
3667084 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
3667102 AAATGATGTTCA
1 AAATGATGTTCA
3667114 AATTGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:3667637 original size:72 final size:71
Alignment explanation
Indices: 3667550--3667708 Score: 221
Period size: 72 Copynumber: 2.2 Consensus size: 71
3667540 AACTAGTTTA
* * * *
3667550 ATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATCTAT-GTGTAAT
1 ATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTATCTATACT-AAAT
3667614 CTACTTTT
65 -TACTTTT
* * *
3667622 ATTAATAGTTGTTTATGTTTGGTCTTTGGTTATTGAATTTATGTTCTACTTATTTATACTAAATT
1 ATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTATCTATACTAAATT
*
3667687 AGTTTT
66 ACTTTT
3667693 ATCAATAGTTGTTTAT
1 ATCAATAGTTGTTTAT
3667709 ATATGATTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
71 21 0.27
72 55 0.71
73 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (71 bp):
ATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTATCTATACTAAATT
ACTTTT
Found at i:3674455 original size:228 final size:228
Alignment explanation
Indices: 3673978--3675312 Score: 1042
Period size: 228 Copynumber: 5.9 Consensus size: 228
3673968 ATGCAGTGTG
* * * * * * * * *
3673978 GACTCCTTCTGGATATTGTAATCAGCTAGAGTTCGACCATCCTCCAA-CTCCTTCCCAGCAAATA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCAT-CTTCAAGCTGCTTTCCAGCAAAAA
* * * * * * *
3674042 TCAACCTCTGCTGGTCTGGTGGAATCCCCTCCTTGTCCTGAATCTTCGCTTTCACATTGTCGATT
65 TCAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATT
* * * * * * * * * *
3674107 GTGTCCGAGCTCTCGAACTCCAGGGTGATGGTTTTCCCAGTCAAGGTCTTCACGAATATCTGCAT
130 GTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCTGCAT
* * * * * *
3674172 CCCCCCTCTAAGTCGCAAA-ACCAAATGCAGGGTC
195 CCCACCACGAAGACG-AAACACCAAATGGAGGGTA
* * * ** * *
3674206 GATTCCTTT-TGGATGTTATAATCCGCAAGTGTCCTCCCATCCTCGAGCTGCTTTCCAGCAAAAA
1 GACT-CTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAA
* * *
3674270 TCAACCTCTGCTGGTCAGGTGGGATACCC-TCCTTATCTTGGATCTTGGCCTTCACATTATCAAT
65 TCAACCTCTGCTGGTCTGGTGGGAT-CCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * *
3674334 TGTGTCTGAGCTCTCCACCTCCAATGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCTGCA
129 TGTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCTGCA
* * * * * * *
3674399 TTCCACCACGCAGTCGGAGCACCAAGTGAAGGGTA
194 TCCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * * *
3674434 GACTCTTTCTGGATATTATAATCTGCAAGTGTCCTACCATCTTCGAGCTG-TTTGCCAGCAAAAA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTT-CCAGCAAAAA
* * * * * * *
3674498 TCAACCTCTGCTGATCTGGTGGAATCCCTTCCTTGTCCTGGATCTTAGCTTTTACATTGTCAATG
65 TCAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATT
* * * * * * * * *
3674563 GTGTCAGAACTCTCAACTTCCAAAGTAATAGTCTTT-CCGGTGAGAGTCTTCACAAAAATTTGCA
130 GTGTCAGAACTCTCCACCTCCAAGGTGATAGT-TTTCCCAGTCAAAGTTTTCACAAAAATCTGCA
* * * *
3674627 TGCCACCACGGAGACGTAACACCAAATGGAGGGTC
194 TCCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * *
3674662 GATTCCTTCTGAATGTTATAGTCCGCAAGAGTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAAT
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAAT
* * * * *
3674727 CAACCTCTGCTGGTCCGGTGGGATCCCTTCCTTATCCTGAATCTTGGCCTTAACATTATCAATCG
66 CAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATTG
* * * * * ** *
3674792 TATCAGAACTCTCCACCTCCAACGTAATAGTTTTTCCAGTGAGGGTTTTTACAAAAATCTGCATC
131 TGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCTGCATC
* * ** *
3674857 CCACCCCTAAGACGAAGGA-CAAGGTGGAGGGTA
196 CCACCACGAAGACGAAACACCAA-ATGGAGGGTA
* * * *
3674890 GACTCTTTCTGGATGTTGTAATCCGCAAGAGTTCGGCCATCTTCAAGCTG-TTTACCGGCAAAGA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTT-CCAGCAAAAA
* * *
3674954 T-AAGCCTCTGTTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCAAT
65 TCAA-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * * * * * * * *
3675018 TGTATCAGAACTTTCCACCTCGAGGGTGATGGTCTTGCCAGT-AAGAGTTTTCACGAATATCTGC
129 TGTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTCCCAGTCAA-AGTTTTCACAAAAATCTGC
* * ** * * ** *
3675082 ATGCCACCCCTTAGACGAAGCACTAGGTGGAGGGTG
193 ATCCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * * * * * * *
3675118 GACTCCTTT-TGGATATTGTAGTCAGCAAGAGTTCGGCCATCCTCAAGTTGTTTTCCGGCAAAGA
1 GACT-CTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAA
* * * * * * * * * * *
3675182 T-AAGCCTTTGTTGGTCAGGAGGAATCCCTTCTTTGTCTTGGATTTTAGCCTTGACATTATCGAT
65 TCAA-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * * * * * * * *
3675246 AGTATCAGAACTTTCTACCT-CAAGGGTGATGGTCTTACCAGT-AAGGGTTTTCACAAAGATCTG
129 TGTGTCAGAACTCTCCACCTCCAA-GGTGATAGTTTTCCCAGTCAA-AGTTTTCACAAAAATCTG
3675309 CATC
192 CATC
3675313 TGCTGTCAAC
Statistics
Matches: 916, Mismatches: 173, Indels: 36
0.81 0.15 0.03
Matches are distributed among these distances:
227 27 0.03
228 869 0.95
229 20 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (228 bp):
GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAAT
CAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATTG
TGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCTGCATC
CCACCACGAAGACGAAACACCAAATGGAGGGTA
Found at i:3674806 original size:456 final size:453
Alignment explanation
Indices: 3673945--3675312 Score: 1357
Period size: 456 Copynumber: 3.0 Consensus size: 453
3673935 CAATTAGAAA
* * * * * * * * * * *
3673945 CCACCACGGAGGCGAAGGACAAGATGCAGTGTGGACTCCTTCTGGATATTGTAATCAGCTAGAGT
1 CCACCACGAAGACGAAGCACAAGGTGAAGGGTAGACTCTTTCTGGATATTATAATCCGCAAGAGT
* * ** * * *
3674010 TCGACCATCCTCCAA-CTCCTTCCCAGCAAATATCAACCTCTGCTGGTCTGGTGGAATCCCCTCC
66 CCGACCAT-CTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCC
* * * * *
3674074 TTGTCCTGAATCTTCGCTTTCACATTGTCGATTGTGTCCGAGCTCTCGAACTCCAGGGTGATGGT
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTC-AACTCCAGGGTGATGGT
* * * * * *
3674139 -TTTCCCAGTCAAG-GTCTTCACGAATATCTGCATCCCCCCTCTAAGTCGCAAAACCAAATGCAG
194 CTTT-CCAGT-AAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACG-AACACCAAATGGAG
* * * ** *
3674202 GGTCGATTCCTTTTGGATGTTATAATCCGCAAGTGTCCTCCCATCCTCGAGCTGCTTTCCAGCAA
256 GGTCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCAAGCTGCTTTCCAGCAA
*
3674267 AAATCAACCTCTGCTGGTCAGGTGGGATACCC-TCCTTATCTTGGATCTTGGCCTTCACATTATC
321 AAATCAACCTCTGCTGGTCAGGTGGGAT-CCCTTCCTTATCTTGGATCTTGGCCTTAACATTATC
* * * * * * *
3674331 AATTGTGTCTGAGCTCTCCACCTCCAATGTGATAGTTTTCCCAGTCAAAGTTTTCACAAAAATCT
385 AATAGTATCAGAACTCTCCACCTCCAACGTGATAGTTTTACCAGT-AAGGTTTTCACAAAAATCT
*
3674396 GCATT
449 GCATC
* * * * *
3674401 CCACCACGCAGTCGGAGCACCAA-GTGAAGGGTAGACTCTTTCTGGATATTATAATCTGCAAGTG
1 CCACCACGAAGACGAAGCA-CAAGGTGAAGGGTAGACTCTTTCTGGATATTATAATCCGCAAGAG
* * * *
3674465 TCCTACCATCTTCGAGCTGTTTGCCAGCAAAAATCAACCTCTGCTGATCTGGTGGAATCCCTTCC
65 TCCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCC
* * ** * *
3674530 TTGTCCTGGATCTTAGCTTTTACATTGTCAATGGTGTCAGAACTCTCAACTTCCAAAGTAATAGT
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTCAAC-TCCAGGGTGATGGT
* * * * * **
3674595 CTTTCCGGTGAGAGTCTTCACAAAAATTTGCATGCCACCACGGAGACGTAACACCAAATGGAGGG
194 CTTTCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACG-AACACCAAATGGAGGG
* * *
3674660 TCGATTCCTTCTGAATGTTATAGTCCGCAAGAGTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAA
258 TCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCAAGCTGCTTTCCAGCAAAA
* * *
3674725 ATCAACCTCTGCTGGTCCGGTGGGATCCCTTCCTTATCCTGAATCTTGGCCTTAACATTATCAAT
323 ATCAACCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAAT
* * * * *
3674790 CGTATCAGAACTCTCCACCTCCAACGTAATAGTTTTTCCAGTGAGGGTTTTTACAAAAATCTGCA
388 AGTATCAGAACTCTCCACCTCCAACGTGATAGTTTTACCAGT-AAGGTTTTCACAAAAATCTGCA
3674855 TC
452 TC
* * * * * *
3674857 CCACCCCTAAGACGAAGGACAAGGTGGAGGGTAGACTCTTTCTGGATGTTGTAATCCGCAAGAGT
1 CCACCACGAAGACGAAGCACAAGGTGAAGGGTAGACTCTTTCTGGATATTATAATCCGCAAGAGT
* * * * * *
3674922 TCGGCCATCTTCAAGCTGTTTACCGGCAAAGAT-AAGCCTCTGTTGGTCTGGTGGGATCCCTTCC
66 CCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAA-CCTCTGCTGGTCTGGTGGAATCCCTTCC
* * * * * * * * *
3674986 TTGTCTTGGATCTTGGCCTTGACATTATCAATTGTATCAGAACTTTCCACCTCGAGGGTGATGGT
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCT-CAACTCCAGGGTGATGGT
* * * * * **
3675051 CTTGCCAGTAAGAGTTTTCACGAATATCTGCATGCCACCCCTTAGACGAAGCACTAGGTGGAGGG
194 CTTTCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACGAA-CACCAAATGGAGGG
* * * * * * * * *
3675116 TGGACTCCTTTTGGATATTGTAGTCAGCAAGAGTTCGGCCATCCTCAAGTTGTTTTCCGGCAAAG
258 TCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCAAGCTGCTTTCCAGCAAAA
* * * * * * * * * *
3675181 AT-AAGCCTTTGTTGGTCAGGAGGAATCCCTTCTTTGTCTTGGATTTTAGCCTTGACATTATCGA
323 ATCAA-CCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAA
* * * * * *
3675245 TAGTATCAGAACTTTCTACCT-CAAGGGTGATGGTCTTACCAGTAAGGGTTTTCACAAAGATCTG
387 TAGTATCAGAACTCTCCACCTCCAA-CGTGATAGTTTTACCAGTAA-GGTTTTCACAAAAATCTG
3675309 CATC
450 CATC
3675313 TGCTGTCAAC
Statistics
Matches: 742, Mismatches: 157, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
455 25 0.03
456 708 0.95
457 9 0.01
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (453 bp):
CCACCACGAAGACGAAGCACAAGGTGAAGGGTAGACTCTTTCTGGATATTATAATCCGCAAGAGT
CCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCCT
TGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTCAACTCCAGGGTGATGGTCT
TTCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACGAACACCAAATGGAGGGTCG
ATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCAAGCTGCTTTCCAGCAAAAATC
AACCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAATAGT
ATCAGAACTCTCCACCTCCAACGTGATAGTTTTACCAGTAAGGTTTTCACAAAAATCTGCATC
Found at i:3679778 original size:228 final size:227
Alignment explanation
Indices: 3679301--3680635 Score: 1036
Period size: 228 Copynumber: 5.9 Consensus size: 227
3679291 ATGCAGTGTG
* * * * * * * * *
3679301 GACTCCTTCTGGATATTGTAATCAGCTAGAGTTCGACCATCCTCCAA-CTCCTTCCCAGCAAATA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCAT-CTTCAAGCTGCTTTCCAGCAAAAA
* * * * * * *
3679365 TCAACCTCTGCTGGTCTGGTGGAATCCCCTCCTTGTCCTGAATCTTCGCTTTCACATTGTCGATT
65 TCAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATT
* * * * * * * * * * *
3679430 GTGTCCGAGCTCTCGAACTCCAGGGTGATGGTTTTCCCAGTCAAGGTCTTCACGAATATCTGCAT
130 GTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGT-AAAGTTTTCACAAAAATCTGCAT
* * * * * *
3679495 CCCCCCTCTAAGTCGCAAA-ACCAAATGCAGGGTC
194 CCCACCACGAAGACG-AAACACCAAATGGAGGGTA
* * * ** * *
3679529 GATTCCTTT-TGGATGTTATAATCCGCAAGTGTCCTCCCATCCTCGAGCTGCTTTCCAGCAAAAA
1 GACT-CTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAA
* * *
3679593 TCAACCTCTGCTGGTCAGGTGGGATACCC-TCCTTATCTTGGATCTTGGCCTTCACATTATCAAT
65 TCAACCTCTGCTGGTCTGGTGGGAT-CCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * *
3679657 TGTGTCTGAGCTCTCCACCTCCAATGTGATAGTTTTTCCAGTCAAAGTTTTCACAAAAATCTGCA
129 TGTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGT-AAAGTTTTCACAAAAATCTGCA
* * * * * * *
3679722 TTCCACCACGCAGTCGGAGCACCAAGTGAAGGGTA
193 TCCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * * *
3679757 GACTCTTTCTGGATATTATAATCTGCAAGTGTCCTACCATCTTCGAGCTG-TTTGCCAGCAAAAA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTT-CCAGCAAAAA
* * * * * * *
3679821 TCAACCTCTGCTGATCTGGTGGAATCCCTTCCTTGTCCTGGATCTTAGCTTTTACATTGTCAATG
65 TCAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATT
* * * * * * * *
3679886 GTGTCAGAACTCTCAACTTCCAAAGTAATAGTCTTTCCGGTAAGAGTCTTCACAAAAATTTGCAT
130 GTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGTAA-AGTTTTCACAAAAATCTGCAT
* * * *
3679951 GCCACCACGGAGACGTAACACCAAATGGAGGGTC
194 CCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * *
3679985 GATTCCTTCTGAATGTTATAGTCCGCAAGAGTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAAT
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAAT
* * * * *
3680050 CAACCTCTGCTGGTCCGGTGGGATCCCTTCCTTATCCTGAATCTTGGCCTTAACATTATCAATCG
66 CAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATTG
* * * ** *
3680115 TATCAGAACTCTCCACCTCCAACGTAATAGTTTTTCCAGTGAGGGTTTTTACAAAAATCTGCATC
131 TGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGT-AAAGTTTTCACAAAAATCTGCATC
* * ** *
3680180 CCACCCCTAAGACGAAGGA-CAAGGTGGAGGGTA
195 CCACCACGAAGACGAAACACCAA-ATGGAGGGTA
* * * *
3680213 GACTCTTTCTGGATGTTGTAATCCGCAAGAGTTCGGCCATCTTCAAGCTG-TTTACCGGCAAAGA
1 GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTT-CCAGCAAAAA
* * *
3680277 T-AAGCCTCTGTTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACATTATCAAT
65 TCAA-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * * * * * * * *
3680341 TGTATCAGAACTTTCCACCTCGAGGGTGATGGTCTTGCCAGTAAGAGTTTTCACGAATATCTGCA
129 TGTGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGTAA-AGTTTTCACAAAAATCTGCA
* * ** ** * ** * *
3680406 TGCCACCCCTTAGACGAAGGACTAGGTGGACGGTG
193 TCCCACCACGAAGACGAAACACCAAATGGAGGGTA
* * * * * * * * * * *
3680441 GACTCCTTT-TGGATATTGTAGTCGGCAAGAGTTCGGCCATCCTCGAGTTGTTTTCCGGCAAAGA
1 GACT-CTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAA
* * * * * * * * * *
3680505 T-AAGCCTTTGTTGGTCAGGAGGGATCCCTTCTTTGTCTTGGATTTTAGCCTTGACATTATCGAT
65 TCAA-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAAT
* * * * * * * * *
3680569 AGTATCAGAACTTTCTACCT-CAAGGGTGATGGTCTTACCAGTAAGGGTTTTCACAAAGATCTGC
129 TGTGTCAGAACTCTCCACCTCCAA-GGTGATAGTTTTTCCAGTAA-AGTTTTCACAAAAATCTGC
3680633 ATC
192 ATC
3680636 TGCTATCAAC
Statistics
Matches: 914, Mismatches: 175, Indels: 36
0.81 0.16 0.03
Matches are distributed among these distances:
227 26 0.03
228 870 0.95
229 18 0.02
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (227 bp):
GACTCTTTCTGGATGTTATAATCCGCAAGAGTTCGACCATCTTCAAGCTGCTTTCCAGCAAAAAT
CAACCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCCTGGATCTTGGCCTTCACATTATCAATTG
TGTCAGAACTCTCCACCTCCAAGGTGATAGTTTTTCCAGTAAAGTTTTCACAAAAATCTGCATCC
CACCACGAAGACGAAACACCAAATGGAGGGTA
Found at i:3680387 original size:456 final size:455
Alignment explanation
Indices: 3679268--3680635 Score: 1404
Period size: 456 Copynumber: 3.0 Consensus size: 455
3679258 CAATTAGAAA
* * * * * * * *
3679268 CCACCACGGAGGCGAAGGACAAGATGCAGTGTGGACTCCTTCTGGATATTGTAATCAGCTAGAGT
1 CCACCACGAAGACGAAGGACAAGGTGAAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGAGT
* ** * * *
3679333 TCGACCATCCTCCAA-CTCCTTCCCAGCAAATATCAACCTCTGCTGGTCTGGTGGAATCCCCTCC
66 TCGACCAT-CTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCC
* * * * *
3679397 TTGTCCTGAATCTTCGCTTTCACATTGTCGATTGTGTCCGAGCTCTCGAA-CTCCAGGGTGATGG
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTC-AACCTCCAGGGTGATGG
* * * * * *
3679461 TTTTCCCAGTCAAG-GTCTTCACGAATATCTGCATCCCCCCTCTAAGTCGCAAAACCAAATGCAG
194 TCTTCCCAGT-AAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACG-AAAACCAAATGGAG
* * * **
3679525 GGTCGATTCCTTTTGGATGTTATAATCCGCAAGTGTCCTCCCATCCTCGAGCTGCTTTCCAGCAA
257 GGTCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCGAGCTGCTTTCCAGCAA
*
3679590 AAATCAACCTCTGCTGGTCAGGTGGGATACCC-TCCTTATCTTGGATCTTGGCCTTCACATTATC
322 AAATCAACCTCTGCTGGTCAGGTGGGAT-CCCTTCCTTATCTTGGATCTTGGCCTTAACATTATC
* * * * * *
3679654 AATTGTGTCTGAGCTCTCCACCTCCAATGTGATAGTTTTTCCAGTCAA-AGTTTTCACAAAAATC
386 AATAGTATCAGAACTCTCCACCTCCAACGTGATAGTTTTTCCAGT-AAGGGTTTTCACAAAAATC
*
3679718 TGCATT
450 TGCATC
* * * * * * *
3679724 CCACCACGCAGTCGGAGCACCAA-GTGAAGGGTAGACTCTTTCTGGATATTATAATCTGCAAGTG
1 CCACCACGAAGACGAAGGA-CAAGGTGAAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGAG
* * * * *
3679788 TCCTACCATCTTCGAGCTGTTTGCCAGCAAAAATCAACCTCTGCTGATCTGGTGGAATCCCTTCC
65 TTCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCC
* * * ** * *
3679853 TTGTCCTGGATCTTAGCTTTTACATTGTCAATGGTGTCAGAACTCTCAACTTCCAAAGTAATAGT
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTCAACCTCCAGGGTGATGGT
* * * * * ** *
3679918 CTTTCCGGTAAGAGTCTTCACAAAAATTTGCATGCCACCACGGAGACGTAACACCAAATGGAGGG
195 CTTCCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACG-AAAACCAAATGGAGGG
* * * *
3679983 TCGATTCCTTCTGAATGTTATAGTCCGCAAGAGTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAA
259 TCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCGAGCTGCTTTCCAGCAAAA
* * *
3680048 ATCAACCTCTGCTGGTCCGGTGGGATCCCTTCCTTATCCTGAATCTTGGCCTTAACATTATCAAT
324 ATCAACCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAAT
* * * *
3680113 CGTATCAGAACTCTCCACCTCCAACGTAATAGTTTTTCCAGTGAGGGTTTTTACAAAAATCTGCA
389 AGTATCAGAACTCTCCACCTCCAACGTGATAGTTTTTCCAGTAAGGGTTTTCACAAAAATCTGCA
3680178 TC
454 TC
* * * * *
3680180 CCACCCCTAAGACGAAGGACAAGGTGGAGGGTAGACTCTTTCTGGATGTTGTAATCCGCAAGAGT
1 CCACCACGAAGACGAAGGACAAGGTGAAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGAGT
* * * * *
3680245 TCGGCCATCTTCAAGCTGTTTACCGGCAAAGAT-AAGCCTCTGTTGGTCTGGTGGGATCCCTTCC
66 TCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAA-CCTCTGCTGGTCTGGTGGAATCCCTTCC
* * * * * * * * *
3680309 TTGTCTTGGATCTTGGCCTTGACATTATCAATTGTATCAGAACTTTCCACCTCGAGGGTGATGGT
130 TTGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTCAACCTCCAGGGTGATGGT
* * * * * * ** *
3680374 CTTGCCAGTAAGAGTTTTCACGAATATCTGCATGCCACCCCTTAGACGAAGGACTAGGTGGACGG
195 CTTCCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACGAA-AACCAAATGGAGGG
* * * * * * * * *
3680439 TGGACTCCTTTTGGATATTGTAGTCGGCAAGAGTTCGGCCATCCTCGAGTTGTTTTCCGGCAAAG
259 TCGATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCGAGCTGCTTTCCAGCAAAA
* * * * * * * * *
3680504 AT-AAGCCTTTGTTGGTCAGGAGGGATCCCTTCTTTGTCTTGGATTTTAGCCTTGACATTATCGA
324 ATCAA-CCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAA
* * * * * * *
3680568 TAGTATCAGAACTTTCTACCT-CAAGGGTGATGGTCTTACCAGTAAGGGTTTTCACAAAGATCTG
388 TAGTATCAGAACTCTCCACCTCCAA-CGTGATAGTTTTTCCAGTAAGGGTTTTCACAAAAATCTG
3680632 CATC
452 CATC
3680636 TGCTATCAAC
Statistics
Matches: 742, Mismatches: 159, Indels: 22
0.80 0.17 0.02
Matches are distributed among these distances:
455 25 0.03
456 714 0.96
457 3 0.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (455 bp):
CCACCACGAAGACGAAGGACAAGGTGAAGGGTAGACTCTTTCTGGATATTGTAATCAGCAAGAGT
TCGACCATCTTCAAGCTGTTTACCAGCAAAAATCAACCTCTGCTGGTCTGGTGGAATCCCTTCCT
TGTCCTGGATCTTAGCTTTCACATTGTCAATTGTGTCAGAACTCTCAACCTCCAGGGTGATGGTC
TTCCCAGTAAGAGTCTTCACGAATATCTGCATGCCACCACTAAGACGAAAACCAAATGGAGGGTC
GATTCCTTTTGGATGTTATAGTCCGCAAGAGTTCGGCCATCCTCGAGCTGCTTTCCAGCAAAAAT
CAACCTCTGCTGGTCAGGTGGGATCCCTTCCTTATCTTGGATCTTGGCCTTAACATTATCAATAG
TATCAGAACTCTCCACCTCCAACGTGATAGTTTTTCCAGTAAGGGTTTTCACAAAAATCTGCATC
Found at i:3683186 original size:56 final size:56
Alignment explanation
Indices: 3683119--3683226 Score: 216
Period size: 56 Copynumber: 1.9 Consensus size: 56
3683109 AATAAAATAG
3683119 CATAAAGATAATAATAAAATATTCCACCAATCATATTTCAACAGCAAATATTTTAA
1 CATAAAGATAATAATAAAATATTCCACCAATCATATTTCAACAGCAAATATTTTAA
3683175 CATAAAGATAATAATAAAATATTCCACCAATCATATTTCAACAGCAAATATT
1 CATAAAGATAATAATAAAATATTCCACCAATCATATTTCAACAGCAAATATT
3683227 CATACTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.30
Consensus pattern (56 bp):
CATAAAGATAATAATAAAATATTCCACCAATCATATTTCAACAGCAAATATTTTAA
Found at i:3686163 original size:228 final size:228
Alignment explanation
Indices: 3685800--3687097 Score: 1059
Period size: 228 Copynumber: 5.7 Consensus size: 228
3685790 TAAAGTTCGA
* * *
3685800 CCATCCTCCAA-CTGCTTTCCAGCAAAGATCAACCTCTGCTGGTCCGGAGGAATCCCCTCCTTGT
1 CCATCCT-CAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGT
* * * * * * * *
3685864 CCTGAATCTTAGATTTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGGGTGATGGTTTTC
65 CCTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTA
* * * *
3685929 CCAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCTAAGGCGCAAAACCAAATGCAGGGTGGA
130 CCAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTTGA
* *
3685994 TTCCTTTTGGATGTTATAGTCCGCAAGCGTCCTC
195 CTCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
* *
3686028 CCATCCTCAAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGTCTGGAGGAATTCCCTCCTTGTC
1 CCATCCTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * *
3686093 CTGAATCTTCGCTTTAACATTGTCAATGGTGTCCGAGCTCTCGACCTCCAGTGTTACGGTTTTAC
66 CTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTAC
* * *
3686158 CAGTCAGGGTCTTAACGAATATCTGCATCCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTTGAC
131 CAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTTGAC
*
3686223 TCCTTTTGGATGTTATAATCCGCAAGAGTCCTC
196 TCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
* * * * *
3686256 CCATCCTCGAGTTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCAGGTGGGATACCCTCCTTGTC
1 CCATCCTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * * * * * * * *
3686321 TTGGATCTT-GGTCTTCACGTTATCAATTGTGTCTGAGCTCTCCACCTCCAATGTAATAGTTTTT
66 CTGAATCTTCGCT-TTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTA
* * * * * * * * *
3686385 CCAGTCAAAGTTTTCACAAAAATCTGCATTCCACCACGCAGTCGCAGCACCAAGTGCAGGGTTGA
130 CCAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTTGA
3686450 CTCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
195 CTCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
* * * * *
3686484 CCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGATCTGGTGGGATACCCTCCTTGTC
1 CCATCCTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
* * * * ** * *
3686549 CTGAATCTTCGCCTTAACATTATCAATGGTATCAGAACTCTCCACCTCCAAAGTGATGGTTTTTC
66 CTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTAC
* * * * * * * * * * * * * *
3686614 CGGTGAGGGTTTTTACAAATATCTGCATCCCACCCCGAAGACGAAGGA-CAAGGTGGAGGGTAGA
131 CAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAA-GTGCAGGGTTGA
* * * * * **
3686678 CT-CTTTCTGGATGTTGTAATCAGCGAGGGTTCGG
195 CTCCTTT-TGGATGTTATAATCCGCAAGCGTCCTC
* * * * * * *
3686712 CCATCTTCAAGTTG-TTTACCTGCAAAGAT-AAGCCTCTGTTGGTCTAGAGGGAT-CCCTTCCTT
1 CCATCCTCAAGCTGCTTT-CCAGCAAAAATCAA-CCTCTGCTGGTCTGGAGGAATACCC-TCCTT
* * * * * * * * * * * * * *
3686774 GTCTTGGATCTTGGCCTTGACATTATCAATCGTATCAGAACTTTCCACCTCGAGGGTGATGGTCT
63 GTCCTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTT
* * * * * * * ** * * * * * *
3686839 TGCCCGT-AAGGGTTTTCACAAATATCTGCATGCCACCCCTTAGACGAAGGACTAGGTGGAGGGT
128 TACCAGTCAA-GGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGT
* * * * * * **
3686903 GGACTCCTTTTGGATGTTGTAGTCGGCAAGAGTTCGG
192 TGACTCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
* * * * * * * *
3686940 CCATCCTCGAGTTGTTTTCCGGCAAAAAT-AAGCCTCTGTTGGTCTGGAGGAATGCCTTCTTTGT
1 CCATCCTCAAGCTGCTTTCCAGCAAAAATCAA-CCTCTGCTGGTCTGGAGGAATACCCTCCTTGT
* * * * * * * * * * * * *
3687004 CTTGGATTTTGGCCTTGACATTATCAATAGTATCGGAGCTTTCCACCTCAAGGGTGATGGTTTTA
65 CCTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTA
* * *
3687069 CCAGT-AAGGGTTTTCACAAAGATCTGCAT
130 CCAGTCAA-GGTCTTCACGAATATCTGCAT
3687098 CTGCTCCCAA
Statistics
Matches: 912, Mismatches: 145, Indels: 26
0.84 0.13 0.02
Matches are distributed among these distances:
227 21 0.02
228 880 0.96
229 11 0.01
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (228 bp):
CCATCCTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCTGGAGGAATACCCTCCTTGTC
CTGAATCTTCGCTTTAACATTATCAATGGTGTCCGAGCTCTCCACCTCCAGTGTAATGGTTTTAC
CAGTCAAGGTCTTCACGAATATCTGCATTCCTCCTCGAAGGCGCAGAACCAAGTGCAGGGTTGAC
TCCTTTTGGATGTTATAATCCGCAAGCGTCCTC
Found at i:3686691 original size:456 final size:455
Alignment explanation
Indices: 3685812--3687098 Score: 1388
Period size: 456 Copynumber: 2.8 Consensus size: 455
3685802 ATCCTCCAAC
* * * * *
3685812 TGCTTTCCAGCAAAGATCAACCTCTGCTGGTCCGGAGGAATCCCCTCCTTGTCCTGAATCTTAGA
1 TGCTTTCCAGCAAAGATCAACCTCTGCTGGTCAGGAGGGAT-CCCTCCTTGTCTTGGATCTT-GG
* * *
3685877 T-TTCACATTGTCAATCGTGTCCGAGCTCTCCACCTCCAGGGTGATGGTTTTCCCAGTCAAGGTC
64 TCTTCACATTATCAATCGTGTCAGAGCTCTCCACCTCCAGGGTGATGGTTTTCCCAGTCAAGGTT
* * * * * * *
3685941 TTCACGAATATCTGCATTCCTCCTCTAAGGCGCAAAACCAAATGCAGGGTGGATTCCTTTTGGAT
129 TTCACAAATATCTGCATTCCACCACTAAGACGCAGAACCAAGTGCAGGGTGGACTCCTTTTGGAT
*
3686006 GTTATAGTCCGCAAGCGTCCTCCCATCCTCAAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGT
194 GTTATAGTCCGCAAGCGTCCTCCCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGT
* * * * * *
3686071 CTGGAGGAATTCCCTCCTTGTCCTGAATCTTCGCTTTAACATTGTCAATGGTGTCCGAGCTCTCG
259 CTGGAGGAATACCCTCCTTGTCCTGAATCTTCGCCTTAACATTATCAATGGTATCAGAGCTCTCC
** * * * * * * * *
3686136 ACCTCCAGTGTTACGGTTTTACCAGTCAGGGTCTTAACGAATATCTGCATCCCTCCTCGAAGGCG
324 ACCTCCAAAGTGATGGTTTTACCAGTAAGGGTTTTAACAAATATCTGCATCCCACCCCGAAGACG
* * * * *
3686201 CAGAACCAAGTGCAGGGTTGACTCCTTTTGGATGTTATAATCCGCAAGAGTCCTCCCATCCTCGA
389 AAGAACCAAGTGCAGGGTAGACTCCTTTTGGATGTTATAATCAGCAAGAGTCCGCCCATCCTCAA
3686266 GT
454 GT
* *
3686268 TGCTTTCCAGCAAAAATCAACCTCTGCTGGTCAGGTGGGATACCCTCCTTGTCTTGGATCTTGGT
1 TGCTTTCCAGCAAAGATCAACCTCTGCTGGTCAGGAGGGAT-CCCTCCTTGTCTTGGATCTTGGT
* * * ** * * * *
3686333 CTTCACGTTATCAATTGTGTCTGAGCTCTCCACCTCCAATGTAATAGTTTTTCCAGTCAAAGTTT
65 CTTCACATTATCAATCGTGTCAGAGCTCTCCACCTCCAGGGTGATGGTTTTCCCAGTCAAGGTTT
* ** * * *
3686398 TCACAAAAATCTGCATTCCACCACGCAGTCGCAGCACCAAGTGCAGGGTTGACTCCTTTTGGATG
130 TCACAAATATCTGCATTCCACCACTAAGACGCAGAACCAAGTGCAGGGTGGACTCCTTTTGGATG
* *
3686463 TTATAATCCGCAAGCGTCCTCCCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGATC
195 TTATAGTCCGCAAGCGTCCTCCCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGTC
* * *
3686528 TGGTGGGATACCCTCCTTGTCCTGAATCTTCGCCTTAACATTATCAATGGTATCAGAACTCTCCA
260 TGGAGGAATACCCTCCTTGTCCTGAATCTTCGCCTTAACATTATCAATGGTATCAGAGCTCTCCA
* * * *
3686593 CCTCCAAAGTGATGGTTTTTCCGGTGAGGGTTTTTACAAATATCTGCATCCCACCCCGAAGACGA
325 CCTCCAAAGTGATGGTTTTACCAGTAAGGGTTTTAACAAATATCTGCATCCCACCCCGAAGACGA
* * * * * * * *
3686658 AGGA-CAAGGTGGAGGGTAGACT-CTTTCTGGATGTTGTAATCAGCGAGGGTTCGGCCATCTTCA
390 AGAACCAA-GTGCAGGGTAGACTCCTTT-TGGATGTTATAATCAGCAAGAGTCCGCCCATCCTCA
3686721 AGT
453 AGT
* *
3686724 TG-TTTACCTGCAAAGAT-AAGCCTCTGTTGGTCTA-GAGGGATCCCTTCCTTGTCTTGGATCTT
1 TGCTTT-CCAGCAAAGATCAA-CCTCTGCTGGTC-AGGAGGGATCCC-TCCTTGTCTTGGATCTT
* * * * * * *
3686786 GGCCTTGACATTATCAATCGTATCAGAACTTTCCACCTCGAGGGTGATGGTCTTGCCC-GT-AAG
62 GGTCTTCACATTATCAATCGTGTCAGAGCTCTCCACCTCCAGGGTGATGGT-TTTCCCAGTCAA-
* * * * * * * *
3686849 GGTTTTCACAAATATCTGCATGCCACCCCTTAGACGAAGGACTAGGTGGAGGGTGGACTCCTTTT
125 GGTTTTCACAAATATCTGCATTCCACCACTAAGACGCAGAACCAAGTGCAGGGTGGACTCCTTTT
* * * * ** * *
3686914 GGATGTTGTAGTCGGCAAGAGTTCGGCCATCCTCGAGTTGTTTTCCGGCAAAAAT-AAGCCTCTG
190 GGATGTTATAGTCCGCAAGCGTCCTCCCATCCTCGAGCTGCTTTCCGGCAAAAATCAA-CCTCTG
* * * * * * * * * * *
3686978 TTGGTCTGGAGGAATGCCTTCTTTGTCTTGGATTTTGGCCTTGACATTATCAATAGTATCGGAGC
254 CTGGTCTGGAGGAATACCCTCCTTGTCCTGAATCTTCGCCTTAACATTATCAATGGTATCAGAGC
* * * *
3687043 TTTCCACCT-CAAGGGTGATGGTTTTACCAGTAAGGGTTTTCACAAAGATCTGCATC
319 TCTCCACCTCCAA-AGTGATGGTTTTACCAGTAAGGGTTTTAACAAATATCTGCATC
3687099 TGCTCCCAAC
Statistics
Matches: 688, Mismatches: 132, Indels: 22
0.82 0.16 0.03
Matches are distributed among these distances:
455 24 0.03
456 659 0.96
457 5 0.01
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (455 bp):
TGCTTTCCAGCAAAGATCAACCTCTGCTGGTCAGGAGGGATCCCTCCTTGTCTTGGATCTTGGTC
TTCACATTATCAATCGTGTCAGAGCTCTCCACCTCCAGGGTGATGGTTTTCCCAGTCAAGGTTTT
CACAAATATCTGCATTCCACCACTAAGACGCAGAACCAAGTGCAGGGTGGACTCCTTTTGGATGT
TATAGTCCGCAAGCGTCCTCCCATCCTCGAGCTGCTTTCCGGCAAAAATCAACCTCTGCTGGTCT
GGAGGAATACCCTCCTTGTCCTGAATCTTCGCCTTAACATTATCAATGGTATCAGAGCTCTCCAC
CTCCAAAGTGATGGTTTTACCAGTAAGGGTTTTAACAAATATCTGCATCCCACCCCGAAGACGAA
GAACCAAGTGCAGGGTAGACTCCTTTTGGATGTTATAATCAGCAAGAGTCCGCCCATCCTCAAGT
Found at i:3695132 original size:13 final size:13
Alignment explanation
Indices: 3695114--3695138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3695104 AAACTTCGAG
3695114 TAATTTTGTATAT
1 TAATTTTGTATAT
3695127 TAATTTTGTATA
1 TAATTTTGTATA
3695139 GTTATATTGG
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TAATTTTGTATAT
Found at i:3708086 original size:87 final size:87
Alignment explanation
Indices: 3707988--3708577 Score: 402
Period size: 87 Copynumber: 6.8 Consensus size: 87
3707978 ATCTACTCTG
* * * * *
3707988 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
* *
3708053 ATAGTGTCTTCGATCTGCTCCG
66 ATACTGTCTTCGATCTGCTCCA
*** * *
3708075 CTGTAATCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAA
1 CTGTAATCTCAGGGAGATAAGATCCT-TTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAA
* *
3708139 GAT-CTGAAATTCTT-TAGTCTGTTCCA
65 GATACTG----TCTTCGA-TCTGCTCCA
* ** * * *
3708165 CTGTAATCTCAGGGAAATAAGA-CC--TGGTGCGATCTGCTCTACTGTAACTTCAGGGAGATAAG
1 CTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * * ** *
3708227 ATCCTTTATTTTAATCCGCTCCA
66 ATACTGT-CTTCGATCTGCTCCA
* * ** * * * *
3708250 CTGTAA-CTTTAGGGAGATAGGATAGTGT-CTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATA
1 CTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACT-TCAGGGAGATA
* * *
3708312 AGATCTCTGGCTTCAATCTGCTCCA
64 AGAT-ACTGTCTTCGATCTGCTCCA
* * * * * *
3708337 CTGTGACCTCAGGGAGATAAGAT-CTGAAATTCTTT-AGTCTGTTCCACTGTAA-TCTCAGGGAA
1 CTGTAATCTCAGGGAGATAAGATCCT----TTATTTCAATCTGCTCCACTGTAACT-TCAGGGAG
* * * *
3708399 ATAAGA-CCTG-GTGCGATCTGCTCTA
61 ATAAGATACTGTCTTCGATCTGCTCCA
* * *
3708424 CTGTAA-CTTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAG
1 CTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAA
* *
3708488 GATAGTGTCTTCGATCTGCTCCG
65 GATACTGTCTTCGATCTGCTCCA
*** * *
3708511 CTGTAATCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTGACCTCAGGGAGATAA
1 CTGTAATCTCAGGGAGATAAGATCCT-TTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAA
3708575 GAT
65 GAT
3708578 CTGAAATTCT
Statistics
Matches: 394, Mismatches: 79, Indels: 60
0.74 0.15 0.11
Matches are distributed among these distances:
84 7 0.02
85 52 0.13
86 13 0.03
87 245 0.62
88 12 0.03
89 1 0.00
90 62 0.16
91 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (87 bp):
CTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
ATACTGTCTTCGATCTGCTCCA
Found at i:3708249 original size:131 final size:131
Alignment explanation
Indices: 3708065--3708360 Score: 307
Period size: 131 Copynumber: 2.3 Consensus size: 131
3708055 AGTGTCTTCG
* * *** * **
3708065 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTCTGGCTTCAATCTACTCCACTGTAACCTC
1 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACCTC
*
3708129 AGGGAGATAAGATCTGAAAT-TCTTTAG-TCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-CT
65 AGGGAGATAAGA--T--AATGTC-TTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCT
*
3708190 GG-TGCG
125 GGCTGCA
* * * *
3708196 ATCTGCTCTACTGTAACTTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTTA
1 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACCTCA
* * * * * *
3708261 GGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
66 GGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGCTGC
3708326 A
131 A
*
3708327 ATCTGCTCCACTGTGACCTCAGGGAGATAAGATC
1 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
3708361 TGAAATTCTT
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
127 5 0.04
128 30 0.22
129 2 0.01
130 4 0.03
131 93 0.68
132 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (131 bp):
ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACCTCA
GGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGCTGC
A
Found at i:3708320 original size:218 final size:218
Alignment explanation
Indices: 3707936--3708625 Score: 1256
Period size: 218 Copynumber: 3.2 Consensus size: 218
3707926 TGTTGTGTTC
* * * * * *
3707936 AGTCTATTCCACTG-CATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTGCTGTAACCTCAG
1 AGTCTGTTCCACTGTAATC-TCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAG
*
3708000 AGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
65 GGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
* *
3708065 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTACTCCACTGTAACCTCA
130 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCA
3708130 GGGAGATAAGATCTGAAATTCTTT
195 GGGAGATAAGATCTGAAATTCTTT
3708154 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
1 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
*
3708219 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATAGTGTCTTCGA
66 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
3708284 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
131 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
3708349 GGAGATAAGATCTGAAATTCTTT
196 GGAGATAAGATCTGAAATTCTTT
3708372 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
1 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
3708437 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
66 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
3708502 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
131 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
3708567 GGAGATAAGATCTGAAATTCTTT
196 GGAGATAAGATCTGAAATTCTTT
* *
3708590 AGTCTGTTCCACTGTAATCTCAGGGGAATAGGACCT
1 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCT
3708626 TTTATAATGA
Statistics
Matches: 458, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
218 455 0.99
219 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (218 bp):
AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
GGAGATAAGATCTGAAATTCTTT
Found at i:3708416 original size:131 final size:131
Alignment explanation
Indices: 3708281--3708579 Score: 315
Period size: 131 Copynumber: 2.3 Consensus size: 131
3708271 ATAGTGTCTT
* * * *
3708281 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCACTGTGACC
1 CGATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACC
*
3708345 TCAGGGAGATAAGATCTGAAAT-TCTTTAG-TCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-
65 TCAGGGAGATAAGA--T--AATGTC-TTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCT
3708406 CTGG-TG
125 CTGGCTG
* * * * *
3708412 CGATCTGCTCTACTGTAACTTCAGGGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACC
* * * * *
3708476 TCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGC
65 TCAGGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGC
*
3708541 TT
130 TG
* *
3708543 CAATCTGCTCCACTGTGACCTCAGGGAGATAAGATCT
1 CGATCTGCTCCACTGT-AACTCAGGGAGATAAGATCT
3708580 GAAATTCTTT
Statistics
Matches: 140, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
127 5 0.04
128 30 0.21
129 2 0.01
130 6 0.04
131 95 0.68
132 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (131 bp):
CGATCTGCTCCACTGTAACTCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGCT
G
Found at i:3721424 original size:21 final size:21
Alignment explanation
Indices: 3721382--3721424 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3721372 ACTAATGATA
* *
3721382 ATAAAACTAATTAATTTTAAG
1 ATAAAACTAATTAATCTAAAG
3721403 ATAAAAC-AATTAATACTAAAG
1 ATAAAACTAATTAAT-CTAAAG
3721424 A
1 A
3721425 AACGGGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAAAACTAATTAATCTAAAG
Found at i:3723868 original size:27 final size:27
Alignment explanation
Indices: 3723828--3723882 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3723818 CCACATCCAG
*
3723828 TAAGTTAGGGCACGACATCTCGGACTT
1 TAAGTTAGGACACGACATCTCGGACTT
3723855 TAAGTTAGGACACGACATCTCGGACTT
1 TAAGTTAGGACACGACATCTCGGACTT
3723882 T
1 T
3723883 TGAGAGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (27 bp):
TAAGTTAGGACACGACATCTCGGACTT
Done.