Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 52 of 335
Found at i:18692430 original size:48 final size:48
Alignment explanation
Indices: 18692359--18692619 Score: 235
Period size: 48 Copynumber: 5.7 Consensus size: 48
18692349 ATGAGATCTC
* *
18692359 GTGTAAGACTATGTTTGGGACATGGCATCGGCGTTGATATGTGTTCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTTCCA
*
18692407 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTTCCA
* * * * *
18692455 GTGTAAGACCATATCTGGGATATGGCATCGGCATCGATATGTGATTTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTG-TTCCA
* * * * *
18692504 -TGTAAGACCATATCTAGG--AT---AT-GGCATTGATATGAGATTTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTG-TTCCA
* * * * *
18692546 -TGTAAGACTATGTCTGGGACATGGTAT---C---GATATGAGGTCCC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTTCCA
*
18692587 GTGTAAGACCATGTCTAGGACATGGCATCGGCG
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCG
18692620 CCGACATCAG
Statistics
Matches: 181, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
41 2 0.01
42 65 0.36
43 2 0.01
44 2 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 101 0.56
49 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTTCCA
Found at i:18692543 original size:42 final size:42
Alignment explanation
Indices: 18692484--18692614 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
18692474 ATATGGCATC
* * *
18692484 GGCATCGATATGTGATTTCATGTAAGACCATATCTAGGATAT
1 GGCATTGATATGAGATTTCATGTAAGACCATATCTAGGACAT
* * *
18692526 GGCATTGATATGAGATTTCATGTAAGACTATGTCTGGGACAT
1 GGCATTGATATGAGATTTCATGTAAGACCATATCTAGGACAT
* * * ** * *
18692568 GGTATCGATATGAGGTCCCGTGTAAGACCATGTCTAGGACAT
1 GGCATTGATATGAGATTTCATGTAAGACCATATCTAGGACAT
18692610 GGCAT
1 GGCAT
18692615 CGGCGCCGAC
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (42 bp):
GGCATTGATATGAGATTTCATGTAAGACCATATCTAGGACAT
Found at i:18692642 original size:132 final size:132
Alignment explanation
Indices: 18692455--18692701 Score: 334
Period size: 132 Copynumber: 1.9 Consensus size: 132
18692445 ATGTGTGCCA
* * * * ** * *
18692455 GTGTAAGACCATATCTGGGATATGGCATCGGCATCGATATGTGATTTCATGTAAGACCATATCTA
1 GTGTAAGACCATATCTAGGACATGGCATCGGCACCGACATCAGACTTCATATAAGACCATATCTA
* ** *
18692520 GGATATGGCATTGATAT-GAGATTTCATGTAAGACTATGTCTGGGACATGGTATCGATATGAGGT
66 GGATATGGCATCGATATAGAGACCT-ATGTAAGACAATGTCTGGGACATGGTATCGATATGAGGT
18692584 CCC
130 CCC
* * *
18692587 GTGTAAGACCATGTCTAGGACATGGCATCGGCGCCGACATCAGACTTCGTATAAGACCATATCTA
1 GTGTAAGACCATATCTAGGACATGGCATCGGCACCGACATCAGACTTCATATAAGACCATATCTA
*
18692652 GGATATGGCATCGATATATAGACCTATGTAAGACAATGTCTGGGACATGG
66 GGATATGGCATCGATATAGAGACCTATGTAAGACAATGTCTGGGACATGG
18692702 CTTTGGCATT
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
132 94 0.96
133 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (132 bp):
GTGTAAGACCATATCTAGGACATGGCATCGGCACCGACATCAGACTTCATATAAGACCATATCTA
GGATATGGCATCGATATAGAGACCTATGTAAGACAATGTCTGGGACATGGTATCGATATGAGGTC
CC
Found at i:18694281 original size:46 final size:44
Alignment explanation
Indices: 18694222--18694336 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
18694212 ACAGGACAGA
* *
18694222 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
18694268 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
18694312 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
18694337 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:18694317 original size:44 final size:45
Alignment explanation
Indices: 18694222--18694355 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
18694212 ACAGGACAGA
* *
18694222 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
18694268 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
18694312 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
18694356 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:18695983 original size:42 final size:42
Alignment explanation
Indices: 18695936--18696084 Score: 172
Period size: 42 Copynumber: 3.5 Consensus size: 42
18695926 TTACTTCCTA
** * *
18695936 TTCAGCTCTTTTAATATTCTGTTTAATCCTTATAGGTTTCCG
1 TTCAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGGTTTCCG
* *
18695978 TTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCCA
1 TTCAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGGTTTCCG
** * *
18696020 TTCAGCTCTTACAAGCTTCTGTTCAACCCTTATGGGTTTCTG
1 TTCAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGGTTTCCG
* ** *
18696062 TTTAGCTCTCATGAGCTTCTGTT
1 TTCAGCTCTTTTAAGCTTCTGTT
18696085 AAGCTTTCGA
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (42 bp):
TTCAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGGTTTCCG
Found at i:18696060 original size:21 final size:21
Alignment explanation
Indices: 18695952--18696063 Score: 62
Period size: 21 Copynumber: 5.3 Consensus size: 21
18695942 TCTTTTAATA
* * *
18695952 TTCTGTTTAATCCTTATAGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * * *
18695973 TTCCGTTCAGCTCTTTTGAGC
1 TTCTGTTCAACCCTTATGGGT
*
18695994 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
** * * *** *
18696015 TTCCATTCAGCTCTTACAAGC
1 TTCTGTTCAACCCTTATGGGT
18696036 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
18696057 TTCTGTT
1 TTCTGTT
18696064 TAGCTCTCAT
Statistics
Matches: 58, Mismatches: 33, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:18696081 original size:21 final size:19
Alignment explanation
Indices: 18696057--18696105 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18696047 CCTTATGGGT
*
18696057 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTAAGCTCTC--GAGC
*
18696078 TTCTGTTAAGCTTTCGAGC
1 TTCTGTTAAGCTCTCGAGC
18696097 TTCTGTTAA
1 TTCTGTTAA
18696106 CGATATACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.50
21 13 0.50
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCTGTTAAGCTCTCGAGC
Found at i:18699907 original size:39 final size:39
Alignment explanation
Indices: 18699862--18699939 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
18699852 ATGCAAGACA
18699862 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
18699901 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
18699940 TAACATTCCG
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:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:18701197 original size:46 final size:44
Alignment explanation
Indices: 18701138--18701252 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
18701128 ACAGGACAGA
* *
18701138 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
18701184 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
18701228 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
18701253 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:18701233 original size:44 final size:45
Alignment explanation
Indices: 18701138--18701271 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
18701128 ACAGGACAGA
* *
18701138 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
18701184 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
18701228 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
18701272 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:18705430 original size:33 final size:33
Alignment explanation
Indices: 18705369--18705433 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
18705359 ACTTTACCCT
**
18705369 TCCATTTCTTTCTCAGGTCTAGACCTTTCTTCA
1 TCCATTTCTTTCTCACCTCTAGACCTTTCTTCA
* * *
18705402 TCCATTTCTTTCTCACCTTTGGAGCTTTCTTC
1 TCCATTTCTTTCTCACCTCTAGACCTTTCTTC
18705434 TTTTTTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.12, C:0.31, G:0.09, T:0.48
Consensus pattern (33 bp):
TCCATTTCTTTCTCACCTCTAGACCTTTCTTCA
Found at i:18715404 original size:39 final size:39
Alignment explanation
Indices: 18715350--18715437 Score: 176
Period size: 39 Copynumber: 2.3 Consensus size: 39
18715340 AACAGATGCT
18715350 ACTTTGCATAGACAATCAATCAGCAGTAAGATTGTCTAA
1 ACTTTGCATAGACAATCAATCAGCAGTAAGATTGTCTAA
18715389 ACTTTGCATAGACAATCAATCAGCAGTAAGATTGTCTAA
1 ACTTTGCATAGACAATCAATCAGCAGTAAGATTGTCTAA
18715428 ACTTTGCATA
1 ACTTTGCATA
18715438 AAACTTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (39 bp):
ACTTTGCATAGACAATCAATCAGCAGTAAGATTGTCTAA
Found at i:18718245 original size:6 final size:6
Alignment explanation
Indices: 18718188--18718242 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
18718178 GAATGAAAGC
*
18718188 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GACGTT
1 GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT GGCGTT
*
18718236 GACGTT G
1 GGCGTT G
18718243 ACGATGGGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.04, C:0.16, G:0.47, T:0.33
Consensus pattern (6 bp):
GGCGTT
Found at i:18719215 original size:27 final size:27
Alignment explanation
Indices: 18719185--18719245 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
18719175 TAACTCATTC
18719185 ATACGAAAGTGCTTTGCCTTGAACAAA
1 ATACGAAAGTGCTTTGCCTTGAACAAA
18719212 ATACGAAAGTGCTTTGCCTTGAACAAA
1 ATACGAAAGTGCTTTGCCTTGAACAAA
18719239 A-ACGAAA
1 ATACGAAA
18719246 CAAACACTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (27 bp):
ATACGAAAGTGCTTTGCCTTGAACAAA
Found at i:18722147 original size:28 final size:28
Alignment explanation
Indices: 18722114--18722174 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
18722104 AAATATATAA
18722114 ACTATTAAAATGATAAACTTGTATTTTT
1 ACTATTAAAATGATAAACTTGTATTTTT
18722142 ACTATTAAAATGATAAACTTGTATTTTT
1 ACTATTAAAATGATAAACTTGTATTTTT
18722170 ACTAT
1 ACTAT
18722175 CATCAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (28 bp):
ACTATTAAAATGATAAACTTGTATTTTT
Found at i:18722997 original size:15 final size:16
Alignment explanation
Indices: 18722963--18723002 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
18722953 CTTTAAAAAA
* *
18722963 TTAATATTTCTCTTTT
1 TTAATATTTATCTATT
18722979 TTAATATTTAT-TATT
1 TTAATATTTATCTATT
18722994 TTAATATTT
1 TTAATATTT
18723003 TACTGTGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATATTTATCTATT
Found at i:18723234 original size:37 final size:35
Alignment explanation
Indices: 18723166--18723235 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
18723156 TAAATTAAAA
* * * *
18723166 TTTTATATTTTTAAATGGTTAAAGTGTAATTTTAC
1 TTTTATAATTTTAAATGGTCAAAATGAAATTTTAC
18723201 TTTTACTAATTTTAAATGGTCAAAATAGAAATTTT
1 TTTTA-TAATTTTAAATGGTCAAAAT-GAAATTTT
18723236 TTCATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 17 0.59
37 7 0.24
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (35 bp):
TTTTATAATTTTAAATGGTCAAAATGAAATTTTAC
Found at i:18723568 original size:18 final size:18
Alignment explanation
Indices: 18723547--18723581 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18723537 TCATTAATTT
* *
18723547 TAAATTTTATTATTAAAA
1 TAAATTGTACTATTAAAA
18723565 TAAATTGTACTATTAAA
1 TAAATTGTACTATTAAA
18723582 TATTTATTAA
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:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAATTGTACTATTAAAA
Found at i:18725056 original size:26 final size:25
Alignment explanation
Indices: 18725023--18725074 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
18725013 TGTGAAAATT
*
18725023 AAACC-AAATCAAAATTTCATATATA
1 AAACCAAAATCAAAA-CTCATATATA
*
18725048 AAACACAAAATTAAAACTCATATATA
1 AAAC-CAAAATCAAAACTCATATATA
18725074 A
1 A
18725075 TATTAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 11 0.48
27 8 0.35
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (25 bp):
AAACCAAAATCAAAACTCATATATA
Found at i:18726207 original size:36 final size:35
Alignment explanation
Indices: 18726142--18726210 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
18726132 AAATAAAAAA
* **
18726142 ATAAAAAATAAAAGTATATACAATTTTTTTAAATC
1 ATAAAAAATAAAAATATATACAAAGTTTTTAAATC
18726177 ATAAAAAACTAAAAATATATTA-AAAGTTTTTAAA
1 ATAAAAAA-TAAAAATATA-TACAAAGTTTTTAAA
18726211 AACTACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 8 0.28
36 19 0.66
37 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (35 bp):
ATAAAAAATAAAAATATATACAAAGTTTTTAAATC
Found at i:18730269 original size:18 final size:18
Alignment explanation
Indices: 18730232--18730270 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18730222 TTAGAAATCA
*
18730232 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
18730250 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
18730268 AAA
1 AAA
18730271 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:18749902 original size:2 final size:2
Alignment explanation
Indices: 18749895--18749921 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18749885 TAAAGGTCGT
18749895 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18749922 GATCTCAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18750569 original size:42 final size:42
Alignment explanation
Indices: 18750510--18750617 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 42
18750500 GATGTCACTA
* *
18750510 TCCCAGACAGGGTCTTACACGAAATC-AAGTACGATGCCAACG
1 TCCCAGACATGATCTTACACGAAATCAAAGT-CGATGCCAACG
* * *
18750552 TCCCAGACATGCTCTTACACATAAATCATAAGTCGATGTCAACG
1 TCCCAGACATGATCTTACAC-GAAATCA-AAGTCGATGCCAACG
*
18750596 TCCCAGACGTGATCTTACACGA
1 TCCCAGACATGATCTTACACGA
18750618 TAACACATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
42 18 0.32
43 6 0.11
44 28 0.50
45 4 0.07
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
TCCCAGACATGATCTTACACGAAATCAAAGTCGATGCCAACG
Found at i:18751832 original size:16 final size:13
Alignment explanation
Indices: 18751801--18751863 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
18751791 AAATAGATAT
18751801 TTATTATTTATCA
1 TTATTATTTATCA
18751814 TTATTATTCTATCAAA
1 TTATTATT-TATC--A
*
18751830 TTATAATTTAT-A
1 TTATTATTTATCA
* *
18751842 TTATTAAATTATAA
1 TTATT-ATTTATCA
18751856 TTATTATT
1 TTATTATT
18751864 ATTAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 5 0.12
13 15 0.37
14 10 0.24
15 3 0.07
16 8 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTTATCA
Found at i:18751863 original size:20 final size:20
Alignment explanation
Indices: 18751808--18751869 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
18751798 TATTTATTAT
* *
18751808 TTATCATTATTATTCTATCAAA
1 TTATAATTATTA-T-TATTAAA
18751830 TTATAATT-TATATTATTAAA
1 TTATAATTAT-TATTATTAAA
18751850 TTATAATTATTATTATTAAA
1 TTATAATTATTATTATTAAA
18751870 AATAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 24 0.67
21 3 0.08
22 9 0.25
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAATTATTATTATTAAA
Found at i:18751878 original size:20 final size:20
Alignment explanation
Indices: 18751831--18751874 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
18751821 TCTATCAAAT
*
18751831 TATAATT-TATATTATTAAAT
1 TATAATTAT-TATTATTAAAA
18751851 TATAATTATTATTATTAAAA
1 TATAATTATTATTATTAAAA
18751871 -ATAA
1 TATAA
18751875 ATTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTATTATTATTAAAA
Found at i:18752123 original size:3 final size:3
Alignment explanation
Indices: 18752115--18752141 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18752105 TAAGATATTT
18752115 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
18752142 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18752146 original size:3 final size:3
Alignment explanation
Indices: 18752140--18752189 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
18752130 ATAATAATAA
18752140 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18752188 TA
1 TA
18752190 ATTTATTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18752217 original size:13 final size:14
Alignment explanation
Indices: 18752207--18752240 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
18752197 AAAGTAAAAG
18752207 AATAAAATAAATAA
1 AATAAAATAAATAA
18752221 AAT-AAATAAATAA
1 AATAAAATAAATAA
*
18752234 AACAAAA
1 AATAAAA
18752241 GAAAGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:18756420 original size:17 final size:18
Alignment explanation
Indices: 18756383--18756424 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
18756373 TATATATTTT
* *
18756383 TAAAAATATCAATTACTA
1 TAAAAATATCAAGTACAA
18756401 TAAAAATATC-AGTACAA
1 TAAAAATATCAAGTACAA
18756418 TAAAAAT
1 TAAAAAT
18756425 TTCTAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATATCAAGTACAA
Found at i:18758888 original size:2 final size:2
Alignment explanation
Indices: 18758881--18758906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18758871 GATGAGTATC
18758881 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
18758907 CTGTGTCCCG
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:18767879 original size:32 final size:32
Alignment explanation
Indices: 18767841--18767908 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
18767831 GTCATTTCTA
18767841 TTTTGATCATTTTTAATTTAATTTATTAATAT
1 TTTTGATCATTTTTAATTTAATTTATTAATAT
18767873 TTTTGATCATTTTTAATTTAATTTATTAATAT
1 TTTTGATCATTTTTAATTTAATTTATTAATAT
18767905 TTTT
1 TTTT
18767909 ATTTTTCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (32 bp):
TTTTGATCATTTTTAATTTAATTTATTAATAT
Found at i:18774911 original size:32 final size:32
Alignment explanation
Indices: 18774851--18774913 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
18774841 ACCTTTTTTT
*
18774851 TTTTTTAATATATTATTTAATATTTAAATTTA
1 TTTTTTAATATATTATTTAATATCTAAATTTA
* *
18774883 TTTTTTAATCT-TTAATTTGATATCTAAATTT
1 TTTTTTAATATATT-ATTTAATATCTAAATTT
18774914 TTCCAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (32 bp):
TTTTTTAATATATTATTTAATATCTAAATTTA
Found at i:18775057 original size:33 final size:33
Alignment explanation
Indices: 18775018--18775082 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
18775008 TAAATACTTT
*
18775018 TACTTAAAAACATGTATTAAATAAATATTAATC
1 TACTTAAAAACATATATTAAATAAATATTAATC
*
18775051 TACTTAAATACATATATTAAATAAATATTAAT
1 TACTTAAAAACATATATTAAATAAATATTAAT
18775083 TTATGTATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (33 bp):
TACTTAAAAACATATATTAAATAAATATTAATC
Found at i:18775576 original size:15 final size:15
Alignment explanation
Indices: 18775553--18775598 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
18775543 TTAGGGTTAG
*
18775553 AGAAAAAGAAAAGGA
1 AGAAGAAGAAAAGGA
*
18775568 AGAAGAAGAAAAAGA
1 AGAAGAAGAAAAGGA
* *
18775583 AGAAGGAGAAGAGGA
1 AGAAGAAGAAAAGGA
18775598 A
1 A
18775599 AAATAGAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAGGA
Found at i:18775577 original size:21 final size:21
Alignment explanation
Indices: 18775553--18775601 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
18775543 TTAGGGTTAG
18775553 AGAAAAAGAA-AAGGAAGAAGA
1 AGAAAAAGAAGAAGG-AGAAGA
18775574 AGAAAAAGAAGAAGGAGAAGA
1 AGAAAAAGAAGAAGGAGAAGA
*
18775595 GGAAAAA
1 AGAAAAA
18775602 TAGAGATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AGAAAAAGAAGAAGGAGAAGA
Found at i:18776774 original size:21 final size:21
Alignment explanation
Indices: 18776721--18776775 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
18776711 TTGGGGCAGC
*
18776721 TTGTTGAGTTGGGGTACTCTT
1 TTGTTGAGTTGGGGTACTCTG
* *
18776742 TTGCTGATTTGGGGTAGCT-TG
1 TTGTTGAGTTGGGGTA-CTCTG
18776763 TTGTTGAGTTGGG
1 TTGTTGAGTTGGG
18776776 ACACCAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.09, C:0.07, G:0.38, T:0.45
Consensus pattern (21 bp):
TTGTTGAGTTGGGGTACTCTG
Found at i:18777410 original size:2 final size:2
Alignment explanation
Indices: 18777403--18777464 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
18777393 CAACAATGAT
18777403 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
18777445 AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC
18777465 CCTAAAAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18777522 original size:25 final size:27
Alignment explanation
Indices: 18777467--18777525 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
18777457 ACACACACCC
* * *
18777467 TAAAAAACAGTCACTATATGCATATTA
1 TAAAAAATACTCACTACATGCATATTA
18777494 TAAAAAATACTCACTACATGCATATTA
1 TAAAAAATACTCACTACATGCATATTA
18777521 -AAAAA
1 TAAAAA
18777526 TAGTCAACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (27 bp):
TAAAAAATACTCACTACATGCATATTA
Found at i:18778489 original size:39 final size:39
Alignment explanation
Indices: 18778435--18778539 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
18778425 AGTCATTTAG
* *
18778435 TAACTATCAAATATTCAGTGCAGTAGTTTAGTTATTCAA
1 TAACTATCAATTATTCAGTACAGTAGTTTAGTTATTCAA
* * *
18778474 TAACTATTAATTATTCTA-TACAGTAATTTAGTTATTCAG
1 TAACTATCAATTATTC-AGTACAGTAGTTTAGTTATTCAA
*
18778513 TATCTATCAATTATTCAGTACAGTAGT
1 TAACTATCAATTATTCAGTACAGTAGT
18778540 CATCGACTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 54 0.96
40 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (39 bp):
TAACTATCAATTATTCAGTACAGTAGTTTAGTTATTCAA
Found at i:18778979 original size:11 final size:11
Alignment explanation
Indices: 18778963--18778997 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
18778953 CTATTTCCCC
18778963 TTTTTTCTTTT
1 TTTTTTCTTTT
*
18778974 TTTTTTCTTCT
1 TTTTTTCTTTT
*
18778985 TTCTTTCTTTT
1 TTTTTTCTTTT
18778996 TT
1 TT
18778998 CCTGCTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:18780073 original size:38 final size:39
Alignment explanation
Indices: 18779989--18780123 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
18779979 ACCAATATGG
*
18779989 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
18780028 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
18780066 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
18780107 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
18780124 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:18781695 original size:5 final size:5
Alignment explanation
Indices: 18781685--18781728 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
18781675 GTTTCTTTTA
18781685 AATAT AATAT AATAT AATAT AATAT AATAT -A-AT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A
18781729 CTTAATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 33 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:18782182 original size:21 final size:20
Alignment explanation
Indices: 18782131--18782183 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 20
18782121 TTTTCTTAAC
18782131 TTAAT-ATATTATAATATAA
1 TTAATAATATTATAATATAA
*
18782150 TTATTATAAATATCTATCATATAA
1 TTA--AT-AATAT-TATAATATAA
18782174 TTAATAATAT
1 TTAATAATAT
18782184 AATACAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 3 0.11
21 7 0.25
22 2 0.07
23 4 0.14
24 12 0.43
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATAATATTATAATATAA
Found at i:18782635 original size:3 final size:3
Alignment explanation
Indices: 18782627--18782689 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
18782617 ATTTTATTTC
*
18782627 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATTCA AT- TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA
*
18782672 ATA ACA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
18782690 GATATGCTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
2 5 0.10
3 42 0.82
4 2 0.04
5 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18784314 original size:18 final size:19
Alignment explanation
Indices: 18784276--18784316 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
18784266 TGGTTCATGT
18784276 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
18784295 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
18784313 TTTC
1 TTTC
18784317 TCATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:18784506 original size:39 final size:38
Alignment explanation
Indices: 18784439--18784573 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
18784429 ACCAATATGG
* * *
18784439 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
18784478 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
18784516 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
18784557 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
18784574 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:18784839 original size:18 final size:19
Alignment explanation
Indices: 18784813--18784851 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
18784803 TTTCAATTCA
18784813 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
18784832 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
18784850 AT
1 AT
18784852 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:18786166 original size:5 final size:5
Alignment explanation
Indices: 18786156--18786192 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
18786146 TTATGTTTAT
18786156 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
18786193 TAAAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:18787042 original size:16 final size:16
Alignment explanation
Indices: 18787021--18787055 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18787011 GAATTAGGGT
18787021 CTGAATTTAGCCTGGA
1 CTGAATTTAGCCTGGA
*
18787037 CTGAATTTAGTCTGGA
1 CTGAATTTAGCCTGGA
18787053 CTG
1 CTG
18787056 GTAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (16 bp):
CTGAATTTAGCCTGGA
Found at i:18787520 original size:20 final size:20
Alignment explanation
Indices: 18787497--18787537 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18787487 AAATATTAGG
18787497 TAAGTATAATTCTTGTTACA
1 TAAGTATAATTCTTGTTACA
18787517 TAAGTATAATTCTTGTTACA
1 TAAGTATAATTCTTGTTACA
18787537 T
1 T
18787538 GAGCTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TAAGTATAATTCTTGTTACA
Found at i:18789587 original size:15 final size:15
Alignment explanation
Indices: 18789555--18789604 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
18789545 CTATCCTATT
**
18789555 AGACACATCACTTTC
1 AGACACATCACTACC
**
18789570 AGATGCATCACTACC
1 AGACACATCACTACC
18789585 AGACACATCACTACC
1 AGACACATCACTACC
18789600 AGACA
1 AGACA
18789605 TGTCTTCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:18789921 original size:89 final size:89
Alignment explanation
Indices: 18789819--18789985 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
18789809 ACACAACCAT
* *
18789819 TTTTGTCATATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAACAAACATTAGT
1 TTTTGCCACATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAACAAACATTAGT
18789884 TTGATAATGGCATTCAAATTTTGA
66 TTGATAATGGCATTCAAATTTTGA
*
18789908 TTTTGCCACATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAATAAACATTAGT
1 TTTTGCCACATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAACAAACATTAGT
18789973 TTGATAATGGCAT
66 TTGATAATGGCAT
18789986 CCATACAATG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (89 bp):
TTTTGCCACATACAATATAGTAGCTTGGATACAAACAATGGCAGATATACACAACAAACATTAGT
TTGATAATGGCATTCAAATTTTGA
Found at i:18790011 original size:48 final size:48
Alignment explanation
Indices: 18789942--18790066 Score: 196
Period size: 48 Copynumber: 2.6 Consensus size: 48
18789932 TTGGATACAA
* * *
18789942 ACAATGGCAGATATACACAATAAACATTAGTTTGATAATGGCATCCAT
1 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
*
18789990 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGTATCCAT
1 ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
* *
18790038 ACGATGGCAGATACAAACAGTAAACATCA
1 ACAATGGCAGATACAAACAATAAACATCA
18790067 TGCACATGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (48 bp):
ACAATGGCAGATACAAACAATAAACATCAGTTTGATAATGGCATCCAT
Found at i:18790272 original size:6 final size:6
Alignment explanation
Indices: 18790136--18790271 Score: 85
Period size: 6 Copynumber: 21.7 Consensus size: 6
18790126 ATCCAAATTG
* * * * * *
18790136 AAATCA AAATCA AAATCT AAAGCT AAATCG AGATCA AAATTA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
** **
18790184 AAATCA AAATCA GTTAGTGTTTCA AAATTG AAATCA AAATCA AAAT-A
1 AAATCA AAATCA ---A---AATCA AAATCA AAATCA AAATCA AAATCA
* * *
18790231 GAAATCA AAATCA AAATCA GAATCG AAATCA AAATTA AAAT
1 -AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
18790272 TGAAATCGAA
Statistics
Matches: 100, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
5 1 0.01
6 93 0.93
7 1 0.01
9 2 0.02
12 3 0.03
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:18790278 original size:24 final size:23
Alignment explanation
Indices: 18790214--18790282 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
18790204 TTCAAAATTG
*
18790214 AAATCAAAATCAAAATAGAAATCA
1 AAATCAAAATC-AAATCGAAATCA
18790238 AAATCAAAATCAGAATCGAAATCA
1 AAATCAAAATCA-AATCGAAATCA
* *
18790262 AAATTAAAATTGAAATCGAAA
1 AAATCAAAA-TCAAATCGAAA
18790283 AAACCCTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.19
Consensus pattern (23 bp):
AAATCAAAATCAAATCGAAATCA
Found at i:18790322 original size:6 final size:6
Alignment explanation
Indices: 18790300--18790333 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
18790290 AAATAACCCT
18790300 AAATCA AAAT-A ACAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA A-AATCA AAATCA AAATCA AAAT
18790334 TGAAATCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:18790364 original size:68 final size:62
Alignment explanation
Indices: 18790238--18790355 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
18790228 ATAGAAATCA
* * * *
18790238 AAATCAAAATCAGAATCGAAATCAAAATTAAAATTGAAATCGAAAAAACCCTAAATAACCCT
1 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAAAAACCCTAAATAACCCT
*
18790300 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAATAACCCTAAAT
1 AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAAAAACCCTAAAT
18790356 CAAAATAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.58, C:0.17, G:0.05, T:0.19
Consensus pattern (62 bp):
AAATCAAAATAACAATCAAAATCAAAATCAAAATTGAAATCGAAAAAACCCTAAATAACCCT
Found at i:18790818 original size:21 final size:21
Alignment explanation
Indices: 18790794--18790833 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18790784 AACATGGCAA
18790794 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
18790815 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
18790834 GGTCCCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:18797803 original size:29 final size:29
Alignment explanation
Indices: 18797723--18797809 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
18797713 TTGAGTTCAA
*
18797723 AAAGGTCTGGCTCTTATTTGAGCACTTCCC
1 AAAGGTTTGGCT-TTATTTGAGCACTTCCC
* * * *
18797753 AAATGTTTTGGCCATTACTTGAGCACTT-CG
1 AAA-GGTTTGG-CTTTATTTGAGCACTTCCC
18797783 AAAGGTTTGGCTTTCATTTGAGCACTT
1 AAAGGTTTGGCTTT-ATTTGAGCACTT
18797810 TTGCAAAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
28 3 0.07
29 17 0.37
30 7 0.15
31 18 0.39
32 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAGGTTTGGCTTTATTTGAGCACTTCCC
Found at i:18809933 original size:17 final size:19
Alignment explanation
Indices: 18809890--18809936 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
18809880 GTTTTATCAA
18809890 ATAAATT-ATTAAAAATTC
1 ATAAATTAATTAAAAATTC
18809908 ATAAA--AATTAAAAATT-
1 ATAAATTAATTAAAAATTC
18809924 A-AAATTAATTAAA
1 ATAAATTAATTAAA
18809937 TTGATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.12
16 1 0.04
17 17 0.65
18 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATTAATTAAAAATTC
Found at i:18815148 original size:107 final size:108
Alignment explanation
Indices: 18815025--18815240 Score: 389
Period size: 107 Copynumber: 2.0 Consensus size: 108
18815015 TAAACAAAAA
18815025 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
*
18815090 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAAATTTTGTTAATTACTCTGATAAAATTTTTG
* *
18815132 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
*
18815197 AATTGTCTTAAAAATTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAAATTTTGTTAATTACTCTGATAAAATTTTTG
18815240 A
1 A
18815241 CGTGTTTTTT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 91 0.88
108 13 0.12
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
AATTGTATTAAAAATTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:18817817 original size:16 final size:15
Alignment explanation
Indices: 18817788--18817831 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
18817778 TTAAAATACA
18817788 ATTATAAAAT-AATATT
1 ATTA-AAAATAAATA-T
18817804 ATTAAAAATAAATAT
1 ATTAAAAATAAATAT
18817819 ATGTAAAAATAAA
1 AT-TAAAAATAAA
18817832 CACTATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATTAAAAATAAATAT
Found at i:18826917 original size:2 final size:2
Alignment explanation
Indices: 18826910--18826935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18826900 GCTTTCAGAA
18826910 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
18826936 GAATATGGTA
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:18830105 original size:44 final size:44
Alignment explanation
Indices: 18829995--18830125 Score: 171
Period size: 43 Copynumber: 3.0 Consensus size: 44
18829985 AGCTCGTACA
18829995 ATGCCAACGTCCCAAACGTGGTCTTACACGT-AATCACATATCG
1 ATGCCAACGTCCCAAACGTGGTCTTACACGTAAATCACATATCG
* * * * *
18830038 ATGTC-ACTATTCCAGACAG-GGTCTTACACGTAAATCACAAATCG
1 ATGCCAAC-GTCCCAAAC-GTGGTCTTACACGTAAATCACATATCG
18830082 ATGCCAACGTCCCAAACGTGGTCTTACACG-AAATCACATATCG
1 ATGCCAACGTCCCAAACGTGGTCTTACACGTAAATCACATATCG
18830125 A
1 A
18830126 AACCCTATGT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 2 0.03
43 36 0.49
44 33 0.45
45 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (44 bp):
ATGCCAACGTCCCAAACGTGGTCTTACACGTAAATCACATATCG
Found at i:18832043 original size:20 final size:17
Alignment explanation
Indices: 18832003--18832045 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
18831993 TTAAAAGATT
*
18832003 TTTAAAAAAAAAAACAG
1 TTTAAAAAAAAAAACAA
18832020 TTTAAAAAAATAAAAGCCAA
1 TTTAAAAAAA-AAAA--CAA
18832040 TTTAAA
1 TTTAAA
18832046 TATTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
20 8 0.36
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (17 bp):
TTTAAAAAAAAAAACAA
Found at i:18834965 original size:14 final size:14
Alignment explanation
Indices: 18834942--18834971 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18834932 TTGAAAATAT
18834942 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
18834956 GTTGATTTGGATTG
1 GTTGAATTGGATTG
18834970 GT
1 GT
18834972 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:18842968 original size:22 final size:24
Alignment explanation
Indices: 18842916--18842970 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
18842906 TATTTTAACG
18842916 TATT-TATATATTAATTTTTTTGA
1 TATTATATATATTAATTTTTTTGA
*
18842939 AACTTTATATATATT-ATTTTTTT-A
1 TA--TTATATATATTAATTTTTTTGA
18842963 TATTATAT
1 TATTATAT
18842971 TTTTTTACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
22 6 0.22
23 1 0.04
24 2 0.07
25 10 0.37
26 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTATATATATTAATTTTTTTGA
Found at i:18842971 original size:15 final size:17
Alignment explanation
Indices: 18842942--18842977 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
18842932 TTTTTGAAAC
18842942 TTTATATATATTATTTT
1 TTTATATATATTATTTT
18842959 TTTATAT-TA-TATTTT
1 TTTATATATATTATTTT
18842974 TTTA
1 TTTA
18842978 CGTTACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATATATTATTTT
Found at i:18843543 original size:15 final size:15
Alignment explanation
Indices: 18843505--18843558 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
18843495 AAAAAAATTG
*
18843505 TAAGTGTTGAAAAA-
1 TAAGTATTGAAAAAT
* *
18843519 TAAATGTTGAAAAAT
1 TAAGTATTGAAAAAT
*
18843534 TAAGTATTGAAAATT
1 TAAGTATTGAAAAAT
*
18843549 TAACTATTGA
1 TAAGTATTGA
18843559 GTTTAAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 13 0.38
15 21 0.62
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (15 bp):
TAAGTATTGAAAAAT
Found at i:18844699 original size:34 final size:34
Alignment explanation
Indices: 18844656--18844723 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
18844646 AATAAAGATA
18844656 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
1 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
18844690 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
1 GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
18844724 TCCCTTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (34 bp):
GTGTGAAAGAGTGGCAAGATAGATACCTTTCTTT
Found at i:18844936 original size:6 final size:6
Alignment explanation
Indices: 18844925--18844949 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18844915 TGCTTGTATT
18844925 ATAATC ATAATC ATAATC ATAATC A
1 ATAATC ATAATC ATAATC ATAATC A
18844950 GAGTCGGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAATC
Found at i:18850407 original size:84 final size:83
Alignment explanation
Indices: 18850242--18850396 Score: 256
Period size: 83 Copynumber: 1.9 Consensus size: 83
18850232 GTCAACCGAG
* * *
18850242 GCTATGAAGGAGGAGAAGACTCCATTTGATGAGCAAATGTTTGGCACAAAAGACTGGGATAGTCA
1 GCTATGAAGGAGGAGAAGACTCCATTTGATCAACAAATATTTGGCACAAAAGACTGGGATAGTCA
18850307 AGTGTGCAAGTCAGATTT
66 AGTGTGCAAGTCAGATTT
* *
18850325 GCTATGAAGGAGGAGAAGACTCCATTTGATCAACGAATATTTAGGCACAAAAGACTGGGATTGTC
1 GCTATGAAGGAGGAGAAGACTCCATTTGATCAACAAATATTT-GGCACAAAAGACTGGGATAGTC
18850390 AAGTGTG
65 AAGTGTG
18850397 TGAGTGAGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 38 0.58
84 28 0.42
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (83 bp):
GCTATGAAGGAGGAGAAGACTCCATTTGATCAACAAATATTTGGCACAAAAGACTGGGATAGTCA
AGTGTGCAAGTCAGATTT
Found at i:18852715 original size:61 final size:62
Alignment explanation
Indices: 18852643--18852760 Score: 177
Period size: 61 Copynumber: 1.9 Consensus size: 62
18852633 ATTGAAGTAA
*
18852643 TATAAAGTAGTATTTAAATATTAAGTT-GAAAAAAATAAAATTTAATAATTACAATATTTAAG
1 TATAAAGTAGTATTTAAATATTAA-TTAGAAAAAAATAAAATTAAATAATTACAATATTTAAG
* * *
18852705 TATAAA-TAGTATTTAAATATTAATTAGATAAAAATAAACTTAAATAATTATAATAT
1 TATAAAGTAGTATTTAAATATTAATTAGAAAAAAATAAAATTAAATAATTACAATAT
18852761 ATAATACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 2 0.04
61 43 0.84
62 6 0.12
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (62 bp):
TATAAAGTAGTATTTAAATATTAATTAGAAAAAAATAAAATTAAATAATTACAATATTTAAG
Found at i:18853196 original size:21 final size:20
Alignment explanation
Indices: 18853156--18853193 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18853146 AGTTTATTTT
*
18853156 TTTTTTAAATTTAATCAATA
1 TTTTTTAAATATAATCAATA
18853176 TTTTTT-AATATATATCAA
1 TTTTTTAAATATA-ATCAA
18853194 ATAGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTTAAATATAATCAATA
Found at i:18855554 original size:12 final size:12
Alignment explanation
Indices: 18855539--18855564 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18855529 GGGGAAAAGG
18855539 GAGAAAGAAAAA
1 GAGAAAGAAAAA
18855551 GAGAAAGAAAAA
1 GAGAAAGAAAAA
18855563 GA
1 GA
18855565 AGTAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAAAA
Found at i:18859061 original size:31 final size:29
Alignment explanation
Indices: 18859018--18859076 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
18859008 TTCGTGATAA
18859018 TTTTTTTTTATTAATGGAATAAAAAAACT
1 TTTTTTTTTATTAATGGAATAAAAAAACT
*
18859047 TTTTTTTTGGTATTAATGGAGTAAAAAAAC
1 TTTTTTTT--TATTAATGGAATAAAAAAAC
18859077 CTAAAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (29 bp):
TTTTTTTTTATTAATGGAATAAAAAAACT
Found at i:18859339 original size:14 final size:14
Alignment explanation
Indices: 18859330--18859359 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18859320 TGATGTCTAA
18859330 TTAATAATGTGAAT
1 TTAATAATGTGAAT
18859344 TTAATAATGTGAAT
1 TTAATAATGTGAAT
18859358 TT
1 TT
18859360 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAATAATGTGAAT
Found at i:18859396 original size:18 final size:18
Alignment explanation
Indices: 18859369--18859419 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
18859359 TTTTTATAAA
18859369 AAAT-TAAAATAT-TTTT
1 AAATATAAAATATATTTT
*
18859385 AAATAATAAAATTTATTTT
1 AAAT-ATAAAATATATTTT
*
18859404 AAATATAAAAGATATT
1 AAATATAAAATATATT
18859420 AAAGAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.14
18 17 0.59
19 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATAAAATATATTTT
Found at i:18863775 original size:2 final size:2
Alignment explanation
Indices: 18863768--18863815 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
18863758 TCCTTCACTC
18863768 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
18863810 AT AT AT
1 AT AT AT
18863816 CATACTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18873991 original size:21 final size:21
Alignment explanation
Indices: 18873944--18873991 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
18873934 TCATTAATAG
* * * *
18873944 TATAAAAAATAGATTAATTTT
1 TATAAAAAATAAATAAATATA
*
18873965 TTTAAAAAATAAATAAATATA
1 TATAAAAAATAAATAAATATA
18873986 TATAAA
1 TATAAA
18873992 GTCTAGATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TATAAAAAATAAATAAATATA
Found at i:18875458 original size:23 final size:23
Alignment explanation
Indices: 18875432--18875503 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
18875422 ATAATAAATA
* *
18875432 TATATATGTATTTTATTTTTAAT
1 TATATATATATTTTAATTTTAAT
*
18875455 TATATTTATATTTTAATTTTAAT
1 TATATATATATTTTAATTTTAAT
* * * *
18875478 TTTA-ATATA-ATCAATTTTTAT
1 TATATATATATTTTAATTTTAAT
18875499 TATAT
1 TATAT
18875504 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 12 0.31
22 4 0.10
23 23 0.59
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (23 bp):
TATATATATATTTTAATTTTAAT
Found at i:18875535 original size:12 final size:12
Alignment explanation
Indices: 18875518--18875551 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18875508 CAAATTGTGT
18875518 ATTGTTTTAAGA
1 ATTGTTTTAAGA
*
18875530 ATTGTTTTAATA
1 ATTGTTTTAAGA
*
18875542 TTTGTTTTAA
1 ATTGTTTTAA
18875552 ATGTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (12 bp):
ATTGTTTTAAGA
Found at i:18876304 original size:2 final size:2
Alignment explanation
Indices: 18876297--18876332 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18876287 AAACTTTAAC
*
18876297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18876333 TTTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18882587 original size:13 final size:14
Alignment explanation
Indices: 18882561--18882590 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
18882551 TCATTTAGTA
18882561 AATTAAGCTTGATT
1 AATTAAGCTTGATT
18882575 AATTAAG-TTGATT
1 AATTAAGCTTGATT
18882588 AAT
1 AAT
18882591 CTTAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.43
Consensus pattern (14 bp):
AATTAAGCTTGATT
Found at i:18886657 original size:46 final size:46
Alignment explanation
Indices: 18886607--18886735 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
18886597 TGGTTGAGCA
*
18886607 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
18886653 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
18886699 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18886736 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:18890783 original size:46 final size:44
Alignment explanation
Indices: 18890679--18890786 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
18890669 TGTCTTTGAC
** * * *
18890679 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
18890723 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
18890769 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
18890787 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:18897271 original size:46 final size:44
Alignment explanation
Indices: 18897167--18897274 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
18897157 TGTCTTTGAC
** * * *
18897167 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
18897211 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
18897257 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
18897275 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:18901850 original size:93 final size:92
Alignment explanation
Indices: 18901692--18901862 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
18901682 GGATGGTTGA
* *
18901692 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
18901757 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
18901784 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
18901849 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
18901863 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 24 0.32
93 51 0.68
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:18901860 original size:46 final size:46
Alignment explanation
Indices: 18901696--18901869 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
18901686 GGTTGAGCAT
* *
18901696 CCGAACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
18901741 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
18901786 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
18901834 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18901870 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 23 0.21
46 41 0.38
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:18904636 original size:56 final size:56
Alignment explanation
Indices: 18904574--18904709 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
18904564 ACCATGGCAT
* * *
18904574 CGATATATATGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTC
*
18904630 CGATATATGTGTGCGAGTAAGAGCACATTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTC
*
18904686 CGATTTATGTGTGCGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
18904710 CTGTCTGGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTC
Found at i:18905920 original size:21 final size:21
Alignment explanation
Indices: 18905896--18905960 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
18905886 AAGTCTAGCT
* *
18905896 GAAGCATATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
*
18905917 GAAGC-C-CGAAG-GCT-AACT
1 GAAGCACAC-AAGTGCTAAACG
18905935 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
18905956 GAAGC
1 GAAGC
18905961 CCAAAGGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAACG
Found at i:18905937 original size:39 final size:39
Alignment explanation
Indices: 18905878--18905978 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
18905868 ATCATGATTT
* * * *
18905878 GAAGCCCGAAGTCTAGCTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
18905917 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
18905956 GAAGCCCAAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
18905979 TCATCAGAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:18906034 original size:20 final size:20
Alignment explanation
Indices: 18905969--18906042 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
18905959 GCCCAAAGGC
*
18905969 TAACTGAAGCTCAT-CAGAGT
1 TAACTGAAACTCATAC-GAGT
* * * *
18905989 TGAACTGAAACCCCAAAAGGGT
1 T-AACTGAAA-CTCATACGAGT
18906011 TAACTGAAACTCATACGAGT
1 TAACTGAAACTCATACGAGT
*
18906031 TAACAGAAACTC
1 TAACTGAAACTC
18906043 GTAAGAGCTA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
20 19 0.46
21 15 0.37
22 7 0.17
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
TAACTGAAACTCATACGAGT
Found at i:18907644 original size:18 final size:19
Alignment explanation
Indices: 18907610--18907645 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18907600 AATGCAATTT
18907610 ATATATGATGTAAGTGAAA
1 ATATATGATGTAAGTGAAA
*
18907629 ATATATG-TGTATGTGAA
1 ATATATGATGTAAGTGAA
18907646 TAGTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
ATATATGATGTAAGTGAAA
Found at i:18909183 original size:2 final size:2
Alignment explanation
Indices: 18909176--18909200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18909166 AGATTTTAAT
18909176 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18909201 TTATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18909356 original size:18 final size:18
Alignment explanation
Indices: 18909335--18909390 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 18
18909325 ATGTATTAGA
18909335 TATTAAATAAATATTTAT
1 TATTAAATAAATATTTAT
18909353 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAA-ATATTTAT
*
18909374 TCATTAAATAATTATTT
1 T-ATTAAATAAATATTT
18909391 TATAAGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
18 2 0.06
19 7 0.23
20 10 0.32
21 11 0.35
22 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTAAATAAATATTTAT
Found at i:18909558 original size:23 final size:23
Alignment explanation
Indices: 18909529--18909575 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
18909519 GTATATATAT
*
18909529 AAAAAAAGGAATA-AAAGAAAGA
1 AAAAAAAAGAATAGAAAGAAAGA
*
18909551 AAAAAAAAGAATAGAAAGGAAGA
1 AAAAAAAAGAATAGAAAGAAAGA
18909574 AA
1 AA
18909576 CAAAGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAAAAGAATAGAAAGAAAGA
Found at i:18911617 original size:46 final size:46
Alignment explanation
Indices: 18911565--18911779 Score: 324
Period size: 46 Copynumber: 4.7 Consensus size: 46
18911555 GCTCTTTGAA
* *
18911565 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
18911611 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
18911657 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
18911703 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
18911749 A-GAAAGTGAGTAAAACCATAGTTGAAAGATA
1 ATGAAA-TGTGTAAGACCATGGTTGAAAGATA
18911780 TTATGGCATC
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
45 4 0.03
46 153 0.97
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:18913700 original size:24 final size:24
Alignment explanation
Indices: 18913631--18913716 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 24
18913621 GTTAACCCAC
* *
18913631 ACACATAGTGCC-TTAATAATCCAT
1 ACACATAGTGCCATTCA-AATCCAA
*
18913655 ACACATA-TCGACGATTCAAATCCAA
1 ACACATAGT-G-CCATTCAAATCCAA
**
18913680 ACACATAGTGCCATTCAAATCCGC
1 ACACATAGTGCCATTCAAATCCAA
18913704 ACACATAGTGCCA
1 ACACATAGTGCCA
18913717 AGGTCATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.02
24 32 0.62
25 15 0.29
26 4 0.08
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.22
Consensus pattern (24 bp):
ACACATAGTGCCATTCAAATCCAA
Found at i:18918182 original size:53 final size:53
Alignment explanation
Indices: 18918101--18918251 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
18918091 CTTACACGGT
* *
18918101 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
18918156 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
18918209 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
18918252 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:18923059 original size:29 final size:29
Alignment explanation
Indices: 18923027--18923161 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
18923017 ATACCCTCCG
** * *
18923027 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
18923056 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
18923085 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
18923114 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
18923143 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
18923162 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:18923094 original size:58 final size:58
Alignment explanation
Indices: 18922973--18923162 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
18922963 TACTCGATTT
* * * *** *
18922973 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
18923031 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
18923089 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
18923147 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
18923163 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:18928879 original size:53 final size:53
Alignment explanation
Indices: 18928798--18928948 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
18928788 CTTACACGGT
* *
18928798 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
18928853 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
18928906 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
18928949 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:18931882 original size:40 final size:36
Alignment explanation
Indices: 18931819--18931946 Score: 179
Period size: 35 Copynumber: 3.5 Consensus size: 36
18931809 GTGGGAAATG
**
18931819 CCATACCTACATTTCTTAACTCAGTATGGATTTGAGAATA
1 CCATACCTACATTTCACAACTCAGTATGGA--T--GAATA
*
18931859 CCATACCTACATTTCACAGCTCAGTATGGAT-AATA
1 CCATACCTACATTTCACAACTCAGTATGGATGAATA
18931894 CCATACCTACATTTCACAACTCAGTATGGATG-ATA
1 CCATACCTACATTTCACAACTCAGTATGGATGAATA
18931929 CCATACCTACATTTCACA
1 CCATACCTACATTTCACA
18931947 CTTTGCCATG
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
35 55 0.66
38 1 0.01
40 27 0.33
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (36 bp):
CCATACCTACATTTCACAACTCAGTATGGATGAATA
Found at i:18931894 original size:35 final size:35
Alignment explanation
Indices: 18931779--18931946 Score: 176
Period size: 35 Copynumber: 4.6 Consensus size: 35
18931769 TCCTCATTGA
*** * *
18931779 AATACCATACCTACATTTTTTTAACTCGGTGTGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
18931815 AATGCCATACCTACATTTCTTAACTCAGTATGGATTT
1 AATACCATACCTACATTTCACAACTCAGTATGGA--T
*
18931852 GAGAATACCATACCTACATTTCACAGCTCAGTATGGAT
1 ---AATACCATACCTACATTTCACAACTCAGTATGGAT
18931890 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
18931925 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
18931947 CTTTGCCATG
Statistics
Matches: 116, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
34 3 0.03
35 68 0.59
36 14 0.12
38 1 0.01
40 30 0.26
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:18935381 original size:24 final size:24
Alignment explanation
Indices: 18935336--18935382 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18935326 TTTAATGCTA
* *
18935336 TGCTGTCAGATTTATGATTCAAAT
1 TGCTGTCAGATTTATAAATCAAAT
18935360 TGCTGTCAGCATTTA-AAATCAAA
1 TGCTGTCAG-ATTTATAAATCAAA
18935383 GTTCCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (24 bp):
TGCTGTCAGATTTATAAATCAAAT
Found at i:18937506 original size:55 final size:55
Alignment explanation
Indices: 18937446--18937550 Score: 122
Period size: 55 Copynumber: 1.9 Consensus size: 55
18937436 TTTTGAGATT
* * *
18937446 TTTTTTAAAAATTAATCCTTGAATTTAATC-ATTATTTTTATATTAAAATTTCAAA
1 TTTTTTAAAAATTAATCCTTAAATTTAA-CAATCATTTCTATATTAAAATTTCAAA
** * * *
18937501 TTTTTTTCAATTTAATCTTTAAATTTAACAATCATTTCTATATTGAAATT
1 TTTTTTAAAAATTAATCCTTAAATTTAACAATCATTTCTATATTAAAATT
18937551 AATCTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.02
55 40 0.98
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (55 bp):
TTTTTTAAAAATTAATCCTTAAATTTAACAATCATTTCTATATTAAAATTTCAAA
Found at i:18943290 original size:66 final size:66
Alignment explanation
Indices: 18943169--18943303 Score: 182
Period size: 66 Copynumber: 2.0 Consensus size: 66
18943159 GATCCAAGCT
* * * * *
18943169 CCAGACCTGCTTCCATCGATCCTAATTATAGAGCGGATCCAAGCTCCAGATCTGCTTCCATTGAT
1 CCAGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAGCTCCAGAGCTGCTCCCATTGAT
18943234 C
66 C
* * *
18943235 CCAGACCCGCTTCCATTGATCCCAACTATAGAGCGGATCC-GGCCTCTAGAGCTGCTCCCATTGA
1 CCAGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAG-CTCCAGAGCTGCTCCCATTGA
18943299 TC
65 TC
18943301 CCA
1 CCA
18943304 ATTATAGAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (66 bp):
CCAGACCCGCTTCCATCGATCCCAACTATAGAGCGGATCCAAGCTCCAGAGCTGCTCCCATTGAT
C
Found at i:18943298 original size:45 final size:45
Alignment explanation
Indices: 18943247--18943448 Score: 282
Period size: 45 Copynumber: 4.5 Consensus size: 45
18943237 AGACCCGCTT
* *
18943247 CCATTGATCCCAACTATAGAGCGGATCCG-GCCTCTAGAGCTGCTC
1 CCATTGATCCCAATTATAGAGCGGATCCGAG-CTCTAGAGGTGCTC
* * *
18943292 CCATTGATCCCAATTATAGAGTGGATCCGAGCTCTAGAGTTGCTT
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
* * *
18943337 CCATTGATCCCAATTATAGAGCGGATCCAAGCGCTAGAGGTGCTT
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
*
18943382 CCATTGAGCCCAATTATAGAGCGGATCCGAG-TGCTAGAGGTGCTC
1 CCATTGATCCCAATTATAGAGCGGATCCGAGCT-CTAGAGGTGCTC
*
18943427 CGATTGATCCCAATTATAGAGC
1 CCATTGATCCCAATTATAGAGC
18943449 TGCTCCAGAG
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
45 140 0.99
46 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (45 bp):
CCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAGGTGCTC
Found at i:18945752 original size:18 final size:18
Alignment explanation
Indices: 18945731--18945767 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18945721 TATCTTATCC
18945731 TTTTCTTGAGTCTCTGAT
1 TTTTCTTGAGTCTCTGAT
18945749 TTTTCTTGAGTCTCTGAT
1 TTTTCTTGAGTCTCTGAT
18945767 T
1 T
18945768 ACCTTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (18 bp):
TTTTCTTGAGTCTCTGAT
Found at i:18953485 original size:22 final size:21
Alignment explanation
Indices: 18953446--18953487 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18953436 TAATAATAAA
*
18953446 TTTTAATTAATATTTTAATTT
1 TTTTAATTAATATGTTAATTT
*
18953467 TTTTAATTTATAATGTTAATT
1 TTTTAATTAAT-ATGTTAATT
18953488 GAAAGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAATTAATATGTTAATTT
Found at i:18956616 original size:2 final size:2
Alignment explanation
Indices: 18956605--18956639 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18956595 TCATCGATTC
18956605 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18956640 AAAGAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18957979 original size:21 final size:21
Alignment explanation
Indices: 18957963--18958041 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
18957953 ATATAAGGGT
* *
18957963 TGAACGGAAGCTCATAAGAGC
1 TGAACGAAAACTCATAAGAGC
* * *
18957984 TGAACGGAAACTCATAAGGGT
1 TGAACGAAAACTCATAAGAGC
* *
18958005 TAAAC-AAAAGCTCAAAAGAGC
1 TGAACGAAAA-CTCATAAGAGC
18958026 TGAACGAAAACTCATA
1 TGAACGAAAACTCATA
18958042 TGAGTTAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.85
22 4 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
TGAACGAAAACTCATAAGAGC
Found at i:18957980 original size:42 final size:42
Alignment explanation
Indices: 18957921--18958041 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
18957911 GCCCGAAGGC
*
18957921 TGAACAGAAGCATATAAGTGCTAAACAGAAACAT-ATAAGGGT
1 TGAACAGAAGCATATAAGAGCTAAACAGAAAC-TCATAAGGGT
* * *
18957963 TGAACGGAAGC-TCATAAGAGCTGAACGGAAACTCATAAGGGT
1 TGAACAGAAGCAT-ATAAGAGCTAAACAGAAACTCATAAGGGT
* * * *
18958005 TAAACAAAAGC-TCAAAAGAGCTGAAC-GAAAACTCATA
1 TGAACAGAAGCAT-ATAAGAGCTAAACAG-AAACTCATA
18958042 TGAGTTAAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 3 0.04
42 65 0.96
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
TGAACAGAAGCATATAAGAGCTAAACAGAAACTCATAAGGGT
Found at i:18958049 original size:42 final size:42
Alignment explanation
Indices: 18957970--18958059 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
18957960 GGTTGAACGG
* * *
18957970 AAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTAAACAA
1 AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
* *
18958012 AAGCTCAAAAGAGCTGAACGAAAACTCATATGAGTTAAACAT
1 AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
18958054 AAGCTC
1 AAGCTC
18958060 GTGAGAACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGCTCAAAAGAGCTGAACGAAAACTCATAAGAGTTAAACAA
Found at i:18972404 original size:30 final size:29
Alignment explanation
Indices: 18972370--18972473 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 29
18972360 AAAATTGGGT
18972370 TTAATTAAAATATTTAAAAAAATTATAAGA-
1 TTAATTAAAAT-TTTAAAAAAATTA-AAGAG
* *
18972400 TTAATGAGAATTTTTAAAAAAATTAGAAGAG
1 TTAATTA-AAATTTTAAAAAAATTA-AAGAG
* *
18972431 TTCAATTAAAATTTTCAAAATAATTAAAGAA
1 TT-AATTAAAATTTT-AAAAAAATTAAAGAG
*
18972462 AT-ATTAAAATTT
1 TTAATTAAAATTT
18972474 ATCAAAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
29 10 0.16
30 23 0.37
31 16 0.26
32 13 0.21
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAATTAAAATTTTAAAAAAATTAAAGAG
Found at i:18973342 original size:26 final size:25
Alignment explanation
Indices: 18973295--18973344 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
18973285 AAAATACTTT
*
18973295 AAAATTCTATATAAAAGATTTTTTA
1 AAAATTCTATATAAAACATTTTTTA
18973320 AAAATTACTATATAAAAC-TTTTTTA
1 AAAATT-CTATATAAAACATTTTTTA
18973345 CTTAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAATTCTATATAAAACATTTTTTA
Found at i:18981778 original size:6 final size:6
Alignment explanation
Indices: 18981767--18981791 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18981757 ATGCCCACTC
18981767 TGTCTT TGTCTT TGTCTT TGTCTT T
1 TGTCTT TGTCTT TGTCTT TGTCTT T
18981792 TCCCTCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TGTCTT
Done.