Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 157 of 193
Found at i:48537218 original size:29 final size:28
Alignment explanation
Indices: 48537186--48537286 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 28
48537176 AAAACTTTCA
*
48537186 AAAATTACCATTTTACCCCTGAATCTTTT
1 AAAATT-CCATTTTACCCCTGAATCTTCT
* * * *
48537215 AAAATTCCGTTTTTA-ACCTCAAT-TTCACCA
1 AAAATTCC-ATTTTACCCCTGAATCTT---CT
*
48537245 AAAATTACCATTTTACCCCTGAAGCTTCT
1 AAAATT-CCATTTTACCCCTGAATCTTCT
48537274 AAAATTCCATTTT
1 AAAATTCCATTTT
48537287 TAACCCCGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
27 2 0.04
28 15 0.27
29 18 0.33
30 11 0.20
31 7 0.13
32 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTGAATCTTCT
Found at i:48537247 original size:59 final size:59
Alignment explanation
Indices: 48537184--48537321 Score: 222
Period size: 59 Copynumber: 2.3 Consensus size: 59
48537174 CCAAAACTTT
* * * * *
48537184 CAAAAATTACCATTTTACCCCTGAATCTTTTAAAATTCCGTTTTTAACCTCAATTTCAC
1 CAAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
*
48537243 CAAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
48537302 CAAAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
48537322 TCGGGTATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
Found at i:48537259 original size:30 final size:30
Alignment explanation
Indices: 48537225--48537323 Score: 71
Period size: 30 Copynumber: 3.3 Consensus size: 30
48537215 AAAATTCCGT
48537225 TTTTAACCTCAATTTCACCAAAAATTACCA
1 TTTTAACCTCAATTTCACCAAAAATTACCA
* * * *
48537255 TTTTACCCCTGAAGCTT---CTAAAATT-CCA
1 TTTTA-ACCTCAA-TTTCACCAAAAATTACCA
* * *
48537283 TTTTTAACCCCGATTACACCAAAAATTACCA
1 -TTTTAACCTCAATTTCACCAAAAATTACCA
*
48537314 TTTTACCCTC
1 TTTTAACCTC
48537324 GGGTATCCAT
Statistics
Matches: 49, Mismatches: 13, Indels: 14
0.64 0.17 0.18
Matches are distributed among these distances:
27 1 0.02
28 6 0.12
29 12 0.24
30 20 0.41
31 8 0.16
32 2 0.04
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (30 bp):
TTTTAACCTCAATTTCACCAAAAATTACCA
Found at i:48537343 original size:59 final size:58
Alignment explanation
Indices: 48537184--48537356 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 58
48537174 CCAAAACTTT
* ** * * * * *
48537184 CAAAAATTACCATTTTACCCCTGAATCTTTTAAAATTCCGTTTTTAACCTCAATTTCAC
1 CAAAAATTACCATTTTACCCCTG-AGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
* *
48537243 CAAAAATTACCATTTTACCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCTG-AGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
* * *
48537302 CAAAAATTACCATTTTA-CCCTCG-GGTATCCATAAGTCCCATTTTTCACCCCGATT
1 CAAAAATTACCATTTTACCCCT-GAGCT-TCCA-AAATCCCATTTTTAACCCCGATT
48537357 TCATTATTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
57 2 0.02
58 7 0.07
59 91 0.91
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTGAGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
Found at i:48549520 original size:68 final size:67
Alignment explanation
Indices: 48549270--48549764 Score: 846
Period size: 68 Copynumber: 7.3 Consensus size: 67
48549260 GGTCTCCAAG
48549270 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCAT-CCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
48549335 ACT
65 ACT
*
48549338 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGGCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
*
48549403 CA
66 CT
48549405 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
48549470 CT
66 CT
* *
48549472 TCATCCCTTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCC-TTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
48549537 ACT
65 ACT
48549540 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
48549605 CT
66 CT
* **
48549607 TCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAATA
1 TCATCCC-TTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
48549672 ACA
65 ACT
* *
48549675 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACATGTCCTCATCTCTGAAATTGAAGTAAGAGCA
1 TCAT-CCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
48549740 ACG
65 ACT
48549743 TCATCCTCTTGAAATTGAAGTA
1 TCATCC-CTTGAAATTGAAGTA
48549765 AAGTTGGATA
Statistics
Matches: 405, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
67 200 0.49
68 202 0.50
69 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (67 bp):
TCATCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
CT
Found at i:48549532 original size:135 final size:136
Alignment explanation
Indices: 48549270--48549774 Score: 874
Period size: 135 Copynumber: 3.7 Consensus size: 136
48549260 GGTCTCCAAG
48549270 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
* *
48549335 ACTTCATCCC-TTGAAATTGAAGTAGAGAGGATAACACGGCTTCATCTCTGAAATTGAAGTAAGA
66 ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
48549399 GCAACA
131 GCAACA
48549405 TCAT-CCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
*
48549469 ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAAGA
66 ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
*
48549534 GCAACT
131 GCAACA
48549540 TCAT-CCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
48549604 ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
66 ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
**
48549669 ATAACA
131 GCAACA
* *
48549675 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACATGTCCTCATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
* *
48549740 ACGTCAT-CCTCTTGAAATTGAAGTAAAGTTGGATA
66 ACTTCATCCCT-TTGAAATTGAAGTAGAG-TGGATA
48549775 GCAAAGTCTT
Statistics
Matches: 354, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
134 70 0.20
135 198 0.56
136 80 0.23
137 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (136 bp):
TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCA
ACTTCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
GCAACA
Found at i:48550092 original size:6 final size:6
Alignment explanation
Indices: 48550074--48550181 Score: 80
Period size: 6 Copynumber: 18.0 Consensus size: 6
48550064 TTAAATTGAT
* * *
48550074 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** * *
48550121 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA CATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
48550169 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
48550182 AGTCCAAATG
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.60
7 20 0.25
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:48550104 original size:17 final size:17
Alignment explanation
Indices: 48550074--48550150 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
48550064 TTAAATTGAT
48550074 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
48550090 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
48550107 TTTAAAATTAAATATTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
48550127 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
48550144 TTTAAAT
1 TTTAAAT
48550151 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:48550139 original size:11 final size:11
Alignment explanation
Indices: 48550064--48550150 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
48550054 GACTCTTGAG
* *
48550064 TTAAATTGATT
1 TTAAATTTAAT
48550075 TTAAATTT-AT
1 TTAAATTTAAT
48550085 TTAAATTTAGAT
1 TTAAATTTA-AT
*
48550097 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
48550108 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
48550122 TTAAATTTAAT
1 TTAAATTTAAT
*
48550133 TTGAATTTAAAT
1 TTAAATTT-AAT
48550145 TTAAAT
1 TTAAAT
48550151 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 14 0.23
13 9 0.15
14 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:48550177 original size:12 final size:11
Alignment explanation
Indices: 48550064--48550160 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
48550054 GACTCTTGAG
* *
48550064 TTAAATTGATT
1 TTAAATTAAAT
*
48550075 TTAAATT-TAT
1 TTAAATTAAAT
*
48550085 TTAAATTTAGAT
1 TTAAA-TTAAAT
**
48550097 TTATTTTAAAT
1 TTAAATTAAAT
48550108 TTAAAATTAAATAT
1 TT-AAATT-AA-AT
*
48550122 TTAAATTTAAT
1 TTAAATTAAAT
*
48550133 TTGAATTTAAAT
1 TT-AAATTAAAT
* *
48550145 TTAAATAAAAA
1 TTAAATTAAAT
48550156 TTAAA
1 TTAAA
48550161 ACATTAAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
10 6 0.09
11 31 0.47
12 18 0.27
13 7 0.11
14 4 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:48550229 original size:14 final size:14
Alignment explanation
Indices: 48550210--48550263 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
48550200 CATGGCCCAC
48550210 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
48550224 GGCCCAATTACAAA
1 GGCCCAATTACAAT
*
48550238 GGCCCAATT--AAG
1 GGCCCAATTACAAT
48550250 GGCCCAATTACAAT
1 GGCCCAATTACAAT
48550264 AGTCTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.31
14 24 0.69
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:48550259 original size:26 final size:27
Alignment explanation
Indices: 48550210--48550262 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
48550200 CATGGCCCAC
*
48550210 GGCCCAATTACAATGGCCCAATTACAAA
1 GGCCCAATTA-AAGGGCCCAATTACAAA
48550238 GGCCCAATT-AAGGGCCCAATTACAA
1 GGCCCAATTAAAGGGCCCAATTACAA
48550263 TAGTCTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (27 bp):
GGCCCAATTAAAGGGCCCAATTACAAA
Found at i:48552045 original size:60 final size:60
Alignment explanation
Indices: 48551947--48552128 Score: 258
Period size: 60 Copynumber: 3.0 Consensus size: 60
48551937 CCCTAAATTG
* * *
48551947 TCCAGAAATTATATTTTGACCCCAAAACTTTTCTAAAATCATATTTTAACCCCGAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTAACCCCGAAACTTT
* * **
48552008 TCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTAACCCCGAAACTTT
* *
48552068 TCCAAAATTATATTTTGACCCCAAAAC-TTTCAAAAATTACCATTTTACCCCCGAATCTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTA-CATTTTAACCCCGAAACTTT
48552128 T
1 T
48552129 AAAATTCCGT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 11 0.10
60 93 0.86
61 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTAACCCCGAAACTTT
Found at i:48552113 original size:30 final size:30
Alignment explanation
Indices: 48551947--48552106 Score: 241
Period size: 30 Copynumber: 5.3 Consensus size: 30
48551937 CCCTAAATTG
48551947 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
* * * *
48551978 TCTAAAATCATATTTTAACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
48552008 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
48552038 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
48552068 TCCAAAATTATATTTTGACCCCAAAAC-TT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48552097 TCAAAAATTA
1 TCCAAAATTA
48552107 CCATTTTACC
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
29 11 0.09
30 102 0.88
31 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:48552161 original size:59 final size:59
Alignment explanation
Indices: 48552098--48552238 Score: 219
Period size: 59 Copynumber: 2.4 Consensus size: 59
48552088 CCAAAACTTT
* * * **
48552098 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCAATTTTAC
1 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
*
48552157 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
*
48552216 CAAAAATTACCATTTTCCCCCCG
1 CAAAAATTACCATTTTACCCCCG
48552239 GGTATCCATA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 75 1.00
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACAC
Found at i:48552173 original size:30 final size:29
Alignment explanation
Indices: 48551989--48552231 Score: 106
Period size: 30 Copynumber: 8.2 Consensus size: 29
48551979 CTAAAATCAT
* *
48551989 ATTTTAACCCCGAAACTTTTCCAAAATTA-T
1 ATTTTAACCCCG-AA-TTTTCAAAAATTACC
* * *
48552019 ATTTTGACCCCAAAACTTTTCCAAAATTA-C
1 ATTTTAACCCC-GAA-TTTTCAAAAATTACC
* ** * *
48552049 ATTTTGACCCTAAAACTTTTCCAAAATTA-T
1 ATTTTAACCC-CGAA-TTTTCAAAAATTACC
* * *
48552079 ATTTTGACCCCAAAACTTTCAAAAATTACC
1 ATTTTAACCCC-GAATTTTCAAAAATTACC
* *
48552109 ATTTTACCCCCGAATCTTT-TAAAATT-CC
1 ATTTTAACCCCGAAT-TTTCAAAAATTACC
*
48552137 GTTTTTAACCCC-AATTTTACCAAAAATTACC
1 -ATTTTAACCCCGAATTTT--CAAAAATTACC
* ** *
48552168 ATTTTACCCCCGAAGCTTCTAAAATT-CC
1 ATTTTAACCCCGAATTTTCAAAAATTACC
**
48552196 ATTTTTAACCCCG-ATTACACCAAAAATTACC
1 A-TTTTAACCCCGAATT--TTCAAAAATTACC
48552227 ATTTT
1 ATTTT
48552232 CCCCCCGGGT
Statistics
Matches: 170, Mismatches: 28, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
27 3 0.02
28 9 0.05
29 45 0.26
30 104 0.61
31 9 0.05
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTAACCCCGAATTTTCAAAAATTACC
Found at i:48552191 original size:29 final size:28
Alignment explanation
Indices: 48552100--48552209 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
48552090 AAAACTTTCA
* *
48552100 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATT-CCATTTTAACCCCGAATCTTCT
* * *
48552129 AAAATTCCGTTTTTAACCCC-AATTTTACCA
1 AAAATTCC-ATTTTAACCCCGAATCTT--CT
* *
48552159 AAAATTACCATTTTACCCCCGAAGCTTCT
1 AAAATT-CCATTTTAACCCCGAATCTTCT
48552188 AAAATTCCATTTTTAACCCCGA
1 AAAATTCCA-TTTTAACCCCGA
48552210 TTACACCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
28 10 0.16
29 33 0.52
30 15 0.23
31 6 0.09
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGAATCTTCT
Found at i:48552236 original size:29 final size:29
Alignment explanation
Indices: 48552155--48552238 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
48552145 CCCCAATTTT
48552155 ACCAAAAATTACCATTTTACCCCCGAAGC
1 ACCAAAAATTACCATTTTACCCCCGAAGC
** * *
48552184 TTCTAAAATT-CCATTTTTAACCCCGATTA-C
1 ACCAAAAATTACCA-TTTTACCCCCGA--AGC
*
48552214 ACCAAAAATTACCATTTTCCCCCCG
1 ACCAAAAATTACCATTTTACCCCCG
48552239 GGTATCCATA
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.07
29 18 0.43
30 17 0.40
31 4 0.10
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (29 bp):
ACCAAAAATTACCATTTTACCCCCGAAGC
Found at i:48552257 original size:59 final size:58
Alignment explanation
Indices: 48552098--48552270 Score: 177
Period size: 59 Copynumber: 2.9 Consensus size: 58
48552088 CCAAAACTTT
* ** * * * **
48552098 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCAATTTTAC
1 CAAAAATTACCATTTTACCCCCG-AGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
* *
48552157 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCCG-AGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
* * * *
48552216 CAAAAATTACCATTTTCCCCCCG-GGTATCCATAAGTCCCATTTTTCACCCCGATT
1 CAAAAATTACCATTTTACCCCCGAGCT-TCCA-AAATCCCATTTTTAACCCCGATT
48552271 TCATTATTTA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 95 0.95
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.33
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCGAGCTTCCAAAATCCCATTTTTAACCCCGATTACAC
Found at i:48557254 original size:59 final size:59
Alignment explanation
Indices: 48557180--48557496 Score: 458
Period size: 59 Copynumber: 5.4 Consensus size: 59
48557170 TAGACTCGCG
* * * *
48557180 GGGGCAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
48557239 GGGGTAAAATAGTAATTTTTGGTTAAA-CGGGGTTAAAAATGGAATTTTGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
48557296 GGGAGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAAATGAAATTTTGGAAAGTTTA
1 GGG-GTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTTA
* * * *
48557357 GGGGTAAAATGGTAATTTTTGATGAAATTGGGGTTAAAAATAGAATTTTGGAAAATTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * *
48557416 GGGGTAAATTGATAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
48557475 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
48557497 ACCATTCAGG
Statistics
Matches: 233, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.01
58 51 0.22
59 123 0.53
60 53 0.23
61 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:48557328 original size:30 final size:30
Alignment explanation
Indices: 48557185--48557496 Score: 134
Period size: 30 Copynumber: 10.6 Consensus size: 30
48557175 TCGCGGGGGC
* * *
48557185 AAAATGGTAATTTTCGGTGAAA-TCGAGGTTA
1 AAAATGGTAATTTTTGG-GAAAGTTG-GGGTA
48557216 AAAATGG-AA-TTTT-GGAAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGGGAAAG-TT-GGGGTA
* * *
48557244 AAAATAGTAATTTTTGGTTAAACG--GGGTTA
1 AAAATGGTAATTTTTGG-GAAA-GTTGGGGTA
48557274 AAAATGG-AA-TTTT-GGAAAGTTTGGGAGT-
1 AAAATGGTAATTTTTGGGAAAG-TTGGG-GTA
48557302 AAAATGGTAATTTTTGGTGAAA-TTGGGGTTAA
1 AAAATGGTAATTTTTGG-GAAAGTTGGGG-T-A
*
48557334 AAAAT-G-AAATTTT-GGAAAGTTTAGGGGT-
1 AAAATGGTAATTTTTGGGAAAG-TT-GGGGTA
*
48557362 AAAATGGTAATTTTTGATGAAA-TTGGGGTTA
1 AAAATGGTAATTTTTG-GGAAAGTTGGGG-TA
* * *
48557393 AAAATAG-AA-TTTTGGAAAATTTAGGGGT-
1 AAAATGGTAATTTTTGGGAAAGTT-GGGGTA
* * *
48557421 AAATTGATAATTTTTGGTGAAA-TCGGGGTTA
1 AAAATGGTAATTTTTGG-GAAAGTTGGGG-TA
*
48557452 AAAATAG-AA-TTTT-GGAAAGTTCAGGGGT-
1 AAAATGGTAATTTTTGGGAAAGTT--GGGGTA
48557480 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
48557497 ACCATTCAGG
Statistics
Matches: 214, Mismatches: 25, Indels: 84
0.66 0.08 0.26
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 9 0.04
28 45 0.21
29 46 0.21
30 65 0.30
31 28 0.13
32 16 0.07
33 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGGAAAGTTGGGGTA
Found at i:48557777 original size:163 final size:163
Alignment explanation
Indices: 48557608--48557913 Score: 540
Period size: 163 Copynumber: 1.9 Consensus size: 163
48557598 AAATTTGGGC
48557608 CAATTTTATAATTAAGCAGAAGTTGATTTGAGGATTAAATTAAAACAAATTAAAAATGACAGGGA
1 CAATTTTATAATTAAGCAGAAGTTGATTTGAGGATTAAATTAAAACAAATTAAAAATGACAGGGA
* * *
48557673 CTAGATACATAAAAAAACCAAAAAGTGGCACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGG
66 CTAGATACATAAAAAAACCAAAAAGTGACACGCGGCAGCCTCTAGTGCAGTCAAACAGTCAAAGG
48557738 ACTAAATTAAAAAAGCTTAAAAGATTCTTGAGT
131 ACTAAATTAAAAAAGCTTAAAAGATTCTTGAGT
* *
48557771 CAATTTTGTAATTAAGCAGAAGTTGATTTGAGGATTAAATTAAAACAAATTAAAAATGATAGGGA
1 CAATTTTATAATTAAGCAGAAGTTGATTTGAGGATTAAATTAAAACAAATTAAAAATGACAGGGA
* * *
48557836 CTAGATACATAAATAAACCAAAAAGTGATACGCGGCAGCCTCTAGTGCAGTCAATCAGTCAAAGG
66 CTAGATACATAAAAAAACCAAAAAGTGACACGCGGCAGCCTCTAGTGCAGTCAAACAGTCAAAGG
48557901 ACTAAATTAAAAA
131 ACTAAATTAAAAA
48557914 CCAATTAAAA
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
163 135 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (163 bp):
CAATTTTATAATTAAGCAGAAGTTGATTTGAGGATTAAATTAAAACAAATTAAAAATGACAGGGA
CTAGATACATAAAAAAACCAAAAAGTGACACGCGGCAGCCTCTAGTGCAGTCAAACAGTCAAAGG
ACTAAATTAAAAAAGCTTAAAAGATTCTTGAGT
Found at i:48559529 original size:6 final size:6
Alignment explanation
Indices: 48559482--48559586 Score: 67
Period size: 6 Copynumber: 18.0 Consensus size: 6
48559472 TTTTGGGCTT
* * * *
48559482 TTTAAT TTTAAT TTTAAA ATT--A TTTCAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
** * * *
48559528 TTTAAA AATGAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT TTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
*
48559576 -ATAAA TTTAAA
1 TTTAAA TTTAAA
48559587 AATCATTTTA
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.04
5 10 0.13
6 57 0.76
7 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:48559553 original size:41 final size:42
Alignment explanation
Indices: 48559503--48559586 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
48559493 TTTTAAAATT
*
48559503 ATTTCAAATTTAAAATAAATTTAAATTTAAAAATGAATTTAA
1 ATTTCAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAA
* * *
48559545 ATTT-AAATTTAAAGTAAATTTAATTTTAGAAATAAATTTAA
1 ATTTCAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAA
48559586 A
1 A
48559587 AATCATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (42 bp):
ATTTCAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAA
Found at i:48559585 original size:18 final size:17
Alignment explanation
Indices: 48559488--48559551 Score: 76
Period size: 18 Copynumber: 3.7 Consensus size: 17
48559478 GCTTTTTAAT
* *
48559488 TTTAATTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
48559504 TTTCAAATTTAAAATAAA
1 TTT-AAATTTAAAATAAA
*
48559522 TTTAAATTTAAAAATGAA
1 TTTAAATTT-AAAATAAA
48559540 TTTAAATTTAAA
1 TTTAAATTTAAA
48559552 TTTAAAGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.07
17 19 0.45
18 20 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:48559597 original size:41 final size:41
Alignment explanation
Indices: 48559508--48559612 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
48559498 AAATTATTTC
* **
48559508 AAATTTAAAATAAATTTAAATTTAAAAATGAATTTAAATTT
1 AAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAAT
* * *
48559549 AAATTTAAAGTAAATTTAATTTTAGAAATAAATTTAAAAAT
1 AAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAAT
* * * *
48559590 CATTTTAAACTTAAATTAAAATT
1 AAATTTAAA-ATAAATTTAAATT
48559613 GATCCAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 42 0.81
42 10 0.19
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (41 bp):
AAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAAT
Found at i:48559604 original size:24 final size:24
Alignment explanation
Indices: 48559518--48559610 Score: 75
Period size: 24 Copynumber: 3.7 Consensus size: 24
48559508 AAATTTAAAA
48559518 TAAATTTAAATTTAAAAATGAA-TT
1 TAAATTTAAATTTAAAAAT-AATTT
48559542 TAAATTTAAATTTAAAGTAAATTTAATTT
1 TAAATTTAAATTT-AA--AAA--TAATTT
* *
48559571 TAGAA-ATAAATTTAAAAATCATTT
1 TA-AATTTAAATTTAAAAATAATTT
*
48559595 TAAACTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
48559611 TTGATCCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
23 8 0.14
24 24 0.41
25 2 0.03
26 3 0.05
27 3 0.05
28 4 0.07
29 12 0.21
30 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATTTAAATTTAAAAATAATTT
Found at i:48562446 original size:26 final size:27
Alignment explanation
Indices: 48562399--48562457 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
48562389 TCCCTCTATT
*
48562399 AACTATATTATTTTTAACAATTAAA-A
1 AACTATATTATTTTGAACAATTAAACA
*
48562425 AACTATATTA-TTTGAAGTAATTAAACA
1 AACTATATTATTTTGAA-CAATTAAACA
48562452 AA-TATA
1 AACTATA
48562458 ATTTCCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 21 0.72
27 3 0.10
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (27 bp):
AACTATATTATTTTGAACAATTAAACA
Found at i:48573171 original size:42 final size:42
Alignment explanation
Indices: 48573118--48573205 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
48573108 CACAATGCTG
*
48573118 ATAGTGTAACATCCGCGTTATTGAA-CAGGAGTTGGAACAATA
1 ATAGTGTAACATCCGCGTGATTGAATC-GGAGTTGGAACAATA
* * * *
48573160 ATAGTGTAACATCTGCGTGCTTGAATCGGATTTGGAACAGTA
1 ATAGTGTAACATCCGCGTGATTGAATCGGAGTTGGAACAATA
48573202 ATAG
1 ATAG
48573206 AGTACAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (42 bp):
ATAGTGTAACATCCGCGTGATTGAATCGGAGTTGGAACAATA
Found at i:48575090 original size:6 final size:6
Alignment explanation
Indices: 48575079--48575117 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
48575069 TGATCAAAAT
48575079 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
48575118 TATGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
TGAAAG
Found at i:48575321 original size:37 final size:38
Alignment explanation
Indices: 48575221--48575322 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
48575211 AACCTTGAGT
* **
48575221 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** ** *
48575262 CGATGAGGTACTGGGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
48575299 CGATGAGACACTGGGTGTCACTTT
1 CGATGAGACACTGGGTGTCACTTT
48575323 TTTGCTTCGA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
37 20 0.41
38 14 0.29
41 15 0.31
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:48579488 original size:16 final size:15
Alignment explanation
Indices: 48579469--48579521 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
48579459 AAATTCTAGG
48579469 TATTTTAGATTTTTTA
1 TATTTTA-ATTTTTTA
*
48579485 TATTTTTATATTTTTA
1 TATTTTAAT-TTTTTA
* *
48579501 TATTTTAAATATTTA
1 TATTTTAATTTTTTA
48579516 TATTTT
1 TATTTT
48579522 TAGTTTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TATTTTAATTTTTTA
Found at i:48579490 original size:8 final size:8
Alignment explanation
Indices: 48579479--48579523 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
48579469 TATTTTAGAT
48579479 TTTTTATA
1 TTTTTATA
48579487 TTTTTATA
1 TTTTTATA
48579495 TTTTTATA
1 TTTTTATA
*
48579503 -TTTTAAA
1 TTTTTATA
*
48579510 TATTTATA
1 TTTTTATA
48579518 TTTTTA
1 TTTTTA
48579524 GTTTAGAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:48579491 original size:17 final size:16
Alignment explanation
Indices: 48579471--48579524 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
48579461 ATTCTAGGTA
48579471 TTTTAGATTTTTTATAT
1 TTTTAGA-TTTTTATAT
*
48579488 TTTTATATTTTTATA-
1 TTTTAGATTTTTATAT
* *
48579503 TTTTAAATATTTATAT
1 TTTTAGATTTTTATAT
48579519 TTTTAG
1 TTTTAG
48579525 TTTAGAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 13 0.41
16 13 0.41
17 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTAGATTTTTATAT
Found at i:48579515 original size:23 final size:23
Alignment explanation
Indices: 48579480--48579523 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
48579470 ATTTTAGATT
* *
48579480 TTTTATATTTTTATATTTTTATA
1 TTTTAAATATTTATATTTTTATA
48579503 TTTTAAATATTTATATTTTTA
1 TTTTAAATATTTATATTTTTA
48579524 GTTTAGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTAAATATTTATATTTTTATA
Found at i:48579719 original size:9 final size:8
Alignment explanation
Indices: 48579695--48579754 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
48579685 AAAAGAAACC
48579695 TTAAATTT
1 TTAAATTT
*
48579703 TGAAATTT
1 TTAAATTT
48579711 TTAATATTT
1 TTAA-ATTT
48579720 TTAAAGTTT
1 TTAAA-TTT
48579729 TTAAATTT
1 TTAAATTT
48579737 TT---TTT
1 TTAAATTT
*
48579742 TTTAATTT
1 TTAAATTT
48579750 TTAAA
1 TTAAA
48579755 ACGCATGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.11
8 23 0.52
9 16 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTAAATTT
Found at i:48580766 original size:30 final size:29
Alignment explanation
Indices: 48580730--48580813 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 29
48580720 AAAAAATGAG
48580730 AAAGAACAAGAACAAGAAAGGTTTGAAACA
1 AAAGAACAAGAACAAGAAAGGTTT-AAACA
48580760 AAAGAACAAGAACAAGAAAGGTCTTAAACA
1 AAAGAACAAGAACAAGAAAGGT-TTAAACA
* * *
48580790 AAAGAACAAAAAGAAGAGAGGTTT
1 AAAGAACAAGAACAAGAAAGGTTT
48580814 TTTTAATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 2 0.04
30 46 0.92
31 2 0.04
ACGTcount: A:0.60, C:0.10, G:0.20, T:0.11
Consensus pattern (29 bp):
AAAGAACAAGAACAAGAAAGGTTTAAACA
Found at i:48582493 original size:24 final size:23
Alignment explanation
Indices: 48582432--48582501 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 23
48582422 TCTACCACTC
48582432 TTATATGGATTAAAAAGTTCGAA
1 TTATATGGATTAAAAAGTTCGAA
48582455 TTATATGGATTAAAAAGTTTC-AA
1 TTATATGGATTAAAAAG-TTCGAA
* *
48582478 TTATATTGATTGAAAAGTTCGAA
1 TTATATGGATTAAAAAGTTCGAA
48582501 T
1 T
48582502 GAGAACTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.07
23 37 0.86
24 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (23 bp):
TTATATGGATTAAAAAGTTCGAA
Found at i:48586274 original size:12 final size:12
Alignment explanation
Indices: 48586273--48586339 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
48586263 ATAACAATAA
48586273 AACAACAATAAA-
1 AACAACAA-AAAT
48586285 AACAACAAAAAT
1 AACAACAAAAAT
*
48586297 AGCAACAAAAAT
1 AACAACAAAAAT
* ** *
48586309 AATAGTAAAAAC
1 AACAACAAAAAT
48586321 AACAACAAAAAT
1 AACAACAAAAAT
48586333 AACAACA
1 AACAACA
48586340 TCAAAACAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
11 3 0.07
12 41 0.93
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:48586387 original size:21 final size:20
Alignment explanation
Indices: 48586363--48586469 Score: 78
Period size: 21 Copynumber: 5.3 Consensus size: 20
48586353 AAAAAGCATC
*
48586363 AAAACAACAACCAAAACAGT
1 AAAAAAACAACCAAAACAGT
*
48586383 AAAAAATC-A--AAAA-AGT
1 AAAAAAACAACCAAAACAGT
* *
48586399 AAAAAAATAATACCAAAACAGG
1 AAAAAAA-CA-ACCAAAACAGT
* *
48586421 AAAAATAGCAACCAAAACAGG
1 AAAAA-AACAACCAAAACAGT
* *
48586442 AAAAATAGCAACCAAAATAGT
1 AAAAA-AACAACCAAAACAGT
48586463 AAAAAAA
1 AAAAAAA
48586470 ACAGCACCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.13
17 4 0.06
19 2 0.03
20 7 0.10
21 39 0.56
22 8 0.11
23 1 0.01
ACGTcount: A:0.68, C:0.15, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAAACAACCAAAACAGT
Found at i:48586399 original size:16 final size:16
Alignment explanation
Indices: 48586374--48586404 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48586364 AAACAACAAC
*
48586374 CAAAACAGTAAAAAAT
1 CAAAAAAGTAAAAAAT
48586390 CAAAAAAGTAAAAAA
1 CAAAAAAGTAAAAAA
48586405 ATAATACCAA
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:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
CAAAAAAGTAAAAAAT
Found at i:48586416 original size:50 final size:47
Alignment explanation
Indices: 48586316--48586418 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 47
48586306 AATAATAGTA
* * * *
48586316 AAAACAACAACAAAAATAACAACATCAAAACAGTAAAAAAAAGCATC
1 AAAACAACAACAAAAATAACAAAATCAAAAAAGTAAAAAAAAACACC
*
48586363 AAAACAACAACCAAAACAGTAA-AAAATCAAAAAAGTAAAAAAATAATACC
1 AAAACAACAA-CAAAA-A-TAACAAAATCAAAAAAGTAAAAAAA-AACACC
48586413 AAAACA
1 AAAACA
48586419 GGAAAAATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
47 10 0.21
48 5 0.11
49 20 0.43
50 12 0.26
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.09
Consensus pattern (47 bp):
AAAACAACAACAAAAATAACAAAATCAAAAAAGTAAAAAAAAACACC
Found at i:48586424 original size:20 final size:20
Alignment explanation
Indices: 48586401--48586458 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
48586391 AAAAAAGTAA
48586401 AAAAATA-ATACCAAAACAGG
1 AAAAATACA-ACCAAAACAGG
48586421 AAAAATAGCAACCAAAACAGG
1 AAAAATA-CAACCAAAACAGG
48586442 AAAAATAGCAACCAAAA
1 AAAAATA-CAACCAAAA
48586459 TAGTAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.19
21 28 0.78
22 1 0.03
ACGTcount: A:0.66, C:0.17, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAAATACAACCAAAACAGG
Found at i:48587839 original size:23 final size:23
Alignment explanation
Indices: 48587813--48587857 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48587803 AAATTCGAAT
**
48587813 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
48587836 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
48587858 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:48587903 original size:13 final size:15
Alignment explanation
Indices: 48587887--48587920 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
48587877 TGAGTTCGAA
48587887 TCGAATTC-AATT-T
1 TCGAATTCGAATTAT
48587900 TCGAATTCGAATTAT
1 TCGAATTCGAATTAT
48587915 TCGAAT
1 TCGAAT
48587921 AAACTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 4 0.21
15 7 0.37
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (15 bp):
TCGAATTCGAATTAT
Found at i:48588143 original size:58 final size:58
Alignment explanation
Indices: 48588069--48588183 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
48588059 CCCATCAACA
48588069 AACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTCAAA-AACACTCATC
1 AACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATT-AAATAACACTCATC
* * *
48588127 AACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCTTAAATAACACTCAT
1 AACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAATAACACTCAT
48588184 AAACAACTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
57 3 0.06
58 50 0.94
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (58 bp):
AACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAATAACACTCATC
Found at i:48590906 original size:17 final size:17
Alignment explanation
Indices: 48590876--48590908 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48590866 AAAATTTATT
48590876 AAAAATTTATAAAAATG
1 AAAAATTTATAAAAATG
48590893 AAAATATTTA-AAAAAT
1 AAAA-ATTTATAAAAAT
48590909 AAAGAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAAATTTATAAAAATG
Found at i:48592351 original size:17 final size:18
Alignment explanation
Indices: 48592311--48592352 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
48592301 AAGTGAACCG
*
48592311 AATTTCTTTATTTTTTGTT
1 AATTT-TTTATTTTTTGTA
*
48592330 GATTTTTTA-TTTTTGTA
1 AATTTTTTATTTTTTGTA
48592347 AATTTT
1 AATTTT
48592353 AATAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 12 0.60
18 4 0.20
19 4 0.20
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (18 bp):
AATTTTTTATTTTTTGTA
Found at i:48598980 original size:22 final size:22
Alignment explanation
Indices: 48598955--48599006 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
48598945 CCTTCTTTAT
**
48598955 ATATATAATATAAAATTATTAA
1 ATATATAATATAAAATTAAAAA
*
48598977 ATAT-TAAATATTAAATTAAAAA
1 ATATAT-AATATAAAATTAAAAA
48598999 ATATATAA
1 ATATATAA
48599007 ATATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATATAATATAAAATTAAAAA
Found at i:48598998 original size:29 final size:29
Alignment explanation
Indices: 48598966--48599030 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
48598956 TATATAATAT
48598966 AAAATTAT-TAAATATTAAATATTAAATTA
1 AAAATTATATAAATATT-AATATTAAATTA
* * *
48598995 AAAAATATATAAATATTTATTTTAAATTA
1 AAAATTATATAAATATTAATATTAAATTA
48599024 AAAATTA
1 AAAATTA
48599031 ATATGGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATTATATAAATATTAATATTAAATTA
Found at i:48599020 original size:24 final size:22
Alignment explanation
Indices: 48598961--48599011 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
48598951 TTATATATAT
* **
48598961 AATATAAAATTATTAAATATTA
1 AATATTAAATTAAAAAATATTA
48598983 AATATTAAATTAAAAAATATATA
1 AATATTAAATTAAAAAATAT-TA
48599006 AATATT
1 AATATT
48599012 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATTAAATTAAAAAATATTA
Found at i:48599475 original size:2 final size:2
Alignment explanation
Indices: 48599468--48599492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48599458 AGCTTATTCA
48599468 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
48599493 ACCAAGCCAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48604574 original size:115 final size:115
Alignment explanation
Indices: 48604413--48604908 Score: 613
Period size: 115 Copynumber: 4.4 Consensus size: 115
48604403 TATATTCATC
***
48604413 ATAATTAAAGAAACA-TTCATGTTGACATCCCTATATTTAATG-CAAATAGACATCCAATTTGAG
1 ATAATTAAAGAAACATTTCAACATGACATCCCTATATTT-ATGACAAATAGACATCCAATTTGAG
* * *
48604476 TAACTCATCATCGTGACCTAAAAAAACTAATATATATTATAAACTATACTG
65 TAACTCAACATCGTGACCTAAAAAAACTAATATATATTATAAGCTATACTA
* * *
48604527 ATAATTAAAGAAACATTTCAACATGACATCCCTATTTTTGTGACAAATAAACATCCAATTTGAGT
1 ATAATTAAAGAAACATTTCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
** * *
48604592 AACTCAACATAATGACGTAAAAAAACTAATATATATATTATAAGCTATAGTA
66 AACTCAACATCGTGACCTAAAAAAACT-A-ATATATATTATAAGCTATACTA
* * * *
48604644 ATAATTGAAGAAACATTCCAACATGACAT-CTTATATTTATGACATATAGACATCCAATTTGAGT
1 ATAATTAAAGAAACATTTCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
** *
48604708 AGTTCAACATCGTGA-C--AAAAAATTAATATATATTATAAGCTATACTA
66 AACTCAACATCGTGACCTAAAAAAACTAATATATATTATAAGCTATACTA
48604755 ATAATTAAAGAAACA--T-----TGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
1 ATAATTAAAGAAACATTTCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
* * * ** *
48604813 AACTCAACATTGTGACGTAAAAAACCTTTTATATATTATAAGTTATACTA
66 AACTCAACATCGTGACCTAAAAAAACTAATATATATTATAAGCTATACTA
* * *
48604863 CTAATTAAAAAAACATTCCAACATGACATCCCTATATTTATGACAA
1 ATAATTAAAGAAACATTTCAACATGACATCCCTATATTTATGACAA
48604909 GTATGATTAA
Statistics
Matches: 324, Mismatches: 43, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
104 6 0.02
105 45 0.14
108 39 0.12
111 35 0.11
112 1 0.00
113 7 0.02
114 17 0.05
115 86 0.27
116 42 0.13
117 46 0.14
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (115 bp):
ATAATTAAAGAAACATTTCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
AACTCAACATCGTGACCTAAAAAAACTAATATATATTATAAGCTATACTA
Found at i:48604831 original size:221 final size:224
Alignment explanation
Indices: 48604413--48604908 Score: 655
Period size: 221 Copynumber: 2.2 Consensus size: 224
48604403 TATATTCATC
***
48604413 ATAATTAAAGAAACATT-CATGTTGACATCCCTATATTTAATG-CAAATAGACATCCAATTTGAG
1 ATAATTAAAGAAACATTCCAACATGACATCCCTATATTT-ATGACAAATAGACATCCAATTTGAG
* *
48604476 TAACTCATCATCGTGACCTAAAAAAACTAATATATATTATAAACTATACTGATAATTAAAGAAAC
65 TAACTCAACATCGTGACC-AAAAAAACTAATATATATTATAAACTATACTAATAATTAAAGAAAC
* *
48604541 ATTTCAACATGACATCCCTATTTTTGTGACAAATAAACATCCAATTTGAGTAACTCAACATAATG
129 A-TT----ATGACATCCCTATATTTATGACAAATAAACATCCAATTTGAGTAACTCAACATAATG
*
48604606 ACGTAAAAAAACTAATATATATATTATAAGCTATAGTA
189 ACGTAAAAAAACT--TATATATATTATAAGCTATACTA
* * *
48604644 ATAATTGAAGAAACATTCCAACATGACAT-CTTATATTTATGACATATAGACATCCAATTTGAGT
1 ATAATTAAAGAAACATTCCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
** * *
48604708 AGTTCAACATCGTGA-C-AAAAAATTAATATATATTATAAGCTATACTAATAATTAAAGAAACA-
66 AACTCAACATCGTGACCAAAAAAACTAATATATATTATAAACTATACTAATAATTAAAGAAACAT
* **
48604770 T-TGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGTAACTCAACATTGTGACGTAAA
131 TATGACATCCCTATATTTATGACAAATAAACATCCAATTTGAGTAACTCAACATAATGACGTAAA
* * *
48604834 AAACCTTTTATATATTATAAGTTATACTA
196 AAAACTTATATATATTATAAGCTATACTA
* *
48604863 CTAATTAAAAAAACATTCCAACATGACATCCCTATATTTATGACAA
1 ATAATTAAAGAAACATTCCAACATGACATCCCTATATTTATGACAA
48604909 GTATGATTAA
Statistics
Matches: 236, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
219 46 0.19
220 14 0.06
221 63 0.27
226 1 0.00
228 43 0.18
230 4 0.02
231 57 0.24
232 8 0.03
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (224 bp):
ATAATTAAAGAAACATTCCAACATGACATCCCTATATTTATGACAAATAGACATCCAATTTGAGT
AACTCAACATCGTGACCAAAAAAACTAATATATATTATAAACTATACTAATAATTAAAGAAACAT
TATGACATCCCTATATTTATGACAAATAAACATCCAATTTGAGTAACTCAACATAATGACGTAAA
AAAACTTATATATATTATAAGCTATACTA
Found at i:48606286 original size:28 final size:28
Alignment explanation
Indices: 48606255--48606314 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
48606245 AAAACGAGAC
48606255 TTTTGGA-TACCCGGGGGCAAAATGGTAA
1 TTTTGGACT-CCCGGGGGCAAAATGGTAA
*
48606283 TTTTGGACTCGCGGGGGCAAAATGGTAA
1 TTTTGGACTCCCGGGGGCAAAATGGTAA
48606311 TTTT
1 TTTT
48606315 CGGTGAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (28 bp):
TTTTGGACTCCCGGGGGCAAAATGGTAA
Found at i:48606428 original size:59 final size:58
Alignment explanation
Indices: 48606294--48606434 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 58
48606284 TTTGGACTCG
* * *
48606294 CGGGGGCAAAATGGTAATTTTCGGTGAAATCGGGATCAAAAGGGAATTTTGAAAAATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATCAAAAGAGAATTTTGAAAAATT
* * * * * *
48606352 CGAGGGTAATATAGTAATTTTTGGTGAAATCGAGG-TCGAAAATAGAATTTTGGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCG-GGATC-AAAAGAGAATTTTGAAAAATT
48606411 CGGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
48606435 ACCATCCAGG
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 29 0.42
59 40 0.58
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGATCAAAAGAGAATTTTGAAAAATT
Found at i:48607050 original size:20 final size:20
Alignment explanation
Indices: 48607027--48607065 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
48607017 ATCGACGCTC
48607027 CCGGTCACGCATCT-CCATCT
1 CCGGTCACGC-TCTGCCATCT
*
48607047 CCGGTCGCGCTCTGCCATC
1 CCGGTCACGCTCTGCCATC
48607066 GTCAGACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.10, C:0.46, G:0.21, T:0.23
Consensus pattern (20 bp):
CCGGTCACGCTCTGCCATCT
Found at i:48607526 original size:3 final size:3
Alignment explanation
Indices: 48607518--48607551 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
48607508 TAATGTTGTA
48607518 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
48607552 ATGTCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:48608363 original size:17 final size:17
Alignment explanation
Indices: 48608338--48608426 Score: 110
Period size: 17 Copynumber: 5.2 Consensus size: 17
48608328 ATTTTAATCC
*
48608338 AAAATAAATTCAAATTT
1 AAAATAAATTTAAATTT
*
48608355 AACATAAATTTAAATTCT
1 AAAATAAATTTAAATT-T
*
48608373 -AAATGAATTTAAATTT
1 AAAATAAATTTAAATTT
48608389 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
*
48608406 AAAATAAA-CTAAGATTT
1 AAAATAAATTTAA-ATTT
48608423 AAAA
1 AAAA
48608427 AATTAAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.06
17 58 0.92
18 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:48608368 original size:6 final size:6
Alignment explanation
Indices: 48608342--48608408 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
48608332 TAATCCAAAA
* *
48608342 TAAATT CAAATT TAACA-- TAAATT TAAATT CTAAA-- TGAATT TAAATT
1 TAAATT TAAATT TAA-ATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
48608388 TAAA-A TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
48608409 ATAAACTAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
4 4 0.08
5 7 0.15
6 32 0.67
7 5 0.10
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:48608725 original size:21 final size:19
Alignment explanation
Indices: 48608696--48608740 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
48608686 TAATTCAATT
*
48608696 AATTCAAATTATTTAATTTAA
1 AATTTAAATT-TTTAA-TTAA
*
48608717 AATTTAAATTTTTTATTAA
1 AATTTAAATTTTTAATTAA
48608736 AATTT
1 AATTT
48608741 TCAAATCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTAAATTTTTAATTAA
Found at i:48608746 original size:21 final size:22
Alignment explanation
Indices: 48608698--48608746 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
48608688 ATTCAATTAA
48608698 TTCAAATTATTTAATTTAAAAT
1 TTCAAATTATTTAATTTAAAAT
*
48608720 TT-AAATT-TTTTA-TTAAAATT
1 TTCAAATTATTTAATTTAAAA-T
48608740 TTCAAAT
1 TTCAAAT
48608747 CGAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.25
20 7 0.29
21 9 0.38
22 2 0.08
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTCAAATTATTTAATTTAAAAT
Found at i:48609583 original size:111 final size:115
Alignment explanation
Indices: 48609335--48609622 Score: 345
Period size: 111 Copynumber: 2.5 Consensus size: 115
48609325 GAATTTTAAA
* * ** *
48609335 AAGTCAAAATTCAAAAAACTTCGTATAAAAAAAAAGTGATAATCT-AAACCAGAACCAATCTAGA
1 AAGTCCAAATTCAGAAAACTTCAAATAAAAAAAAA-TGATAATCTAAAACCACAACCAATCTAGA
*
48609399 TAAAAAGAAAATTCAAACCTAAAAATTCTAAAAAGGAAACTCAAACCTTGAGT
65 T-AAAAGAAAATTCAAACCTAAAAATTCTAAAAAGGAAACGC-AACCTTGAGT
* * *
48609452 AAGCCCAAATTCAGAAAACTTCAAATAAAAAAAAATGATAATCTAAAACTACAACCAATCTCGAT
1 AAGTCCAAATTCAGAAAACTTCAAATAAAAAAAAATGATAATCTAAAACCACAACCAATCTAGAT
* * * * * *
48609517 -GAAG-AAATTCAAATCTAAAAATTCTATATATGACA-GC-ACCTTGAGT
66 AAAAGAAAATTCAAACCTAAAAATTCTAAAAAGGAAACGCAACCTTGAGT
* * *
48609563 AAGTCCAAAGTCAGAAAACTTCAAATAAAAAAAAATGATAATCT-AAACCAGAATCAATCT
1 AAGTCCAAATTCAGAAAACTTCAAATAAAAAAAAATGATAATCTAAAACCACAACCAATCT
48609623 GGATGTGATA
Statistics
Matches: 150, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
110 13 0.09
111 51 0.34
113 1 0.01
114 26 0.17
115 3 0.02
116 9 0.06
117 47 0.31
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.22
Consensus pattern (115 bp):
AAGTCCAAATTCAGAAAACTTCAAATAAAAAAAAATGATAATCTAAAACCACAACCAATCTAGAT
AAAAGAAAATTCAAACCTAAAAATTCTAAAAAGGAAACGCAACCTTGAGT
Found at i:48615451 original size:18 final size:18
Alignment explanation
Indices: 48615428--48615464 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48615418 AAAAAAAACT
* *
48615428 TGTATAATAATATTGAAA
1 TGTATAAAAATATTAAAA
48615446 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
48615464 T
1 T
48615465 AAAATTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:48617308 original size:19 final size:21
Alignment explanation
Indices: 48617286--48617334 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
48617276 TTAAAACTTG
48617286 TTAAATGAA-TAAAAATTC-C
1 TTAAATGAATTAAAAATTCAC
** *
48617305 TTAAAAAAATTAAAATTTCAC
1 TTAAATGAATTAAAAATTCAC
48617326 TTAAATGAA
1 TTAAATGAA
48617335 GTTTTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 7 0.30
20 8 0.35
21 8 0.35
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAAATGAATTAAAAATTCAC
Found at i:48617580 original size:21 final size:20
Alignment explanation
Indices: 48617547--48617586 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
48617537 ATATACCCCA
48617547 TTTTTAAATATTTAAGTAAAC
1 TTTTTAAATATTTAA-TAAAC
48617568 TTTTATAAA-ATTTAATAAA
1 TTTT-TAAATATTTAATAAA
48617587 TTAAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTTAAATATTTAATAAAC
Found at i:48627210 original size:32 final size:32
Alignment explanation
Indices: 48627159--48627219 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
48627149 TTACATAATA
48627159 AATTAATATTTTATATTTAAA-ATTATTTATTT
1 AATTAATATTTTATATTTAAATATT-TTTATTT
*
48627191 AATTAAT-TTTATATTTTTAAATATTTTTA
1 AATTAATATTT-TATATTTAAATATTTTTA
48627220 AAAAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 3 0.12
32 20 0.77
33 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
AATTAATATTTTATATTTAAATATTTTTATTT
Found at i:48628610 original size:21 final size:21
Alignment explanation
Indices: 48628551--48628612 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
48628541 ACCTTTTCTA
*
48628551 AAGTTAAAAA-TCAAAACCATT
1 AAGTTAAAAAGT-AAAACTATT
*
48628572 AAATTAAAAAGTAAAACTATT
1 AAGTTAAAAAGTAAAACTATT
48628593 AAGTTAAAAAGTAAAACTAT
1 AAGTTAAAAAGTAAAACTAT
48628613 GTCATTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (21 bp):
AAGTTAAAAAGTAAAACTATT
Found at i:48638870 original size:79 final size:77
Alignment explanation
Indices: 48638729--48638942 Score: 223
Period size: 79 Copynumber: 2.7 Consensus size: 77
48638719 TGATGTCGGC
* * * * * * *
48638729 TTAATTGACTAGAGCTGGGATCACATTTGCGGTTTATCCGCTAGGCATTGGGTGTCAGGATTTGA
1 TTAACTGACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTGTCAAGATTTGA
*
48638794 CGGACGTTGTCAG
66 CGGACATTGT-AG
**
48638807 TTTAACTGACTAGAGTTGGGCTCACATTTGCGGTTTATCTTCTAAGCACTAGGTG-CTAAGATTT
1 -TTAACTGACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTGTC-AAGATTT
* * *
48638871 GATGGATATTGTTG
64 GACGGACATTGTAG
** * * *
48638885 TTAATCCAACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGTCA
1 TTAA-CTGACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTGTCA
48638943 TAACTGTCGG
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
77 4 0.04
78 46 0.41
79 62 0.55
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (77 bp):
TTAACTGACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTAGGTGTCAAGATTTGA
CGGACATTGTAG
Found at i:48640753 original size:39 final size:39
Alignment explanation
Indices: 48640710--48640806 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 39
48640700 AGTCATGCGA
* * * * *
48640710 TGTTTATAGTGTCACTGTCGGTTCGAAATAGC-ATCGCAG
1 TGTTTACAGTGTCACTGCCCGTTCAAAATAGCTA-CACAG
48640749 TGTTTACAGTGTCACTGCCCGTTCAAAATAGCTACACAG
1 TGTTTACAGTGTCACTGCCCGTTCAAAATAGCTACACAG
48640788 TGTTTACAGTGTCACTGCC
1 TGTTTACAGTGTCACTGCC
48640807 AGCTCTGTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (39 bp):
TGTTTACAGTGTCACTGCCCGTTCAAAATAGCTACACAG
Found at i:48646920 original size:58 final size:57
Alignment explanation
Indices: 48646851--48646970 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 57
48646841 AAAAGGAGTT
* *
48646851 GTTTATGAGTGTTATTTTG-GAATAAAATTATATTTAGGTTTGAAAATATTCGGGTTTA
1 GTTTATAAGTG-T-TTTTGAGAATAAAATTATATTTAGGTTTAAAAATATTCGGGTTTA
* * * *
48646909 GTTTATAAGTGTTTTTGAAGGATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATAAGTGTTTTTG-AGAATAAAATTATATTTAGGTTTAAAAATATTCGGGTTTA
48646967 GTTT
1 GTTT
48646971 GTTGATGGGC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
56 5 0.09
57 1 0.02
58 48 0.89
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (57 bp):
GTTTATAAGTGTTTTTGAGAATAAAATTATATTTAGGTTTAAAAATATTCGGGTTTA
Found at i:48647233 original size:23 final size:23
Alignment explanation
Indices: 48647190--48647234 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48647180 AAAAAAATTC
**
48647190 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
48647213 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
48647235 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:48647631 original size:30 final size:29
Alignment explanation
Indices: 48647597--48647675 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
48647587 ATTTAACTTT
*
48647597 AATAAAAATGTTAATTTTAATAGTAATAAA
1 AATAAAAATTTTAATTTT-ATAGTAATAAA
* **
48647627 AATAAAAATATTTTATTTTATTTTAATAAA
1 AATAAAAAT-TTTAATTTTATAGTAATAAA
*
48647657 AATTAAATATTTTAATTTT
1 AA-TAAAAATTTTAATTTT
48647676 CATCAACAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 28 0.68
31 13 0.32
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
AATAAAAATTTTAATTTTATAGTAATAAA
Found at i:48647930 original size:14 final size:15
Alignment explanation
Indices: 48647911--48647940 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
48647901 GGGAATTTTG
48647911 AATTAAAATTT-TAA
1 AATTAAAATTTATAA
48647925 AATTAAAATTTATAA
1 AATTAAAATTTATAA
48647940 A
1 A
48647941 TTATATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAAATTTATAA
Found at i:48651891 original size:18 final size:18
Alignment explanation
Indices: 48651850--48651892 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
48651840 TTCTATAATT
* *
48651850 TAAAAATATTAAATTATA
1 TAAAAATATTAAAATAAA
*
48651868 TTAAAATATTAAAATAAA
1 TAAAAATATTAAAATAAA
48651886 TAAAAAT
1 TAAAAAT
48651893 TATAGTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATATTAAAATAAA
Found at i:48652004 original size:21 final size:20
Alignment explanation
Indices: 48651980--48652023 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
48651970 TTTTTATAAC
48651980 ATATTTAT-TATAATAGTAAAA
1 ATATTTATATA-AATA-TAAAA
48652001 ATATTTATATAAATATAAAA
1 ATATTTATATAAATATAAAA
48652021 ATA
1 ATA
48652024 ACAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 12 0.55
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATTTATATAAATATAAAA
Found at i:48652019 original size:20 final size:21
Alignment explanation
Indices: 48651980--48652023 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
48651970 TTTTTATAAC
48651980 ATATTTATTATAATAGTAAAA
1 ATATTTATTATAATAGTAAAA
48652001 ATATTTA-TATAAATA-TAAAA
1 ATATTTATTAT-AATAGTAAAA
48652021 ATA
1 ATA
48652024 ACAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATTTATTATAATAGTAAAA
Found at i:48652712 original size:2 final size:2
Alignment explanation
Indices: 48652700--48652745 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48652690 AATTAAAATG
*
48652700 TA TA AA TA TA TA 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 TA TA TA
48652742 TA TA
1 TA TA
48652746 AAGGGTTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:48654857 original size:19 final size:19
Alignment explanation
Indices: 48654814--48654883 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
48654804 ATTACAAAAT
*
48654814 AATTCAAAATAATTTTCCAAA
1 AATTCAAAAT-ATTTT-TAAA
*
48654835 AATTCAAAATATTTTTTAA
1 AATTCAAAATATTTTTAAA
*
48654854 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTTTAAA
48654873 AATTTCAAAAT
1 AA-TTCAAAAT
48654884 TTATATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 21 0.48
20 13 0.30
21 10 0.23
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTTTAAA
Found at i:48658660 original size:3 final size:3
Alignment explanation
Indices: 48658652--48658679 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48658642 TTGATTCACT
48658652 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
48658680 CGCACATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:48661032 original size:23 final size:23
Alignment explanation
Indices: 48661002--48661126 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
48660992 ACCCTAGCGC
*
48661002 GCTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCACTGTCT-GT
*
48661025 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTCTGT
* * *
48661048 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTCTGT
* * * *
48661071 ACTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTCTGT
* * *
48661094 ACTCTCTATTATTAGCACTGTGTGT
1 GCTCTC--TGATTAGCACTGTCTGT
48661119 GCTCTCTG
1 GCTCTCTG
48661127 TTGCCTAGCA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
23 66 0.74
24 4 0.04
25 19 0.21
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTCTGT
Found at i:48661122 original size:71 final size:69
Alignment explanation
Indices: 48661033--48661171 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 69
48661023 GTGCTCTCTG
*
48661033 ATTAGCACTGTGTGTGCTCTCTGAT-TAGTACTT-TGTGTACTCTCTGATTAGTACTTTGTGTAC
1 ATTAGCACTGTGTGTGCTCTCTGATCTAGCACTTATGTG--CTCTCTG-TTAGTACTTTG-GTAC
48661096 TCTCTATT
62 TCTCTATT
*
48661104 ATTAGCACTGTGTGTGCTCTCTGTTGCCTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTC
1 ATTAGCACTGTGTGTGCTCTCTGAT--CTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTC
48661169 TCT
64 TCT
48661172 GCTTGTTCCG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
71 33 0.53
72 11 0.18
73 7 0.11
74 7 0.11
75 4 0.06
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (69 bp):
ATTAGCACTGTGTGTGCTCTCTGATCTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTC
TATT
Found at i:48664351 original size:7 final size:7
Alignment explanation
Indices: 48664339--48664363 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48664329 TTTTGGAATT
48664339 TTTTATA
1 TTTTATA
48664346 TTTTATA
1 TTTTATA
48664353 TTTTATA
1 TTTTATA
48664360 TTTT
1 TTTT
48664364 TGAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:48664411 original size:21 final size:21
Alignment explanation
Indices: 48664387--48664426 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48664377 AAATTTTTAA
48664387 TTATATATTTT-TTTAAAATTT
1 TTATAT-TTTTATTTAAAATTT
*
48664408 TTATGTTTTTATTTAAAAT
1 TTATATTTTTATTTAAAAT
48664427 ACGAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATATTTTTATTTAAAATTT
Found at i:48678107 original size:49 final size:50
Alignment explanation
Indices: 48678034--48678132 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 50
48678024 CATCTATTTA
* **
48678034 AAGGTTGAAAAAACATTATTCTAATAAAAGTTAAATAGGTGAAGTGTAGT
1 AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAGTGTAGT
* * *
48678084 AAGGTTG-AACAACATTATTCTAATCAATGTCAAATAGAAGAAGTGTAGT
1 AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAGTGTAGT
48678133 TCTATATGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 36 0.84
50 7 0.16
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.29
Consensus pattern (50 bp):
AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAGTGTAGT
Found at i:48679620 original size:20 final size:21
Alignment explanation
Indices: 48679581--48679620 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48679571 TATAATTTTT
*
48679581 TATATTTTTAATCAATATAATA
1 TATATTTTTAA-CAAAATAATA
48679603 TATATTTTTAA-AAAATAA
1 TATATTTTTAACAAAATAA
48679621 AAGAAGACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATTTTTAACAAAATAATA
Found at i:48680554 original size:14 final size:15
Alignment explanation
Indices: 48680519--48680547 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48680509 TTATTTATAA
48680519 AATAATTATATAATT
1 AATAATTATATAATT
48680534 AATAATTA-ATAATT
1 AATAATTATATAATT
48680548 TTTAATTTTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATTATATAATT
Found at i:48680585 original size:7 final size:7
Alignment explanation
Indices: 48680521--48680588 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
48680511 ATTTATAAAA
48680521 TAATTAT
1 TAATTAT
*
48680528 ATAATTAA
1 -TAATTAT
*
48680536 TAATTAA
1 TAATTAT
*
48680543 TAATTTT
1 TAATTAT
*
48680550 TAATTTT
1 TAATTAT
48680557 TAATT-T
1 TAATTAT
48680563 T-ATT-T
1 TAATTAT
48680568 T-ATTAAT
1 TAATT-AT
48680575 TAATTAT
1 TAATTAT
48680582 TAATTAT
1 TAATTAT
48680589 ATAAATGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
5 8 0.15
6 2 0.04
7 35 0.65
8 9 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATTAT
Found at i:48683008 original size:31 final size:31
Alignment explanation
Indices: 48682973--48683070 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
48682963 ATATAAGAAA
48682973 AAATTCAATATTTCTTAAATTTTATTTAATT
1 AAATTCAATATTTCTTAAATTTTATTTAATT
* * *
48683004 AAATT-TATATTATATTATATTTTTTATTT--TT
1 AAATTCAATATT-TCTTA-A-ATTTTATTTAATT
* * *
48683035 AAAGTCAATTTTTCTTAAAATTTATTTAATT
1 AAATTCAATATTTCTTAAATTTTATTTAATT
48683066 AAATT
1 AAATT
48683071 TATATTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
29 7 0.14
30 6 0.12
31 25 0.49
32 5 0.10
33 8 0.16
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (31 bp):
AAATTCAATATTTCTTAAATTTTATTTAATT
Found at i:48683052 original size:62 final size:64
Alignment explanation
Indices: 48682977--48683101 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 64
48682967 AAGAAAAAAT
*
48682977 TCAATATTTCTTAAATTTTATTTAATTAAATTTATATTATA-T-TATATTTTTTATTTTTAAAG
1 TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTATATTATATATTTTTTATTTTTAAAG
* *
48683039 TCAATTTTTCTTAAAATTTATTTAATTAAATTTATATTGTATTATATATTTTTTATTTTTAAA
1 TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTATATTATATATTTTTTATTTTTAAA
48683102 TTTAACGGTG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 38 0.66
63 1 0.02
64 19 0.33
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (64 bp):
TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTATATTATATATTTTTTATTTTTAAAG
Found at i:48683846 original size:26 final size:26
Alignment explanation
Indices: 48683817--48683867 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
48683807 TTTTAAATCA
*
48683817 AATTTTTTAAAATATATTTTAAAAGG
1 AATTTTTCAAAATATATTTTAAAAGG
* * *
48683843 AATTTTTCATATTATTTTTTAAAAG
1 AATTTTTCAAAATATATTTTAAAAG
48683868 CAATGCTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (26 bp):
AATTTTTCAAAATATATTTTAAAAGG
Found at i:48685936 original size:101 final size:101
Alignment explanation
Indices: 48685752--48685951 Score: 231
Period size: 101 Copynumber: 2.0 Consensus size: 101
48685742 TATTTAAGTG
* * *
48685752 TATATATTAATATATTTATTTACTATTTATTATATAGCAACATACTCATTAATTGCTCATCTATT
1 TATATATTAACATATTTACTTACTATTTATTATACAGCAACATACTCATTAATTGCTCATCTATT
* ** *
48685817 ATTTCCTTGGAAACTCAAAACATTTTTAAAAAATATA
66 ATTTCATACGAAACTCAAAAC-GTTTTAAAAAATATA
* ** * * * *
48685854 TATATATTAACATATTTACTTATTATTT-TTATACATTAATATATTCATTAATTGCTTATTTATT
1 TATATATTAACATATTTACTTACTATTTATTATACAGCAACATACTCATTAATTGCTCATCTATT
* * *
48685918 ATTTTATACGAAATTCAAAACGTTTTAATAAATA
66 ATTTCATACGAAACTCAAAACGTTTTAAAAAATA
48685952 AAAATAAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
100 11 0.14
101 45 0.56
102 25 0.31
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (101 bp):
TATATATTAACATATTTACTTACTATTTATTATACAGCAACATACTCATTAATTGCTCATCTATT
ATTTCATACGAAACTCAAAACGTTTTAAAAAATATA
Found at i:48688718 original size:25 final size:24
Alignment explanation
Indices: 48688681--48688829 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
48688671 ACACTAGCGC
48688681 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
48688704 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
48688729 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
48688752 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
48688775 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
48688798 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
48688821 GCTCTCTGT
1 GCTCTCTGT
48688830 TGCCCAGCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:48688781 original size:46 final size:46
Alignment explanation
Indices: 48688702--48688828 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
48688692 AGCACGTCTC
48688702 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
48688750 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
48688796 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTG
48688829 TTGCCCAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 64 0.86
48 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:48688820 original size:69 final size:68
Alignment explanation
Indices: 48688681--48688874 Score: 214
Period size: 69 Copynumber: 2.8 Consensus size: 68
48688671 ACACTAGCGC
* * * * * *
48688681 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTCAGCACTTAT-GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGATTAGCACT
*
48688746 TTGTGT
63 GTGTGT
* *
48688752 GCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTG
1 GCTCTCTG-TTCAGCAC-TTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTG
48688816 TGTGT
64 TGTGT
48688821 GCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCTG
1 GCTCTCTGTT---CAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTG
48688875 CTTGTTCCGT
Statistics
Matches: 109, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 51 0.47
70 11 0.10
71 36 0.33
72 9 0.08
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (68 bp):
GCTCTCTGTTCAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTGTG
TGT
Found at i:48689460 original size:29 final size:29
Alignment explanation
Indices: 48689418--48689580 Score: 141
Period size: 29 Copynumber: 5.5 Consensus size: 29
48689408 GTGTTACACT
* *
48689418 TAAAC-TTTCCTAAAATCATATTTTTACCC
1 TAAACTTTTCC-AAAATCACATTTTGACCC
* * *
48689447 TAAACTTTTCTAAAATTACATTTTGGCCCC
1 TAAACTTTTCCAAAATCACATTTT-GACCC
* * *
48689477 TGAACTTTTCCAAAATTACAGTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGA-CCC
* *
48689507 TTTAAACCTTTCCAAAATCACATTTT-AACC
1 --TAAACTTTTCCAAAATCACATTTTGACCC
* * *
48689537 TCAAACTTCTCCAAAATCACATCTTAACCC
1 T-AAACTTTTCCAAAATCACATTTTGACCC
48689567 TAAACTTTTCCAAA
1 TAAACTTTTCCAAA
48689581 TTTATGTTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
28 1 0.01
29 49 0.45
30 37 0.34
31 1 0.01
32 20 0.19
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAACTTTTCCAAAATCACATTTTGACCC
Found at i:48691626 original size:20 final size:19
Alignment explanation
Indices: 48691563--48691628 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
48691553 GTATTTCAAC
48691563 ATTTTTTGAATTTTCAAAATA
1 ATTTTTTGAATTTT--AAATA
* * *
48691584 ATTTTAAT-AATTTTATATT
1 ATTTT-TTGAATTTTAAATA
48691603 ATTTTCTTGAATTTTAAATA
1 ATTTT-TTGAATTTTAAATA
48691623 ATTTTT
1 ATTTTT
48691629 AGTACTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 10 0.28
20 14 0.39
21 11 0.31
22 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTTTGAATTTTAAATA
Found at i:48691647 original size:29 final size:30
Alignment explanation
Indices: 48691583--48691645 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
48691573 TTTTCAAAAT
*
48691583 AATTTT-AATAATTTTATATTATTTTCTTG
1 AATTTTAAATAATTTTATAGTATTTTCTTG
48691612 AATTTTAAATAATTTT-TAGTACTTTT-TT-
1 AATTTTAAATAATTTTATAGTA-TTTTCTTG
48691640 AATTTT
1 AATTTT
48691646 TAATTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 12 0.39
30 13 0.42
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTTTAAATAATTTTATAGTATTTTCTTG
Found at i:48692249 original size:16 final size:15
Alignment explanation
Indices: 48692228--48692265 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
48692218 GGCTATAGTA
48692228 TAAATTTATAAAAAAT
1 TAAATTTA-AAAAAAT
*
48692244 TAAATTGAAAAAAAT
1 TAAATTTAAAAAAAT
48692259 TAAATTT
1 TAAATTT
48692266 TAAGGAGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAATTTAAAAAAAT
Found at i:48694405 original size:21 final size:22
Alignment explanation
Indices: 48694376--48694418 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
48694366 AATTGGTTAC
*
48694376 AAAATGAGC-TAGAACATATTT
1 AAAACGAGCATAGAACATATTT
48694397 AAAACGAGCTATAGAACATATT
1 AAAACGAGC-ATAGAACATATT
48694419 CAGATAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAACGAGCATAGAACATATTT
Found at i:48696441 original size:17 final size:18
Alignment explanation
Indices: 48696413--48696463 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
48696403 CAATGCTTTT
48696413 TAAAAATAATTTTTG-T-C
1 TAAAAAT-ATTTTTGATAC
48696430 TCAAAAATATTTTTGATAC
1 T-AAAAATATTTTTGATAC
*
48696449 TAAAAATACTTTTGA
1 TAAAAATATTTTTGA
48696464 AAAATTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.27
18 20 0.67
19 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (18 bp):
TAAAAATATTTTTGATAC
Found at i:48721397 original size:15 final size:17
Alignment explanation
Indices: 48721366--48721404 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
48721356 TTATATTATT
48721366 TTTAAT-TT-TTTTAAA
1 TTTAATATTATTTTAAA
48721381 TTT-ATATTATTTT-AA
1 TTTAATATTATTTTAAA
48721396 TTTAATATT
1 TTTAATATT
48721405 TAATTAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 10 0.48
16 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAATATTATTTTAAA
Found at i:48727071 original size:28 final size:27
Alignment explanation
Indices: 48727021--48727074 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
48727011 GGCAAAACCA
48727021 TTATACTGTTTATGTAGTCAAATAATC
1 TTATACTGTTTATGTAGTCAAATAATC
*
48727048 TTATACTTCGTTTAT-TAGTTAAATAAT
1 TTATAC-T-GTTTATGTAGTCAAATAAT
48727075 TGGTCCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 12 0.50
29 6 0.25
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (27 bp):
TTATACTGTTTATGTAGTCAAATAATC
Found at i:48727387 original size:41 final size:42
Alignment explanation
Indices: 48727342--48727433 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
48727332 TTTGTTTTAG
* *
48727342 TCAAGGAAAAA-AACTTCTACGTGGAGGCGTTTTTATCTCAT
1 TCAAGGAAAAAGAACTTCCACGTGGAGGCATTTTTATCTCAT
** *
48727383 TCAA-GAAAAAGTGCTTCCACGTGGAGGCATTTTTTTCTCAT
1 TCAAGGAAAAAGAACTTCCACGTGGAGGCATTTTTATCTCAT
48727424 TCAAGGAAAA
1 TCAAGGAAAA
48727434 GTGCTTCCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 6 0.14
41 33 0.75
42 5 0.11
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (42 bp):
TCAAGGAAAAAGAACTTCCACGTGGAGGCATTTTTATCTCAT
Found at i:48727434 original size:41 final size:41
Alignment explanation
Indices: 48727355--48727444 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
48727345 AGGAAAAAAA
* *
48727355 CTTCTACGTGGAGGCGTTTTTATCTCATTCAAGAAAAAGTG
1 CTTCCACGTGGAGGCATTTTTATCTCATTCAAGAAAAAGTG
* *
48727396 CTTCCACGTGGAGGCATTTTTTTCTCATTCAAGGAAAAGTG
1 CTTCCACGTGGAGGCATTTTTATCTCATTCAAGAAAAAGTG
48727437 CTTCCACG
1 CTTCCACG
48727445 CGGAAGCGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
CTTCCACGTGGAGGCATTTTTATCTCATTCAAGAAAAAGTG
Found at i:48739323 original size:16 final size:16
Alignment explanation
Indices: 48739304--48739350 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
48739294 CTGATTATAG
48739304 CTCTATTCCATTACAA
1 CTCTATTCCATTACAA
* *
48739320 CTCTATTTCATTACAT
1 CTCTATTCCATTACAA
*
48739336 CTTTATTCCATTACA
1 CTCTATTCCATTACA
48739351 GCGAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (16 bp):
CTCTATTCCATTACAA
Found at i:48743125 original size:22 final size:22
Alignment explanation
Indices: 48743097--48743140 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48743087 AAAATGTAGT
48743097 TGGTGCTAATTTGGCTAACGAA
1 TGGTGCTAATTTGGCTAACGAA
48743119 TGGTGCTAATTTGGCTAACGAA
1 TGGTGCTAATTTGGCTAACGAA
48743141 AGCGGTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (22 bp):
TGGTGCTAATTTGGCTAACGAA
Found at i:48749866 original size:23 final size:21
Alignment explanation
Indices: 48749832--48749882 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
48749822 GTTAATCAAT
**
48749832 AAATAAATTAAAATTTATAAA
1 AAATAAATTAAAAACTATAAA
48749853 AAATCAAATTTAAAAACTATAAA
1 AAAT-AAA-TTAAAAACTATAAA
*
48749876 AATTAAA
1 AAATAAA
48749883 AAAATGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
23 15 0.60
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAATTAAAAACTATAAA
Found at i:48751323 original size:15 final size:15
Alignment explanation
Indices: 48751292--48751320 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48751282 GAGTAAAATT
48751292 TTAACAGTAATTCAA
1 TTAACAGTAATTCAA
48751307 TTAAC-GTAATTCAA
1 TTAACAGTAATTCAA
48751321 ATTCAAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (15 bp):
TTAACAGTAATTCAA
Found at i:48752368 original size:17 final size:17
Alignment explanation
Indices: 48752325--48752368 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
48752315 AATGGAAAAT
48752325 AAAGAAAAAAGAAAAGA
1 AAAGAAAAAAGAAAAGA
** * *
48752342 AAAGTTAAAAGAACATA
1 AAAGAAAAAAGAAAAGA
48752359 AAAGAAAAAA
1 AAAGAAAAAA
48752369 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAGA
Found at i:48755284 original size:43 final size:43
Alignment explanation
Indices: 48755236--48755317 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
48755226 AATGTTAATA
48755236 GCATGAGTTCAAAATTCATCATATGTAAGATTTTAATTGGTTT
1 GCATGAGTTCAAAATTCATCATATGTAAGATTTTAATTGGTTT
48755279 GCATGAGTTCAAAATTCATCATATGTAAGATTTTAATTG
1 GCATGAGTTCAAAATTCATCATATGTAAGATTTTAATTG
48755318 ATTTTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (43 bp):
GCATGAGTTCAAAATTCATCATATGTAAGATTTTAATTGGTTT
Found at i:48759420 original size:39 final size:40
Alignment explanation
Indices: 48759366--48759445 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
48759356 TATGCACTCA
48759366 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
* * *
48759405 ATGGACATCTTTTGAAGATTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
48759445 A
1 A
48759446 CATACCTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:48764367 original size:39 final size:40
Alignment explanation
Indices: 48764313--48764392 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
48764303 TATGCACTCA
48764313 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
*
48764352 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
48764392 A
1 A
48764393 CATACCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 28 0.72
40 11 0.28
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:48764408 original size:39 final size:38
Alignment explanation
Indices: 48764317--48764409 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
48764307 CACTCAATGG
* *
48764317 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
48764356 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
48764394 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
48764410 ACTTGTCCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 5 0.10
39 32 0.67
40 11 0.23
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:48771762 original size:17 final size:18
Alignment explanation
Indices: 48771739--48771789 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
48771729 TTGATTTTTC
48771739 ATAATTTTTTTATAATTT
1 ATAATTTTTTTATAATTT
48771757 AT-ATTTTTTTA-AATTT
1 ATAATTTTTTTATAATTT
* *
48771773 TTAATATTTTTATAATT
1 ATAATTTTTTTATAATT
48771790 AAAGATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 6 0.21
17 17 0.59
18 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATAATTTTTTTATAATTT
Found at i:48772002 original size:21 final size:20
Alignment explanation
Indices: 48771978--48772025 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
48771968 AAATTGATTG
*
48771978 ATTAAATCGAAAAAAATAATA
1 ATTAAAT-GAAAAAAATAAAA
**
48771999 ATTAAATGATTAAAATAAAA
1 ATTAAATGAAAAAAATAAAA
48772019 ATTAAAT
1 ATTAAAT
48772026 TATTGAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
ATTAAATGAAAAAAATAAAA
Found at i:48772456 original size:3 final size:3
Alignment explanation
Indices: 48772448--48772474 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48772438 AACCCAAAAG
48772448 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
48772475 AGAAAGAATA
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:48773794 original size:7 final size:7
Alignment explanation
Indices: 48773782--48773818 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
48773772 GACTTACTCT
48773782 ATCTGCA
1 ATCTGCA
48773789 ATCTGCA
1 ATCTGCA
48773796 ATCTGCA
1 ATCTGCA
48773803 ATCTGCA
1 ATCTGCA
*
48773810 ATCTTCA
1 ATCTGCA
48773817 AT
1 AT
48773819 TCCTTTTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (7 bp):
ATCTGCA
Found at i:48780051 original size:6 final size:6
Alignment explanation
Indices: 48780040--48780078 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
48780030 TGAGCAAAAT
* * *
48780040 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
48780079 TATTAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:48784899 original size:87 final size:87
Alignment explanation
Indices: 48784791--48784949 Score: 266
Period size: 87 Copynumber: 1.8 Consensus size: 87
48784781 TTTTTGGTTT
* *
48784791 TTTTTTTTGCATTCACTTGAGTAATTGAACTTTTAAAATGCATTAAAAAGACCCTCAAACTTTTT
1 TTTTTTTTGCACTCACTTGAGTAATTGAACTTTTAAAATGCATCAAAAAGACCCTCAAACTTTTT
48784856 CAAAAAAGCAATTAAGTCCTTC
66 CAAAAAAGCAATTAAGTCCTTC
* *
48784878 TTTTTTTTGCACTCAAC-TGAGTACTTGAACTTTTAAAATGCATCAAAAAGATCCTCAAACTTTT
1 TTTTTTTTGCACTC-ACTTGAGTAATTGAACTTTTAAAATGCATCAAAAAGACCCTCAAACTTTT
48784942 TCAAAAAA
65 TCAAAAAA
48784950 ATATAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 65 0.97
88 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (87 bp):
TTTTTTTTGCACTCACTTGAGTAATTGAACTTTTAAAATGCATCAAAAAGACCCTCAAACTTTTT
CAAAAAAGCAATTAAGTCCTTC
Done.