Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 170 of 199
Found at i:55058216 original size:28 final size:28
Alignment explanation
Indices: 55058171--55058240 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
55058161 CAAATATAAT
55058171 AAATATATGTTTTTTATT-TTTTAAATTTTA
1 AAATA-AT-TTTTTTATTATTTT-AATTTTA
*
55058201 AAATAATTTTTTTATTATTTTATTTTTA
1 AAATAATTTTTTTATTATTTTAATTTTA
*
55058229 AAATAAATTTTT
1 AAATAATTTTTT
55058241 AGTGTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 26 0.70
29 6 0.16
30 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (28 bp):
AAATAATTTTTTTATTATTTTAATTTTA
Found at i:55058248 original size:27 final size:28
Alignment explanation
Indices: 55058196--55058251 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
55058186 ATTTTTTAAA
* *
55058196 TTTTAAAATAATTTTTTTATTATTTTAT
1 TTTTAAAATAATATTTTTAGTATTTTAT
*
55058224 TTTTAAAATAA-ATTTTTAGTGTTTTAT
1 TTTTAAAATAATATTTTTAGTATTTTAT
55058251 T
1 T
55058252 AAAAGAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTTAAAATAATATTTTTAGTATTTTAT
Found at i:55060710 original size:11 final size:11
Alignment explanation
Indices: 55060694--55060718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55060684 AAAAGCTAAG
55060694 AAAATAAAATA
1 AAAATAAAATA
55060705 AAAATAAAATA
1 AAAATAAAATA
55060716 AAA
1 AAA
55060719 TATGTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:55061670 original size:11 final size:11
Alignment explanation
Indices: 55061656--55061680 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55061646 CTTTTTTATC
55061656 TCTATTTTCAA
1 TCTATTTTCAA
55061667 TCTATTTTCAA
1 TCTATTTTCAA
55061678 TCT
1 TCT
55061681 TTCTTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTATTTTCAA
Found at i:55066385 original size:45 final size:45
Alignment explanation
Indices: 55066335--55066438 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
55066325 GGGTAATAAT
55066335 TTTCTCAATTCAATTTATAACAAATTACACAATCATACATCACCA
1 TTTCTCAATTCAATTTATAACAAATTACACAATCATACATCACCA
*
55066380 TTTCTCAATTCAATTTATAACAAATTACACAATCGTACATCACCA
1 TTTCTCAATTCAATTTATAACAAATTACACAATCATACATCACCA
* *
55066425 ATTATCAATTCAAT
1 TTTCTCAATTCAAT
55066439 CATTCATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (45 bp):
TTTCTCAATTCAATTTATAACAAATTACACAATCATACATCACCA
Found at i:55067367 original size:25 final size:24
Alignment explanation
Indices: 55067322--55067371 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
55067312 TCCACTAACT
*
55067322 TGTTTTATGTTATTTTATTATATTA
1 TGTTTTATGTTATTATATTAT-TTA
55067347 TGTTTTATGTTATTA-ATTTATTTA
1 TGTTTTATGTTATTATA-TTATTTA
55067371 T
1 T
55067372 TTGAAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (24 bp):
TGTTTTATGTTATTATATTATTTA
Found at i:55072038 original size:42 final size:42
Alignment explanation
Indices: 55071991--55072076 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
55071981 TCAAGGTGTC
*
55071991 GGTGGTCAAAGTCCATTTTGTGACAGTGGGTATGTTGCACGT
1 GGTGGTCAAAGTCCATTTTGTGACAGTGGGTATGTAGCACGT
* *
55072033 GGTGGTCAAAGTCCATTTTGTTATAGTGGGTATGTAGCACGT
1 GGTGGTCAAAGTCCATTTTGTGACAGTGGGTATGTAGCACGT
55072075 GG
1 GG
55072077 GCCATATCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.34
Consensus pattern (42 bp):
GGTGGTCAAAGTCCATTTTGTGACAGTGGGTATGTAGCACGT
Found at i:55072702 original size:12 final size:12
Alignment explanation
Indices: 55072687--55072718 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
55072677 ATTTTTATTT
55072687 TTATTTATTTAC
1 TTATTTATTTAC
55072699 TTATTTATTTAC
1 TTATTTATTTAC
55072711 TTAGTTTA
1 TTA-TTTA
55072719 AATTTTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (12 bp):
TTATTTATTTAC
Found at i:55074378 original size:12 final size:12
Alignment explanation
Indices: 55074356--55074387 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
55074346 CATAAAAATT
55074356 TAAACTAAGTAAA
1 TAAA-TAAGTAAA
55074369 TAAATAAGTAAA
1 TAAATAAGTAAA
55074381 TAAATAA
1 TAAATAA
55074388 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (12 bp):
TAAATAAGTAAA
Found at i:55075891 original size:27 final size:27
Alignment explanation
Indices: 55075849--55075910 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
55075839 CTCATTATTC
55075849 TTCTTCATTATCACCGGTACAACAAAG
1 TTCTTCATTATCACCGGTACAACAAAG
* * *
55075876 TTTTTCATTATGACCGGTTCAACAAAG
1 TTCTTCATTATCACCGGTACAACAAAG
55075903 TTCTTCAT
1 TTCTTCAT
55075911 CAGATGGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (27 bp):
TTCTTCATTATCACCGGTACAACAAAG
Found at i:55084957 original size:26 final size:26
Alignment explanation
Indices: 55084940--55085075 Score: 103
Period size: 26 Copynumber: 5.1 Consensus size: 26
55084930 ATCAAATTAT
*
55084940 ATATTTTTATTAAATTATATTTAATA
1 ATATTTTTATTAAATTATAATTAATA
*
55084966 ATATTTTTATTAAATTATATTTAATA
1 ATATTTTTATTAAATTATAATTAATA
* * *
55084992 ATAATTATT-TTAAATTATATTTTATA
1 AT-ATTTTTATTAAATTATAATTAATA
* * * * * * *
55085018 GTATTATATATTATGATTTTAGTAAATTC
1 ATATT-TTTATTA-AATTATAATTAA-TA
*
55085047 ATATATTTTATTAAATTATATTTAATA
1 ATAT-TTTTATTAAATTATAATTAATA
55085074 AT
1 AT
55085076 TATGTTAAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 11
0.75 0.16 0.10
Matches are distributed among these distances:
25 3 0.03
26 46 0.53
27 11 0.13
28 15 0.17
29 10 0.12
30 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (26 bp):
ATATTTTTATTAAATTATAATTAATA
Found at i:55085016 original size:41 final size:41
Alignment explanation
Indices: 55084952--55085075 Score: 98
Period size: 41 Copynumber: 3.0 Consensus size: 41
55084942 ATTTTTATTA
*
55084952 AATTATATTT-AATAATATTTTTATTAAATTATATTTAATAAT
1 AATTAT-TTTAAATTATA-TTTTATTAAATTATATTTAATAAT
* *
55084994 AATTATTTTAAATTATATTTTA-TAGTATTATATATT-ATGAT
1 AATTATTTTAAATTATATTTTATTA-AATTATAT-TTAATAAT
**
55085035 --TT-TAGTAAATTCATATATTTTATTAAATTATATTTAATAAT
1 AATTATTTTAAA-T--TATATTTTATTAAATTATATTTAATAAT
55085076 TATGTTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
38 5 0.07
39 3 0.04
40 4 0.06
41 39 0.58
42 16 0.24
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (41 bp):
AATTATTTTAAATTATATTTTATTAAATTATATTTAATAAT
Found at i:55085056 original size:18 final size:17
Alignment explanation
Indices: 55085002--55085067 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
55084992 ATAATTATTT
55085002 TAAATTATAT-TTTATAG
1 TAAATTATATATTT-TAG
*
55085019 TATTATATATTATGATTTTAG
1 TA-AAT-TA-TAT-ATTTTAG
*
55085040 TAAATTCATATATTTTAT
1 TAAATT-ATATATTTTAG
55085058 TAAATTATAT
1 TAAATTATAT
55085068 TTAATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 6 0.15
18 14 0.35
19 6 0.15
20 6 0.15
21 5 0.12
22 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TAAATTATATATTTTAG
Found at i:55085267 original size:39 final size:41
Alignment explanation
Indices: 55085211--55085316 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
55085201 TTTCCTTATG
* *
55085211 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
55085251 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
55085296 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
55085317 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 23 0.40
45 4 0.07
46 10 0.18
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:55085291 original size:44 final size:46
Alignment explanation
Indices: 55085224--55085316 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
55085214 TTACACCTCT
*
55085224 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
55085268 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
55085314 ATT
1 ATT
55085317 ACGCCTCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 23 0.50
45 4 0.09
46 19 0.41
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:55085319 original size:16 final size:16
Alignment explanation
Indices: 55085298--55085328 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55085288 AGAATTACCT
55085298 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55085314 ATTACGCCTCTATTC
1 ATTACGCCTCTATTC
55085329 TAATACTGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55087356 original size:30 final size:30
Alignment explanation
Indices: 55087274--55087358 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 30
55087264 TTAATATATA
55087274 AATATTTTTATTATTTTATTGTTTTAAAAAATT
1 AATATTTTTATT-TTTTA-T-TTTTAAAAAATT
* * * *
55087307 AATAATATTAATATATTATTTTTAAAAAA-T
1 AAT-ATTTTTATTTTTTATTTTTAAAAAATT
55087337 AATATTTTTATTTTGTTATTTT
1 AATATTTTTATTTT-TTATTTT
55087359 ATTATATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
29 7 0.17
30 11 0.26
31 10 0.24
32 1 0.02
33 7 0.17
34 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
AATATTTTTATTTTTTATTTTTAAAAAATT
Found at i:55090141 original size:41 final size:41
Alignment explanation
Indices: 55090079--55090161 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
55090069 TTCATCTAAG
55090079 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
1 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
* * *
55090120 TAAGAAATGAGATTCAGTTGAAGTTAAGAATGAGGAATGCT
1 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
55090161 T
1 T
55090162 TTAATGTGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (41 bp):
TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
Found at i:55094696 original size:3 final size:3
Alignment explanation
Indices: 55094688--55094728 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
55094678 AAGAAAGGGA
55094688 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55094729 AAGAACAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55099828 original size:12 final size:13
Alignment explanation
Indices: 55099811--55099842 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
55099801 AAAAAATCAA
55099811 CAAAAATATGGTG
1 CAAAAATATGGTG
55099824 CAAAAATATGGTG
1 CAAAAATATGGTG
55099837 CAAAAA
1 CAAAAA
55099843 CACAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (13 bp):
CAAAAATATGGTG
Found at i:55100616 original size:162 final size:162
Alignment explanation
Indices: 55100372--55100885 Score: 848
Period size: 162 Copynumber: 3.2 Consensus size: 162
55100362 TGCAATTGGG
** * *
55100372 AGCAGCTCAGTATCCTCAGAGTTTTCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
1 AGCAGCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* * * *
55100437 AATTTCAACTGATTGCATTCTCTGACTAGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
55100502 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
131 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
** *
55100534 AGCAGCTCTCTATCTTCAGAGTTTGCAATTTTCCAAGACTATTAGCAACACAAATTGGGAAGAGA
1 AGCAGCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* * * *
55100599 AATTTCAATTTATTGCATTTTGTGACTTGTAATTCCCTTAGGCATCGCAAGCTTATGGTTGATAC
66 AATTTCAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
*
55100664 TTGTGAGTCTTGAATTATTTCTTCCATTCCAA
131 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
* *
55100696 AGCAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACGTTGGGAAGAGA
1 AGCAGCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
55100761 AATTTCAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
*
55100826 CTGTGAGTCTTGGATTATTTCTTCCATTCCAA
131 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
*
55100858 AGCACCTCTCTATCTTCAGAGTTTGCAA
1 AGCAGCTCTCTATCTTCAGAGTTTGCAA
55100886 ATTGGGCACA
Statistics
Matches: 324, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 324 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (162 bp):
AGCAGCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
AATTTCAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
Found at i:55101798 original size:22 final size:21
Alignment explanation
Indices: 55101756--55101806 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
55101746 AATGAATTAT
55101756 TAAAGAAAAAATAGAAACAAA
1 TAAAGAAAAAATAGAAACAAA
55101777 TAAAGAAATAATATA-AAAC-AA
1 TAAAGAAA-AA-ATAGAAACAAA
55101798 -AAAGAAAAA
1 TAAAGAAAAA
55101807 TCTTACTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 10 0.36
22 6 0.21
23 3 0.11
ACGTcount: A:0.76, C:0.04, G:0.08, T:0.12
Consensus pattern (21 bp):
TAAAGAAAAAATAGAAACAAA
Found at i:55109094 original size:290 final size:297
Alignment explanation
Indices: 55108531--55109118 Score: 1079
Period size: 290 Copynumber: 2.0 Consensus size: 297
55108521 AAATGCTTCG
55108531 ATCTTACCAAATTTTGAACTTGTTGTTTTTGATTCGAACACAACAGATTGCATACAAGGCCCTCA
1 ATCTTACCAAATTTTGAACTTGTTGTTTTTGATTCGAACACAACAGATTGCATACAAGGCCCTCA
55108596 AAGACTCGGGCTCATGATACCATTTGTTGGAACAATGGTAGCAGCAAACATCAAACAAAGTTACA
66 AAGACTCGGGCTCATGATACCATTTGTTGGAACAATGGTAGCAGCAAACATCAAACAAAGTTACA
55108661 ACACAGTGTTTGTAAGACTGAAGCAAGAAGAATCGAAGCAAAGAAAAAGCAAAGCAATGAACAAA
131 ACACAGTGTTTGTAAGACTGAAGCAAGAAGAATCGAAGCAAAGAAAAAGCAAAGCAATGAACAAA
55108726 AAATGAATACTCAGCAAAGTTGTAACTGAACATTACAAAATTCATTCAAAATTTGAAATAAAAGG
196 AAATGAATACTCAGCAAAGTTGTAACTGAACATTACAAAATTCATTCAAAATTTGAAATAAAAGG
55108791 AGTTACAATTTGTTCATTTGACAGTTACCTACTAATCT
261 AGTTACAATTTGTTCATTTGACAGTTA-CTACTAATCT
55108829 ATCTTACCAAATTTTGAACTTGTTGTTGGTTTGATTCG-AC-C-ACA-ATTGCATACAAGGCCCT
1 ATCTTACCAAATTTTGAACTTGTTGTT--TTTGATTCGAACACAACAGATTGCATACAAGGCCCT
55108890 CAAAGACTCGGGCTCATGATACCATTTGTTGGAACAATGGTAGCAG-AAACATCAAAC-AAGTTA
64 CAAAGACTCGGGCTCATGATACCATTTGTTGGAACAATGGTAGCAGCAAACATCAAACAAAGTTA
55108953 C-ACACAGTGTTTGTAAGACTGAAGCAAGAAGAATCGAAGCAAAG-AAAAGCAAAGCAATGAAC-
129 CAACACAGTGTTTGTAAGACTGAAGCAAGAAGAATCGAAGCAAAGAAAAAGCAAAGCAATGAACA
55109015 AAAAATGAATACTCAGC-AAGTTGTAACTGAACATTACAAAATTCATTCAAAATTTGAAATAAAA
194 AAAAATGAATACTCAGCAAAGTTGTAACTGAACATTACAAAATTCATTCAAAATTTGAAATAAAA
55109079 GGAGTTACAATTTGTTCATTTGACAGTTACTACTAATCT
259 GGAGTTACAATTTGTTCATTTGACAGTTACTACTAATCT
55109118 A
1 A
55109119 ATGCCTCCAC
Statistics
Matches: 288, Mismatches: 0, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
289 11 0.04
290 76 0.26
291 17 0.06
292 18 0.06
293 43 0.15
294 7 0.02
295 11 0.04
296 63 0.22
297 3 0.01
298 28 0.10
299 2 0.01
300 9 0.03
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (297 bp):
ATCTTACCAAATTTTGAACTTGTTGTTTTTGATTCGAACACAACAGATTGCATACAAGGCCCTCA
AAGACTCGGGCTCATGATACCATTTGTTGGAACAATGGTAGCAGCAAACATCAAACAAAGTTACA
ACACAGTGTTTGTAAGACTGAAGCAAGAAGAATCGAAGCAAAGAAAAAGCAAAGCAATGAACAAA
AAATGAATACTCAGCAAAGTTGTAACTGAACATTACAAAATTCATTCAAAATTTGAAATAAAAGG
AGTTACAATTTGTTCATTTGACAGTTACTACTAATCT
Found at i:55114071 original size:41 final size:41
Alignment explanation
Indices: 55114026--55114109 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
55114016 ATGCCAACTG
55114026 CTGTAGTACTTTCTTCAAAAACTGCTTCTGAGACAAACTAA
1 CTGTAGTACTTTCTTCAAAAACTGCTTCTGAGACAAACTAA
55114067 CTGTAGTACTTTCTTCAAAAACTGCTTCTGAGACAAACTAA
1 CTGTAGTACTTTCTTCAAAAACTGCTTCTGAGACAAACTAA
55114108 CT
1 CT
55114110 CTTCCATGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (41 bp):
CTGTAGTACTTTCTTCAAAAACTGCTTCTGAGACAAACTAA
Found at i:55121955 original size:661 final size:658
Alignment explanation
Indices: 55120734--55121957 Score: 1456
Period size: 661 Copynumber: 1.9 Consensus size: 658
55120724 TTTGAAAAAC
* * * *
55120734 AAAAATGATAACTGGAGTCTCCACCAATCCTTTTTGATAAGGTGTGATCGGATCACCTTAAAAAG
1 AAAAATGAAAACGGGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCGGATCACCTCAAAAAG
55120799 TGGTTGTTTTTAATAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAA
66 TGGTTGTTTTTAATAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAA
* * *
55120864 AAAGGGTTCGGGAGTCGGTTACGTACGAGGAAGGATTAGCACCCTCATAATGCCCAAAAATTGGT
131 AAAGGGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTCATAACGCCCAAAAATTGGT
* * *
55120929 ACCTAGTTGATTAGTTAATGTCTTAATGTCGAAAATTAAAAACTTTAAAGAGATTTAAAATACGA
196 ACCTAGTTGATTACTTAATATCTTAATGTCGAAAATTAAAAACCTTAAAGAGATTTAAAATACGA
*** * *
55120994 CCCTATATTTTAAAACTTATATGGAACGAGATACTCGTTAAGATCTTCTCATTTCGGAAAGGAAA
261 CCCTATATTTTAAAACTTATAAAAAACGAGATACTCATTAAGATCTTCTCATTTCAGAAAGGAAA
* ** ** *
55121059 ATGTCACACCCAATGAATTAGGACACGATATTTTGTCTCTTCGAAAATGCGCTTATCTAAGAGCT
326 ATGTCACACCCAATGAATTAGGACACGATATCTTACCTCTTCGAAAATGAACTCATCTAAGAGCT
* * * *
55121124 CGCACAATAAAAGTTAAAAGGATATTCAATTGTTTAAGTCGTATAAAAATTGCAACCCAATACGT
391 CGCACAAGAAAAGTTAAAAGAATATTCAATTGTTTAAGTCATAAAAAAATTGCAACCCAATACGT
* * * * *
55121189 TAGGGCACAATTTCTCAAAATACAAAACATTGAATATTGCCTTTATTTATTATTTAGGAAAATCC
456 TAAGACACAATTTCTCAAAATACAAAACATTAAATATTGAC--TA-TTATTATTTAGAAAAATCC
* *
55121254 TCATCTCGAGAAAACAACGTGTCATATCAATACGTTAGGACACAATGTGTTGAATTCCCGATGAT
518 TCATCTCGAGAAAACAACGTATCATATCAATACATTAGGACACAATGTGTTGAATTCCCGATGAT
55121319 GAGCTTTTTATTTATTTATTTTTATTAAAAGTGTTGACGCCATTTTTTGATAAAAACGGGGTCGA
583 GAGCTTTTTATTTATTTATTTTTATTAAAAGTGTTGACGCCATTTTTTGATAAAAACGGGGTCGA
55121384 CTTGGGTTTTG
648 CTTGGGTTTTG
* * * *
55121395 AAAAATGAAAACGGGAGTCGCCACCAATCCTTTTTTATGAGGTGTGATTGGATCACCTCGAAAAG
1 AAAAATGAAAACGGGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCGGATCACCTCAAAAAG
* * * *
55121460 TGGTTGTTTTTAATAAACCATTTGATTTTATTAAAACAACGGTTTTGGTCCACGAAATTTAGAAA
66 TGGTTGTTTTTAATAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCA-AAA
* *
55121525 AATA-GGTTTGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTCGAT-ACGCCC-AAAATTG
130 AAAAGGGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTC-ATAACGCCCAAAAATTG
* * *
55121587 GTACCTAGTTGATTACTTAATATCTTTAGTGTCGAAAATTTAAAACCTTGAAGA-ATTTCAAAAA
194 GTACCTAGTTGATTACTTAATATC-TTAATGTCGAAAATTAAAAACCTTAAAGAGATTT--AAAA
* * * ** *
55121651 TACGATCCT-TATTTTGAAAGAAAAGTTATAAAAAAGGATCTGCTCATTAAGA-CTT-TAGCATT
256 TACGACCCTATATTTT-----AAAACTTATAAAAAACGAGATACTCATTAAGATCTTCT--CATT
* * ***
55121713 TCAGAAAGAGAAAATGTCATACCCAAT-ACGTTAGGGTGCGATATCTTACCTCTTC-AGAAATGA
314 TCAGAAAG-GAAAATGTCACACCCAATGA-ATTAGGACACGATATCTTACCTCTTCGA-AAATGA
* * * * **
55121776 AC-CAGTCTAA-A-CTCGCATAGGAAAATTTAAAAGAATGTTTGATTGTTTAAGTCATAAAAAAA
376 ACTCA-TCTAAGAGCTCGCACAAGAAAAGTTAAAAGAATATTCAATTGTTTAAGTCAT-AAAAAA
* * ***
55121838 ATTGCAACCCAATCATGTTAAGATACAATTTCTTC-AAATGTTAAACATTAAATATT-AC-A-T-
439 ATTGCAACCCAAT-ACGTTAAGACACAATTTC-TCAAAATACAAAACATTAAATATTGACTATTA
* * * * * * *
55121898 TTATTTCGAAAAATTCTCGTCTCGAGGAATCAACGTATCATGTCCAATGCATTAGGACAC
502 TTATTTAGAAAAATCCTCATCTCGAGAAAACAACGTATCATAT-CAATACATTAGGACAC
55121958 GGCGTACTGA
Statistics
Matches: 469, Mismatches: 74, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
660 68 0.14
661 204 0.43
662 20 0.04
663 1 0.00
664 1 0.00
665 38 0.08
666 57 0.12
667 78 0.17
668 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (658 bp):
AAAAATGAAAACGGGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCGGATCACCTCAAAAAG
TGGTTGTTTTTAATAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAA
AAAGGGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTCATAACGCCCAAAAATTGGT
ACCTAGTTGATTACTTAATATCTTAATGTCGAAAATTAAAAACCTTAAAGAGATTTAAAATACGA
CCCTATATTTTAAAACTTATAAAAAACGAGATACTCATTAAGATCTTCTCATTTCAGAAAGGAAA
ATGTCACACCCAATGAATTAGGACACGATATCTTACCTCTTCGAAAATGAACTCATCTAAGAGCT
CGCACAAGAAAAGTTAAAAGAATATTCAATTGTTTAAGTCATAAAAAAATTGCAACCCAATACGT
TAAGACACAATTTCTCAAAATACAAAACATTAAATATTGACTATTATTATTTAGAAAAATCCTCA
TCTCGAGAAAACAACGTATCATATCAATACATTAGGACACAATGTGTTGAATTCCCGATGATGAG
CTTTTTATTTATTTATTTTTATTAAAAGTGTTGACGCCATTTTTTGATAAAAACGGGGTCGACTT
GGGTTTTG
Found at i:55122500 original size:25 final size:27
Alignment explanation
Indices: 55122453--55122502 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
55122443 TAAAATGACA
*
55122453 TAATATATATAAACAATATACATATTT
1 TAATATATATAAACAATAAACATATTT
55122480 TAATATATATAAA-AA-AAACATAT
1 TAATATATATAAACAATAAACATAT
55122503 ATATACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 13 0.59
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (27 bp):
TAATATATATAAACAATAAACATATTT
Found at i:55122574 original size:26 final size:26
Alignment explanation
Indices: 55122545--55122623 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
55122535 ATTAAATAGG
55122545 TTAGAAAAGAAAAATAAATAAATACA
1 TTAGAAAAGAAAAATAAATAAATACA
55122571 TTAGAAAAGAAAAATAAATAAATACA
1 TTAGAAAAGAAAAATAAATAAATACA
55122597 TTAGAAAAGAAAAATAAATAAATACA
1 TTAGAAAAGAAAAATAAATAAATACA
55122623 T
1 T
55122624 ATATATACAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (26 bp):
TTAGAAAAGAAAAATAAATAAATACA
Found at i:55122735 original size:3 final size:3
Alignment explanation
Indices: 55122720--55122794 Score: 64
Period size: 3 Copynumber: 24.3 Consensus size: 3
55122710 ATAAGAAAAC
* * * *
55122720 ATA ATA CTA ATA ATA ATG TTA ATGA AT- ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
55122765 A-A GATA ATA ATA ATA ATA ACTGA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA A-T-A ATA ATA A
55122795 AATTGCTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
2 3 0.05
3 47 0.81
4 6 0.10
5 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55124354 original size:26 final size:27
Alignment explanation
Indices: 55124302--55124359 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
55124292 CAATATAACA
** *
55124302 AAAATATATGTGTATATATGTAAATTAT
1 AAAATATATGTACATATAAGT-AATTAT
55124330 AAAATATATGTACATATAAGT-ATTAT
1 AAAATATATGTACATATAAGTAATTAT
55124356 AAAA
1 AAAA
55124360 ATGTATAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (27 bp):
AAAATATATGTACATATAAGTAATTAT
Found at i:55124417 original size:44 final size:45
Alignment explanation
Indices: 55124368--55124454 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
55124358 AAATGTATAG
*
55124368 ATGTATGCATA-TA-TTTTAAGACTATAAAATATATGGAAGAATAT
1 ATGTATGCATACTAGTTTTAAG-CTACAAAATATATGGAAGAATAT
* * *
55124412 ATGTATGTATACGTAGTTTTAAGTTACAAAATATATGTAAGAA
1 ATGTATGCATAC-TAGTTTTAAGCTACAAAATATATGGAAGAA
55124455 AAATGTAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 10 0.28
46 19 0.53
47 7 0.19
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (45 bp):
ATGTATGCATACTAGTTTTAAGCTACAAAATATATGGAAGAATAT
Found at i:55124561 original size:23 final size:25
Alignment explanation
Indices: 55124535--55124581 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
55124525 TAAGAAGATT
* *
55124535 TATGATGAAA-TTAA-ATATTAATA
1 TATGAAGAAACTTAATATAATAATA
55124558 TATGAAGAAACTTAATATAATAAT
1 TATGAAGAAACTTAATATAATAAT
55124582 GCATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (25 bp):
TATGAAGAAACTTAATATAATAATA
Found at i:55124640 original size:3 final size:3
Alignment explanation
Indices: 55124632--55124665 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
55124622 TTTAAAACAG
* *
55124632 AAT AAT AAT AAT AAT GAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55124666 TTTTGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55128816 original size:20 final size:20
Alignment explanation
Indices: 55128760--55128818 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
55128750 TTTTCCAGAA
55128760 AAATTGTTTTTACATATATT
1 AAATTGTTTTTACATATATT
* * *
55128780 -AATATATTTATATATATATT
1 AAAT-TGTTTTTACATATATT
55128800 AAATTGTTTTTACATATAT
1 AAATTGTTTTTACATATAT
55128819 AGTAATGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
AAATTGTTTTTACATATATT
Found at i:55128843 original size:40 final size:40
Alignment explanation
Indices: 55128760--55128843 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
55128750 TTTTCCAGAA
* *
55128760 AAATTGTTTTTACATATATTAATATATTTATATATATATT
1 AAATTGTTTTTACATATATTAATAGATTTATATATATAAT
*
55128800 AAATTGTTTTTACATATATAGTAAT-GATTTATTTATA-AAT
1 AAATTGTTTTTACATATAT--TAATAGATTTATATATATAAT
55128840 AAAT
1 AAAT
55128844 AAATCTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 25 0.64
41 10 0.26
42 4 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (40 bp):
AAATTGTTTTTACATATATTAATAGATTTATATATATAAT
Found at i:55132301 original size:25 final size:25
Alignment explanation
Indices: 55132252--55132301 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
55132242 AAGAGAAGAT
*
55132252 GAAGAACGGAAGAAGGAAAATGAAC
1 GAAGAACGGAAGAACGAAAATGAAC
55132277 GAAGAACGGAAGAACGAGAAA-GAAC
1 GAAGAACGGAAGAACGA-AAATGAAC
55132302 CTTACCTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.56, C:0.10, G:0.32, T:0.02
Consensus pattern (25 bp):
GAAGAACGGAAGAACGAAAATGAAC
Found at i:55134376 original size:18 final size:18
Alignment explanation
Indices: 55134337--55134379 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
55134327 GGTTAAATAC
* *
55134337 TTTTTTTTTAAATTATTG
1 TTTTTTATTAAATTAGTG
55134355 -TTTTTATTAAATTAGTG
1 TTTTTTATTAAATTAGTG
55134372 TTTTTTAT
1 TTTTTTAT
55134380 CAAAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTTTATTAAATTAGTG
Found at i:55135837 original size:21 final size:22
Alignment explanation
Indices: 55135804--55135845 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
55135794 ATTTGAGAAT
*
55135804 ATTTTAATTTTTATAATTAATAA
1 ATTTTAA-TTTTACAATTAATAA
55135827 ATTTTAA-TTTACAATTAAT
1 ATTTTAATTTTACAATTAAT
55135846 TTTTACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTAATTTTACAATTAATAA
Found at i:55135942 original size:22 final size:23
Alignment explanation
Indices: 55135898--55135946 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
55135888 CCCATCGGTT
55135898 AAAAACTAGTTATTTTTCCTTTTA
1 AAAAACTAGTTATTTTT-CTTTTA
55135922 AAAAATCTAGTTA-TTTT-TTTTA
1 AAAAA-CTAGTTATTTTTCTTTTA
55135944 AAA
1 AAA
55135947 GTAATGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
24 9 0.38
25 7 0.29
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAAACTAGTTATTTTTCTTTTA
Found at i:55136558 original size:17 final size:17
Alignment explanation
Indices: 55136538--55136583 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
55136528 TGAGTTTTTT
*
55136538 AAAATTAGA-AAATCTTG
1 AAAATTACATAAAT-TTG
55136555 AAAA-TACATAAATTTG
1 AAAATTACATAAATTTG
*
55136571 AAAATTAAATAAA
1 AAAATTACATAAA
55136584 AATAGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (17 bp):
AAAATTACATAAATTTG
Found at i:55138842 original size:24 final size:24
Alignment explanation
Indices: 55138815--55138888 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
55138805 AAGAAACAAT
*
55138815 TTTTTATATTTACGTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
* * *
55138839 TTTTTCATATTAACATTAT-TGATG
1 TTTTT-ATATTTACATTCTGTAATG
* * *
55138863 TTTCTAAATTTACCTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
55138887 TT
1 TT
55138889 AGAGTTAGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
23 9 0.24
24 19 0.50
25 10 0.26
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTTTATATTTACATTCTGTAATG
Found at i:55138842 original size:25 final size:25
Alignment explanation
Indices: 55138814--55138888 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 25
55138804 AAAGAAACAA
*
55138814 TTTTTTATATTTACGTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
* * * *
55138839 TTTTTCATATTAACATTAT-TGATG
1 TTTTTTATATTTACATTCTGTAATG
* * *
55138863 -TTTCTAAATTTACCTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
55138887 TT
1 TT
55138889 AGAGTTAGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
23 12 0.33
24 8 0.22
25 16 0.44
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (25 bp):
TTTTTTATATTTACATTCTGTAATG
Found at i:55140952 original size:20 final size:21
Alignment explanation
Indices: 55140929--55140969 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55140919 CTTTTTTTAA
55140929 ACTTTTTTT-ATTTTTAAAAT
1 ACTTTTTTTAATTTTTAAAAT
55140949 ACTTTTTTTAATTTTTAAAAT
1 ACTTTTTTTAATTTTTAAAAT
55140970 TTTTTTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
ACTTTTTTTAATTTTTAAAAT
Found at i:55140974 original size:31 final size:31
Alignment explanation
Indices: 55140889--55140974 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 31
55140879 AATAAATATA
55140889 TTTTTT-ATTTTTAAAAATATTTTTAAAATACT
1 TTTTTTAATTTTT-AAAAT-TTTTTAAAATACT
**
55140921 TTTTTTAAACTTTTT-TTA-TTTTTAAAATACT
1 TTTTTT-AA-TTTTTAAAATTTTTTAAAATACT
55140952 TTTTTTAATTTTTAAAATTTTTT
1 TTTTTTAATTTTTAAAATTTTTT
55140975 TGGTGTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
29 5 0.11
30 3 0.07
31 24 0.53
32 6 0.13
33 1 0.02
34 1 0.02
35 5 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTTAATTTTTAAAATTTTTTAAAATACT
Found at i:55142245 original size:62 final size:63
Alignment explanation
Indices: 55142115--55142245 Score: 146
Period size: 62 Copynumber: 2.1 Consensus size: 63
55142105 CAAGTTATTA
* *
55142115 AAATAACTAAAAAAAACAAATAACATGAAAGAAGGGAAATTATATATTAAAATAAAAATTTTAT
1 AAATAACTAAAAAAAACAAATAACATGAAAGAA-GGAAATTACATATTAAAATAAAAATTATAT
* * *
55142179 -AATAACT-AAAAAAACAAATAACATGAAATAA-GTAA-TACATA-TAGAATGAAAAACTTCATA
1 AAATAACTAAAAAAAACAAATAACATGAAAGAAGGAAATTACATATTAAAAT-AAAAA-TT-ATA
55142239 T
63 T
55142240 AAATAA
1 AAATAA
55142246 TAGTATATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
58 5 0.09
59 10 0.17
60 5 0.09
61 3 0.05
62 28 0.48
63 7 0.12
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (63 bp):
AAATAACTAAAAAAAACAAATAACATGAAAGAAGGAAATTACATATTAAAATAAAAATTATAT
Found at i:55142452 original size:17 final size:17
Alignment explanation
Indices: 55142432--55142470 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
55142422 TGTGTACATA
55142432 TATAAAAAATAGTATTG
1 TATAAAAAATAGTATTG
* *
55142449 TAT-AAGAATATTATTG
1 TATAAAAAATAGTATTG
55142465 TATAAA
1 TATAAA
55142471 TCTTTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
TATAAAAAATAGTATTG
Found at i:55142526 original size:18 final size:16
Alignment explanation
Indices: 55142503--55142538 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
55142493 AAGTGGATTT
55142503 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
55142521 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
55142537 TA
1 TA
55142539 TATATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:55142704 original size:15 final size:15
Alignment explanation
Indices: 55142686--55142722 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
55142676 ATAACCAAAT
*
55142686 ATAATAATAATATAA
1 ATAATAATAAAATAA
*
55142701 ATAATAATAAAATTA
1 ATAATAATAAAATAA
55142716 ATAATAA
1 ATAATAA
55142723 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAATAAAATAA
Found at i:55142705 original size:12 final size:12
Alignment explanation
Indices: 55142683--55142721 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
55142673 AATATAACCA
55142683 AATAT-AATAAT
1 AATATAAATAAT
55142694 AATATAAATAAT
1 AATATAAATAAT
55142706 AATA-AAATTAAT
1 AATATAAA-TAAT
55142718 AATA
1 AATA
55142722 AATTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATAAATAAT
Found at i:55142722 original size:12 final size:12
Alignment explanation
Indices: 55142690--55142727 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
55142680 CCAAATATAA
55142690 TAATAATATAAA-
1 TAATAATA-AAAT
55142702 TAATAATAAAAT
1 TAATAATAAAAT
55142714 TAATAAT-AAAT
1 TAATAATAAAAT
55142725 TAA
1 TAA
55142728 AATTAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATAATAAAAT
Found at i:55144000 original size:8 final size:8
Alignment explanation
Indices: 55143980--55144028 Score: 68
Period size: 8 Copynumber: 6.4 Consensus size: 8
55143970 CCACCTCCAC
55143980 CTCCACCGA
1 CTCCA-CGA
55143989 -TCCACGA
1 CTCCACGA
55143996 CTCCACGA
1 CTCCACGA
55144004 --CCACGA
1 CTCCACGA
55144010 CTCCACGA
1 CTCCACGA
55144018 CTCCACGA
1 CTCCACGA
55144026 CTC
1 CTC
55144029 AACGGTGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.16
7 3 0.08
8 28 0.76
ACGTcount: A:0.24, C:0.51, G:0.12, T:0.12
Consensus pattern (8 bp):
CTCCACGA
Found at i:55144000 original size:22 final size:22
Alignment explanation
Indices: 55143974--55144023 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
55143964 CCACCTCCAC
*
55143974 CTCCACCTCCACCGA-TCCACGA
1 CTCCACCACCA-CGACTCCACGA
*
55143996 CTCCACGACCACGACTCCACGA
1 CTCCACCACCACGACTCCACGA
55144018 CTCCAC
1 CTCCAC
55144024 GACTCAACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.24, C:0.54, G:0.10, T:0.12
Consensus pattern (22 bp):
CTCCACCACCACGACTCCACGA
Found at i:55144219 original size:17 final size:17
Alignment explanation
Indices: 55144197--55144264 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
55144187 ACAAACAGTA
55144197 GATGTATAATTTCATTT
1 GATGTATAATTTCATTT
*
55144214 GATGTATAATTTCTTTT
1 GATGTATAATTTCATTT
* * *
55144231 GGTTGGATTATTTTTCATTT
1 -GATGTA-TA-ATTTCATTT
55144251 GATGTATAATTTCA
1 GATGTATAATTTCA
55144265 GATATTTGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 21 0.52
18 6 0.15
19 6 0.15
20 7 0.17
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (17 bp):
GATGTATAATTTCATTT
Found at i:55145998 original size:21 final size:22
Alignment explanation
Indices: 55145947--55145998 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
55145937 ACAATGATTA
55145947 ATCTTCAA-TCGAAAAATCACT
1 ATCTTCAATTCGAAAAATCACT
55145968 ATCTTCAATTC-AAAAATCACT
1 ATCTTCAATTCGAAAAATCACT
55145989 ATCTTCAATT
1 ATCTTCAATT
55145999 GTCCGCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (22 bp):
ATCTTCAATTCGAAAAATCACT
Found at i:55148050 original size:165 final size:162
Alignment explanation
Indices: 55147807--55148151 Score: 510
Period size: 165 Copynumber: 2.1 Consensus size: 162
55147797 AACAGTTCTT
* *
55147807 TATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGCAAGAGAAATTTCAACT
1 TATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGCAAGAGAAATTTCAAAT
* * * *
55147872 TATTACATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATGATACTTGTGAG
66 CATTACATTCTGTGACTTGTACTTCCCTCAGGCATTGAAAGCTTATGG-T--TGATACTCGTGAG
* * *
55147937 TCTTGAATTATTTCTTTCATTCCAAAGCATCTCTC
128 TCTTGAATTATTTCTTCCATTACAAAGCACCTCTC
* * * * *
55147972 TATCTTTAGGGTTTGCAATTTCCCAAGACTATTAGCAATACACATTGGGAAGAGAAATTTCAAAT
1 TATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGCAAGAGAAATTTCAAAT
* *
55148037 CATTACTTTCTGTGACTTGTATTTCCCTCAGGCATTGAAAGCTTATGGTTGATACTCGTGAGTCT
66 CATTACATTCTGTGACTTGTACTTCCCTCAGGCATTGAAAGCTTATGGTTGATACTCGTGAGTCT
*
55148102 TGGATTATTTCTTCCATTACAAAGCACCTCTC
131 TGAATTATTTCTTCCATTACAAAGCACCTCTC
55148134 TATCTTCAGAGTTTGCAA
1 TATCTTCAGAGTTTGCAA
55148152 ATTGGGCACA
Statistics
Matches: 161, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 59 0.37
164 1 0.01
165 101 0.63
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (162 bp):
TATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGCAAGAGAAATTTCAAAT
CATTACATTCTGTGACTTGTACTTCCCTCAGGCATTGAAAGCTTATGGTTGATACTCGTGAGTCT
TGAATTATTTCTTCCATTACAAAGCACCTCTC
Found at i:55149879 original size:21 final size:21
Alignment explanation
Indices: 55149855--55149895 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55149845 TGGATAAGTT
55149855 TCCCTCTTTTGAAACCACATA
1 TCCCTCTTTTGAAACCACATA
**
55149876 TCCCTCTTTTGGTACCACAT
1 TCCCTCTTTTGAAACCACAT
55149896 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (21 bp):
TCCCTCTTTTGAAACCACATA
Found at i:55159917 original size:3 final size:3
Alignment explanation
Indices: 55159909--55159959 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
55159899 CAGTGGTATT
55159909 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55159955 ATA AT
1 ATA AT
55159960 TATCAAGCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55161113 original size:18 final size:18
Alignment explanation
Indices: 55161076--55161111 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55161066 ATTATTTATC
*
55161076 TAATAAATATCTTTTAAA
1 TAATAAATATCTCTTAAA
55161094 TAATAAATATCTACTTAA
1 TAATAAATATCT-CTTAA
55161112 TATACAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAATATCTCTTAAA
Found at i:55161203 original size:11 final size:11
Alignment explanation
Indices: 55161187--55161211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55161177 TACATTTGGG
55161187 ATAAATATAAT
1 ATAAATATAAT
55161198 ATAAATATAAT
1 ATAAATATAAT
55161209 ATA
1 ATA
55161212 TATTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:55164903 original size:25 final size:24
Alignment explanation
Indices: 55164858--55164914 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
55164848 TCCACTAACT
*
55164858 TGTTTTAAGTTATTTTATTATATTA
1 TGTTTTAAGTTATTATATTAT-TTA
*
55164883 TGTTTTATGTTATTA-ATTTATTTA
1 TGTTTTAAGTTATTATA-TTATTTA
55164907 --TTTTAAGT
1 TGTTTTAAGT
55164915 AAAAATTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.25
24 4 0.14
25 17 0.61
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (24 bp):
TGTTTTAAGTTATTATATTATTTA
Found at i:55165903 original size:21 final size:19
Alignment explanation
Indices: 55165877--55165930 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
55165867 AGCTCAATTC
55165877 GGTATCAATACTTGGGGTTAA
1 GGTATCAATACTT--GGTTAA
* *
55165898 GGTATCAATACCTTGTTTAG
1 GGTATCAATA-CTTGGTTAA
55165918 GGTATCAATACTT
1 GGTATCAATACTT
55165931 TGATCCCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 14 0.47
21 10 0.33
22 3 0.10
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (19 bp):
GGTATCAATACTTGGTTAA
Found at i:55173313 original size:23 final size:23
Alignment explanation
Indices: 55173269--55173317 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
55173259 CCCGTCGGTT
55173269 AAAACTAGTTATTTTTCCTTTTAA
1 AAAACTAGTTATTTTT-CTTTTAA
*
55173293 AAAATCTAGTTCTTTTT-TTTTAA
1 AAAA-CTAGTTATTTTTCTTTTAA
55173316 AA
1 AA
55173318 GTAATGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 4 0.17
25 11 0.48
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (23 bp):
AAAACTAGTTATTTTTCTTTTAA
Found at i:55173615 original size:18 final size:18
Alignment explanation
Indices: 55173592--55173642 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
55173582 AAAAATTAAA
55173592 TGTTATAATATTTTATTT
1 TGTTATAATATTTTATTT
** *
55173610 TGTTATTTTATTATATTT
1 TGTTATAATATTTTATTT
55173628 TAGTGTA-AATATTTT
1 T-GT-TATAATATTTT
55173643 TTAAATACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 16 0.64
19 7 0.28
20 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
TGTTATAATATTTTATTT
Found at i:55176340 original size:16 final size:16
Alignment explanation
Indices: 55176319--55176349 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55176309 ATGCTTAATT
*
55176319 TTCAAATAGAAATTAA
1 TTCAAAAAGAAATTAA
55176335 TTCAAAAAGAAATTA
1 TTCAAAAAGAAATTA
55176350 CTAAAATCAA
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:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
TTCAAAAAGAAATTAA
Found at i:55179526 original size:24 final size:24
Alignment explanation
Indices: 55179499--55179572 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
55179489 AAGAAACAAT
*
55179499 TTTTTATATTTACGTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
* * *
55179523 TTTTTCATATTAACATTAT-TGATG
1 TTTTT-ATATTTACATTCTGTAATG
* * *
55179547 TTTCTAAATTTACCTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
55179571 TT
1 TT
55179573 AGAGTTAGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
23 9 0.24
24 19 0.50
25 10 0.26
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTTTATATTTACATTCTGTAATG
Found at i:55179526 original size:25 final size:25
Alignment explanation
Indices: 55179498--55179572 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 25
55179488 AAAGAAACAA
*
55179498 TTTTTTATATTTACGTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
* * * *
55179523 TTTTTCATATTAACATTAT-TGATG
1 TTTTTTATATTTACATTCTGTAATG
* * *
55179547 -TTTCTAAATTTACCTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
55179571 TT
1 TT
55179573 AGAGTTAGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
23 12 0.33
24 8 0.22
25 16 0.44
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (25 bp):
TTTTTTATATTTACATTCTGTAATG
Found at i:55180730 original size:16 final size:16
Alignment explanation
Indices: 55180697--55180730 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55180687 AATATTTGTT
* *
55180697 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55180713 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55180729 AA
1 AA
55180731 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55183551 original size:21 final size:21
Alignment explanation
Indices: 55183525--55183565 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55183515 AGACGAGCAA
* *
55183525 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
55183546 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
55183566 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:55185502 original size:16 final size:16
Alignment explanation
Indices: 55185469--55185502 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55185459 GGAGATTGTT
* *
55185469 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55185485 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55185501 AA
1 AA
55185503 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55190994 original size:162 final size:162
Alignment explanation
Indices: 55190744--55191090 Score: 604
Period size: 162 Copynumber: 2.1 Consensus size: 162
55190734 TTGGAAACAG
* *
55190744 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACATATTGGGAAGAGAAATTT
1 CTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
*
55190809 CAACTGATTGCATTCTCTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTGATTGCATTCTCTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGACACTTGTG
55190874 AGTCTTGAATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGAATTATTTCTTCCATTCCAAAGCAC
*
55190906 CTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* * * * *
55190971 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGGCAGTTGTG
66 CAACTGATTGCATTCTCTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGACACTTGTG
*
55191036 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGAATTATTTCTTCCATTCCAAAGCAC
55191068 CTCTCTATCTTCAGAGTTTGCAA
1 CTCTCTATCTTCAGAGTTTGCAA
55191091 ATTAGGCGCA
Statistics
Matches: 175, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
162 175 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (162 bp):
CTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
CAACTGATTGCATTCTCTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGACACTTGTG
AGTCTTGAATTATTTCTTCCATTCCAAAGCAC
Found at i:55191765 original size:21 final size:22
Alignment explanation
Indices: 55191732--55191774 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
55191722 AACGAATTAT
*
55191732 TAAAGAAAAAATA-GAAACAAA
1 TAAAGAAAAAATATAAAACAAA
* *
55191753 TAAATAAATAATATAAAACAAA
1 TAAAGAAAAAATATAAAACAAA
55191775 AACAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (22 bp):
TAAAGAAAAAATATAAAACAAA
Found at i:55196034 original size:16 final size:16
Alignment explanation
Indices: 55195989--55196038 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
55195979 AAAACTAGAG
55195989 TTTTTAAAATATTT-A-
1 TTTTTAAAAT-TTTCAT
* * *
55196004 TGTTTACAATATTCAT
1 TTTTTAAAATTTTCAT
55196020 TTTTTAAAATTTTCAT
1 TTTTTAAAATTTTCAT
55196036 TTT
1 TTT
55196039 AAATTATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 16 0.59
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTAAAATTTTCAT
Found at i:55197546 original size:29 final size:31
Alignment explanation
Indices: 55197497--55197554 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
55197487 TTTTTTTCAA
55197497 CAAAAATTACAAAAAAATTTA-AAATAATTTT
1 CAAAAATTACAAAAAAATTTATAAA-AATTTT
*
55197528 CAAAAA-TA-AAAAATATTTATAAAAATT
1 CAAAAATTACAAAAAAATTTATAAAAATT
55197555 CCAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 14 0.56
30 5 0.20
31 6 0.24
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (31 bp):
CAAAAATTACAAAAAAATTTATAAAAATTTT
Found at i:55200986 original size:10 final size:10
Alignment explanation
Indices: 55200931--55201012 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 10
55200921 AAGTAAACTT
*
55200931 TAAATAAAAA
1 TAAATAATAA
55200941 TTAAATAATAA
1 -TAAATAATAA
55200952 GTAAAT-A-AA
1 -TAAATAATAA
*
55200961 TCAAATCA-AA
1 T-AAATAATAA
55200971 TCAAATAATAA
1 T-AAATAATAA
55200982 TAAATAATAA
1 TAAATAATAA
55200992 T-AATACATAA
1 TAAATA-ATAA
55201002 -AAATGAATAA
1 TAAAT-AATAA
55201012 T
1 T
55201013 CTAGAAAGGG
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
8 1 0.02
9 10 0.16
10 32 0.52
11 18 0.30
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (10 bp):
TAAATAATAA
Found at i:55202318 original size:45 final size:44
Alignment explanation
Indices: 55202227--55202829 Score: 476
Period size: 45 Copynumber: 13.6 Consensus size: 44
55202217 ATCTACTTTG
* * * * *
55202227 CTGCAACCTC-GGAGAGATGAGATTTGTAGCTTCAATTTGCTTCA
1 CTGCAACTTCAGGA-AGATAAGATTTGTATCTTCAATCTGCTCCA
* * *
55202271 CTGTAACTTTAGGAAGATAAGATTTGCTATCTTCAATCTACTCCA
1 CTGCAACTTCAGGAAGATAAGATTTG-TATCTTCAATCTGCTCCA
* * * * *
55202316 CTGCCACTTCAAGAAAATAAGATTTGTA-GTTCTAATTTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTATCTTC-AATCTGCTCCA
* * * *
55202360 CTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTACTCCA
1 CTGCAACTTCAGGAAGATAAGATTTGTATCTTCAATCTGCTCCA
* * * *
55202404 CTGCAACTTCA-GAGAGATAAGATTTATGGT-TTTAATCTGCTCTA
1 CTGCAACTTCAGGA-AGATAAGATTTGT-ATCTTCAATCTGCTCCA
* *
55202448 CTACAACTTTA-GAGAGATAAGATTTGCTATCTTCAATCTGCTCCA
1 CTGCAACTTCAGGA-AGATAAGATTTG-TATCTTCAATCTGCTCCA
* * **
55202493 CTGCAACTTCA-AAGAGATAAGATTTGTGAGT-TT-AATTTGCTTTA
1 CTGCAACTTCAGGA-AGATAAGATTTGT-A-TCTTCAATCTGCTCCA
* * *
55202537 CTGCAACTTTA-GAGAGATAAGATTTGATATCTTTAATCTGCTCAA
1 CTGCAACTTCAGGA-AGATAAGATTTG-TATCTTCAATCTGCTCCA
* *
55202582 CTGCAACTTCAAGAAGATAAGATTTGCTATATTCAATCTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATTTG-TATCTTCAATCTGCTCCA
*
55202627 CTGCAACTTCAGGAAGATAAGATTTACTATCTTCAATCTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATTT-GTATCTTCAATCTGCTCCA
** * * * *
55202672 CTGTGATTTCATGG-AGATAAGATTTGCTATCCTCAACCTGCTCTA
1 CTGCAACTTCA-GGAAGATAAGATTTG-TATCTTCAATCTGCTCCA
** *
55202717 CTGTGACTTCAAGG-AGATAAGATTTGTGAT-TTTAATCTGCTCCA
1 CTGCAACTTC-AGGAAGATAAGATTTGT-ATCTTCAATCTGCTCCA
* * ** * *
55202761 CTACAACTTCA-GAGAGATATGATTTGTGGCTTTAATTTGCTCCA
1 CTGCAACTTCAGGA-AGATAAGATTTGTATCTTCAATCTGCTCCA
* * * *
55202805 CCGTAACTTTAGGGAGATAAGATTT
1 CTGCAACTTCAGGAAGATAAGATTT
55202830 TCCATGAAAA
Statistics
Matches: 456, Mismatches: 80, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
42 1 0.00
43 6 0.01
44 217 0.48
45 226 0.50
46 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (44 bp):
CTGCAACTTCAGGAAGATAAGATTTGTATCTTCAATCTGCTCCA
Found at i:55202353 original size:89 final size:90
Alignment explanation
Indices: 55202238--55202829 Score: 547
Period size: 89 Copynumber: 6.6 Consensus size: 90
55202228 TGCAACCTCG
* *
55202238 GAGAGATGAGATTTGTAGCTTC-AATTTGCTTCACTGTAACTTTAGGAAGATAAGATTTGCTATC
1 GAGAGATAAGATTTGTAG-TTCTAATTTGCTTCACTGCAACTTTAGGAAGATAAGATTTGCTATC
* *
55202302 TTCAATCTACTCCACTGCCACTTCAA
65 TTCAATCTGCTCCACTGCAACTTCAA
* * * * *
55202328 GA-AAATAAGATTTGTAGTTCTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCT
1 GAGAGATAAGATTTGTAGTTCTAATTTGCTTCACTGCAACTTTAGGAAGATAAGATTTGCTATCT
* *
55202391 TTAATCTACTCCACTGCAACTTC-A
66 TCAATCTGCTCCACTGCAACTTCAA
* * * * *
55202415 GAGAGATAAGATTTATGGTTTTAATCTGC-TCTACTACAACTTTA-GAGAGATAAGATTTGCTAT
1 GAGAGATAAGATTTGTAGTTCTAATTTGCTTC-ACTGCAACTTTAGGA-AGATAAGATTTGCTAT
55202478 CTTCAATCTGCTCCACTGCAACTTCAA
64 CTTCAATCTGCTCCACTGCAACTTCAA
* *
55202505 -AGAGATAAGATTTGTGAGTT-TAATTTGCTTTACTGCAACTTTA-GAGAGATAAGATTTGATAT
1 GAGAGATAAGATTTGT-AGTTCTAATTTGCTTCACTGCAACTTTAGGA-AGATAAGATTTGCTAT
* *
55202567 CTTTAATCTGCTCAACTGCAACTTCAA
64 CTTCAATCTGCTCCACTGCAACTTCAA
* * * * *
55202594 GA-AGATAAGATTTGCTATATTC-AATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTACTAT
1 GAGAGATAAGATTTG-TA-GTTCTAATTTGCTTCACTGCAACTTTAGGAAGATAAGATTTGCTAT
** * *
55202657 CTTCAATCTGCTCCACTGTGATTTCAT
64 CTTCAATCTGCTCCACTGCAACTTCAA
* ** ** *
55202684 G-GAGATAAGATTTGCTA-TCCTCAACCTGC-TCTACTGTGACTTCAAGG-AGATAAGATTTG-T
1 GAGAGATAAGATTTG-TAGTTCT-AATTTGCTTC-ACTGCAACTT-TAGGAAGATAAGATTTGCT
* *
55202744 GAT-TTTAATCTGCTCCACTACAACTTC-A
62 -ATCTTCAATCTGCTCCACTGCAACTTCAA
* * * * * *
55202772 GAGAGATATGATTTGTGGCTT-TAATTTGCTCCACCGTAACTTTAGGGAGATAAGATTT
1 GAGAGATAAGATTTGTAG-TTCTAATTTGCTTCACTGCAACTTTAGGAAGATAAGATTT
55202830 TCCATGAAAA
Statistics
Matches: 414, Mismatches: 64, Indels: 50
0.78 0.12 0.09
Matches are distributed among these distances:
87 8 0.02
88 99 0.24
89 194 0.47
90 108 0.26
91 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (90 bp):
GAGAGATAAGATTTGTAGTTCTAATTTGCTTCACTGCAACTTTAGGAAGATAAGATTTGCTATCT
TCAATCTGCTCCACTGCAACTTCAA
Found at i:55212556 original size:17 final size:18
Alignment explanation
Indices: 55212534--55212569 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55212524 TAGTATAAAA
*
55212534 TAAAA-TTTAAATTAATT
1 TAAAATTTTAAAATAATT
55212551 TAAAATTTTAAAATAATT
1 TAAAATTTTAAAATAATT
55212569 T
1 T
55212570 TATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATTTTAAAATAATT
Found at i:55216680 original size:37 final size:37
Alignment explanation
Indices: 55216614--55216690 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
55216604 TCTCTCAACT
55216614 TTATTTTTTATTAAAATTATCTCAACATTTTT-ATAAA
1 TTATTTTTTATTAAAATTATCTCAACATTTTTCA-AAA
**
55216651 TTATTTTTTATTACAAATTAT-TCGGCATTTTTCAAAA
1 TTATTTTTTATTA-AAATTATCTCAACATTTTTCAAAA
55216688 TTA
1 TTA
55216691 GCAATGACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
37 28 0.78
38 8 0.22
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (37 bp):
TTATTTTTTATTAAAATTATCTCAACATTTTTCAAAA
Found at i:55219567 original size:41 final size:41
Alignment explanation
Indices: 55219521--55219624 Score: 208
Period size: 41 Copynumber: 2.5 Consensus size: 41
55219511 ATATAAGGGC
55219521 AAGTTAACAATGAAGAATGCTTAAGAAATGAGATTCAATTG
1 AAGTTAACAATGAAGAATGCTTAAGAAATGAGATTCAATTG
55219562 AAGTTAACAATGAAGAATGCTTAAGAAATGAGATTCAATTG
1 AAGTTAACAATGAAGAATGCTTAAGAAATGAGATTCAATTG
55219603 AAGTTAACAATGAAGAATGCTT
1 AAGTTAACAATGAAGAATGCTT
55219625 TTAATGTGCC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (41 bp):
AAGTTAACAATGAAGAATGCTTAAGAAATGAGATTCAATTG
Found at i:55219573 original size:23 final size:23
Alignment explanation
Indices: 55219547--55219615 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
55219537 ATGCTTAAGA
55219547 AATGAGATTCAATTGAAGTTAAC
1 AATGAGATTCAATTGAAGTTAAC
*
55219570 AATGAAGAATGC--TT-AAG---A-
1 AATG-AG-ATTCAATTGAAGTTAAC
55219588 AATGAGATTCAATTGAAGTTAAC
1 AATGAGATTCAATTGAAGTTAAC
55219611 AATGA
1 AATGA
55219616 AGAATGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 18
0.64 0.04 0.33
Matches are distributed among these distances:
16 3 0.09
17 2 0.06
18 6 0.17
19 4 0.11
22 4 0.11
23 11 0.31
24 2 0.06
25 3 0.09
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (23 bp):
AATGAGATTCAATTGAAGTTAAC
Found at i:55224816 original size:17 final size:18
Alignment explanation
Indices: 55224783--55224819 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55224773 TCAAATTTAT
*
55224783 CAAGTTTTATTTCAAAAA
1 CAAGTTTTATCTCAAAAA
55224801 CAAGTTTTA-CTCAAAAA
1 CAAGTTTTATCTCAAAAA
55224818 CA
1 CA
55224820 TTATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (18 bp):
CAAGTTTTATCTCAAAAA
Found at i:55233095 original size:24 final size:22
Alignment explanation
Indices: 55233067--55233112 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55233057 TTAAAAAATT
55233067 AATAATATTAATATATATTTTTAA
1 AATAAT-TTAAT-TATATTTTTAA
* *
55233091 AATAATTTTATTTTATTTTTAA
1 AATAATTTAATTATATTTTTAA
55233113 TATTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATAATTTAATTATATTTTTAA
Found at i:55235872 original size:24 final size:24
Alignment explanation
Indices: 55235845--55235918 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
55235835 AAGAAACAAT
*
55235845 TTTTTATATTTACGTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
* * *
55235869 TTTTTCATATTAACATTAT-TGATG
1 TTTTT-ATATTTACATTCTGTAATG
* * *
55235893 TTTCTAAATTTACCTTCTGTAATG
1 TTTTTATATTTACATTCTGTAATG
55235917 TT
1 TT
55235919 AGAGTTAGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
23 9 0.24
24 19 0.50
25 10 0.26
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTTTATATTTACATTCTGTAATG
Found at i:55235872 original size:25 final size:25
Alignment explanation
Indices: 55235844--55235918 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 25
55235834 AAAGAAACAA
*
55235844 TTTTTTATATTTACGTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
* * * *
55235869 TTTTTCATATTAACATTAT-TGATG
1 TTTTTTATATTTACATTCTGTAATG
* * *
55235893 -TTTCTAAATTTACCTTCTGTAATG
1 TTTTTTATATTTACATTCTGTAATG
55235917 TT
1 TT
55235919 AGAGTTAGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
23 12 0.33
24 8 0.22
25 16 0.44
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (25 bp):
TTTTTTATATTTACATTCTGTAATG
Found at i:55237077 original size:16 final size:16
Alignment explanation
Indices: 55237044--55237077 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55237034 AATATTTATT
* *
55237044 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
55237060 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
55237076 AA
1 AA
55237078 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:55239490 original size:23 final size:24
Alignment explanation
Indices: 55239451--55239495 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
55239441 ATTTGTAGTA
*
55239451 ATAATAACATGATAATG-ATAAAC
1 ATAATAAAATGATAATGTATAAAC
55239474 ATAATAAAAT-ATGAATGTATAA
1 ATAATAAAATGAT-AATGTATAA
55239496 TAATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (24 bp):
ATAATAAAATGATAATGTATAAAC
Found at i:55239562 original size:13 final size:13
Alignment explanation
Indices: 55239544--55239568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55239534 AAATAATCTA
55239544 ATTTAAAAAATAT
1 ATTTAAAAAATAT
55239557 ATTTAAAAAATA
1 ATTTAAAAAATA
55239569 AATAAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:55239643 original size:4 final size:4
Alignment explanation
Indices: 55239634--55239717 Score: 52
Period size: 4 Copynumber: 21.5 Consensus size: 4
55239624 AAAAATGCAC
* ** **
55239634 AATA AATA AA-A AACA AATA AAT- TTTA AATA AA-A AGGA AAT- AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
55239678 AGTA AATA AATCA AATCA AATCA AAT- AATA AATA AATA AA
1 AATA AATA AAT-A AAT-A AAT-A AATA AATA AATA AATA AA
55239718 AATAATAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
3 12 0.19
4 38 0.59
5 14 0.22
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:55239687 original size:26 final size:26
Alignment explanation
Indices: 55239658--55239719 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
55239648 AAATAAATTT
*
55239658 TAAATAAAAAGGAAAT-AATAAGTAAA
1 TAAATAAAAAGCAAATAAATAA-TAAA
* *
55239684 TAAAT-CAAATCAAATCAAATAATAAA
1 TAAATAAAAAGCAAAT-AAATAATAAA
55239710 TAAATAAAAA
1 TAAATAAAAA
55239720 TAATAATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 7 0.24
26 14 0.48
27 8 0.28
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (26 bp):
TAAATAAAAAGCAAATAAATAATAAA
Found at i:55239720 original size:17 final size:17
Alignment explanation
Indices: 55239700--55239742 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
55239690 AAATCAAATC
55239700 AAATAATAAATAAATAA
1 AAATAATAAATAAATAA
*
55239717 AAATAAT-AATACATAA
1 AAATAATAAATAAATAA
55239733 AAATGAATAA
1 AAAT-AATAA
55239743 TCAAGAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 12 0.52
17 10 0.43
18 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATAATAAATAAATAA
Found at i:55241265 original size:14 final size:14
Alignment explanation
Indices: 55241225--55241275 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
55241215 TTCTTTTACT
55241225 TTTTATTTAC-TTA
1 TTTTATTTACTTTA
*
55241238 CTTTACTTTACTTTA
1 TTTTA-TTTACTTTA
*
55241253 TTTTATTTGCTTTA
1 TTTTATTTACTTTA
*
55241267 TTTTTTTTA
1 TTTTATTTA
55241276 ATTACTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.13
14 20 0.65
15 7 0.23
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTATTTACTTTA
Found at i:55242966 original size:44 final size:44
Alignment explanation
Indices: 55242930--55243621 Score: 638
Period size: 44 Copynumber: 15.6 Consensus size: 44
55242920 TCTACTCCGT
* * *
55242930 TGCAACCTCAGAGAGATGAGATTTGTAGCTTTAATCTGCTTCAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* * *
55242974 TGCAACTTCA-AGGAGATAAGATTTGCTATCTTCAATCTGCTCTAC
1 TGCAACTTCAGA-GAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
* * * *
55243019 TACCACTTCAGGGAAATAAGATTTGTAG-TTGTAATCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTT-TAATCTGCTCCAC
* * *
55243063 TGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
* * * * *
55243108 AGCCACTTCAGGGAAATAAGATTTGTAG-TTCTAATCTGCTCCAT
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTT-TAATCTGCTCCAC
* * * *
55243152 TACAACTTCAGGGAGATAAGATTTATAGCTTTAATCTACTCCAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* * * *
55243196 TGCAACTTCAGAGAGATAAGATTTATGGTTTTAATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* * * *
55243240 TACAACTTCAGAGAGATAAGATTTGCTATCTTCAATATGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
* * * * ** *
55243285 TGCAACTTTAGGGAGATAAGATTTGTGGCTTTAATCTACTTTAT
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* *
55243329 TGCAACTTCAGAGAGATAAGATTTGATATCTTTAATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
* * *
55243374 TGCAACTTCA-AGGATATAAGATTTGCTATCTTCAATCTGCTCCAC
1 TGCAACTTCAGA-GAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
** * * * *
55243419 TGTGACTTCAG-GAAGATAAGATTTGCTATCTTCAATCTACTCTAC
1 TGCAACTTCAGAG-AGATAAGATTTG-TAGCTTTAATCTGCTCCAC
* * * * ** *
55243464 TACGACTTCAGGGAGAAAAGATTTGCTATATTCAATCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTG-TAGCTTTAATCTGCTCCAC
** * * *
55243509 TGTGACTTCAGGGAGATAAGATTTGTGGTTTTAATCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* * *
55243553 TACAACTTCAGAGAGATAGGATTTGTGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
* * * *
55243597 CGCAACTTTAGGGAGATAATATTTG
1 TGCAACTTCAGAGAGATAAGATTTG
55243622 CCACAATAAC
Statistics
Matches: 537, Mismatches: 97, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
43 5 0.01
44 272 0.51
45 257 0.48
46 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
TGCAACTTCAGAGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
Found at i:55243044 original size:89 final size:89
Alignment explanation
Indices: 55242948--55243622 Score: 668
Period size: 89 Copynumber: 7.6 Consensus size: 89
55242938 CAGAGAGATG
*
55242948 AGATTTGTAGCTTTAATCTGCTTCACTGCAACTTCAAGGAGATAAGATTTGCTATCTTCAATCTG
1 AGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTATCTTCAATCTG
* *
55243013 CTCTACTACCACTTCAGGGAAATA
66 CTCCACTACAACTTCAGGGAAATA
*
55243037 AGATTTGTAG-TTGTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCT
1 AGATTTGTAGCTT-TAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTATCTTCAATCT
*
55243101 GCTCCAC-AGCCACTTCAGGGAAATA
65 GCTCCACTA-CAACTTCAGGGAAATA
* * * * * *
55243126 AGATTTGTAG-TTCTAATCTGCTCCATTACAACTTCAGGGAGATAAGATTT-ATAGCTTTAATCT
1 AGATTTGTAGCTT-TAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTATCTTCAATCT
* * * *
55243189 ACTCCACTGCAACTTCAGAGAGATA
65 GCTCCACTACAACTTCAGGGAAATA
* * * * * *
55243214 AGATTTATGGTTTTAATCTGCTCTACTACAACTTC-AGAGAGATAAGATTTGCTATCTTCAATAT
1 AGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGCTATCTTCAATCT
* * *
55243278 GCTCCACTGCAACTTTAGGGAGATA
65 GCTCCACTACAACTTCAGGGAAATA
* * ** * * *
55243303 AGATTTGTGGCTTTAATCTACTTTATTGCAACTTC-AGAGAGATAAGATTTGATATCTTTAATCT
1 AGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGCTATCTTCAATCT
* * * *
55243367 GCTCTACTGCAACTTCAAGGATATA
65 GCTCCACTACAACTTCAGGGAAATA
* * **
55243392 AGATTTGCTATCTTCAATCTGCTCCACTGTGACTTC-AGGAAGATAAGATTTGCTATCTTCAATC
1 AGATTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGCTATCTTCAATC
* * *
55243456 TACTCTACTACGACTTCAGGGAGAA-A
64 TGCTCCACTACAACTTCAGGGA-AATA
** * ** * * *
55243482 AGATTTGCTATATTCAATCTGCTCCACTGTGACTTCAGGGAGATAAGATTTG-TGGT-TTTAATC
1 AGATTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCT-ATCTTCAATC
* *
55243545 TGCTCCACTACAACTTCAGAGAGATA
64 TGCTCCACTACAACTTCAGGGAAATA
* * * * * *
55243571 GGATTTGTGGCTTTAATCTGCTCCACCGCAACTTTAGGGAGATAATATTTGC
1 AGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGC
55243623 CACAATAACT
Statistics
Matches: 499, Mismatches: 74, Indels: 26
0.83 0.12 0.04
Matches are distributed among these distances:
87 1 0.00
88 108 0.22
89 277 0.56
90 110 0.22
91 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (89 bp):
AGATTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGCTATCTTCAATCTG
CTCCACTACAACTTCAGGGAAATA
Found at i:55245464 original size:28 final size:28
Alignment explanation
Indices: 55245424--55245480 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
55245414 TCTCTAGCAT
* *
55245424 CAAATACTAACAGATCATTAAGTGCTAA
1 CAAATACTAACAGATCAGTAAATGCTAA
55245452 CAAATACTAACAGATCAGTAAATGCTAA
1 CAAATACTAACAGATCAGTAAATGCTAA
55245480 C
1 C
55245481 CAGAGAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (28 bp):
CAAATACTAACAGATCAGTAAATGCTAA
Found at i:55246556 original size:12 final size:12
Alignment explanation
Indices: 55246539--55246566 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55246529 TTTTCCAGAA
55246539 AACATTATATCG
1 AACATTATATCG
55246551 AACATTATATCG
1 AACATTATATCG
55246563 AACA
1 AACA
55246567 CACAAACGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (12 bp):
AACATTATATCG
Found at i:55252479 original size:30 final size:31
Alignment explanation
Indices: 55252419--55252480 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
55252409 TGGGTGATTG
*
55252419 TTTTTGGTCAACCAATTATGAATTTGTTTAA
1 TTTTTGATCAACCAATTATGAATTTGTTTAA
* *
55252450 TTTTTGATCATCCAATTAT-AATTTTTTTAA
1 TTTTTGATCAACCAATTATGAATTTGTTTAA
55252480 T
1 T
55252481 CTGGTCACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (31 bp):
TTTTTGATCAACCAATTATGAATTTGTTTAA
Found at i:55252771 original size:25 final size:25
Alignment explanation
Indices: 55252743--55252805 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
55252733 TTAAATTTGT
*
55252743 ATAATAATATTGATATTAAATAAAA
1 ATAATAATATTAATATTAAATAAAA
55252768 ATAACT-ATATTAATATTAAATAAAA
1 ATAA-TAATATTAATATTAAATAAAA
55252793 ATACATAAATATT
1 ATA-AT-AATATT
55252806 TTCAACTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 26 0.79
26 2 0.06
27 5 0.15
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (25 bp):
ATAATAATATTAATATTAAATAAAA
Found at i:55258594 original size:165 final size:165
Alignment explanation
Indices: 55258352--55258692 Score: 619
Period size: 165 Copynumber: 2.1 Consensus size: 165
55258342 TACTTCCCTT
*
55258352 AGACTTTGGAGTAGACATTTGTATGCTACTTGTCGGTCTTGGATTATATCTTCCAACTGCGAGCA
1 AGACTTTGGAGTAGACATTTGTATGCCACTTGTCGGTCTTGGATTATATCTTCCAACTGCGAGCA
* * * *
55258417 GCTCTTTATCTTCAAAGTATGCAATTGCCCAAGGCTATTAGCAACTGACATTGGGAAGATATATT
66 ACTATTTATCTTCAAAGTATGCAATTGCCCAAGCCTATTAGCAACTGACATAGGGAAGATATATT
55258482 TCAAATTATTGCATCTCTCTATTTCAACAATCTTC
131 TCAAATTATTGCATCTCTCTATTTCAACAATCTTC
*
55258517 AGACTTTGGAGTAGACATTTGTATGCCACTTGTCGGTCTTGGATTATATCTTCCAATTGCGAGCA
1 AGACTTTGGAGTAGACATTTGTATGCCACTTGTCGGTCTTGGATTATATCTTCCAACTGCGAGCA
*
55258582 ACTATTTATCTTCAAAGTATGCAATTGCCCAAGCCTATTAGCTACTGACATAGGGAAGATATATT
66 ACTATTTATCTTCAAAGTATGCAATTGCCCAAGCCTATTAGCAACTGACATAGGGAAGATATATT
55258647 TCAAATTATTGCATCTCTCTATTTCAACAATCTTC
131 TCAAATTATTGCATCTCTCTATTTCAACAATCTTC
55258682 AGACTTTGGAG
1 AGACTTTGGAG
55258693 GCTTAAATAA
Statistics
Matches: 169, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 169 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (165 bp):
AGACTTTGGAGTAGACATTTGTATGCCACTTGTCGGTCTTGGATTATATCTTCCAACTGCGAGCA
ACTATTTATCTTCAAAGTATGCAATTGCCCAAGCCTATTAGCAACTGACATAGGGAAGATATATT
TCAAATTATTGCATCTCTCTATTTCAACAATCTTC
Found at i:55262400 original size:16 final size:15
Alignment explanation
Indices: 55262381--55262430 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
55262371 AAACTAGGGG
*
55262381 TTTTTAAAACATTTA
1 TTTTTAAAACATTCA
*
55262396 TTTTTAAAATATTCA
1 TTTTTAAAACATTCA
**
55262411 TTTTTTAAAATTTTCA
1 -TTTTTAAAACATTCA
55262427 TTTT
1 TTTT
55262431 AAATTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAAAACATTCA
Found at i:55262401 original size:15 final size:16
Alignment explanation
Indices: 55262381--55262430 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
55262371 AAACTAGGGG
*
55262381 TTTTTAAAACATTTA-
1 TTTTTAAAACATTCAT
*
55262396 TTTTTAAAATATTCAT
1 TTTTTAAAACATTCAT
**
55262412 TTTTTAAAATTTTCAT
1 TTTTTAAAACATTCAT
55262428 TTT
1 TTT
55262431 AAATTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTAAAACATTCAT
Found at i:55264111 original size:19 final size:20
Alignment explanation
Indices: 55264081--55264120 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
55264071 ACAAAAAGAA
55264081 TTAAAATAATTT-TCAAAAAT
1 TTAAAATAATTTAT-AAAAAT
55264101 TTAAAAT-ATTTATAAAAAT
1 TTAAAATAATTTATAAAAAT
55264120 T
1 T
55264121 CTAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATAATTTATAAAAAT
Found at i:55267657 original size:2 final size:2
Alignment explanation
Indices: 55267650--55267674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55267640 TCAATAAATA
55267650 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55267675 AGAAGGTCTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55269639 original size:162 final size:162
Alignment explanation
Indices: 55269368--55269846 Score: 581
Period size: 162 Copynumber: 3.0 Consensus size: 162
55269358 GGAGTAGACA
** * *
55269368 TATGTATGGCACTTGTAGGTCTTGGATTACATCTTCCAATTGCGAACAACTCTTTATTTTCAAAG
1 TATGTATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAG
* * *** * * * * *
55269433 TTTGCAATTGCCCAAGGGTATTAGTAGCAGATAGTGGGAAGAGATATTTTAAATTATCACATTTT
66 TATGCAATTGTCCAAGACAATTAGCAACAGATAGTAGAAAGAGATACTTTAAATTATCACATTTT
* *
55269498 TCAACCTTTACTTCCCTTAAACTTTGGAGGGT
131 TCAACATTTACTTCCCTTAAACTTTGGAGGCT
** * *
55269530 TATGTATGGCACTTGCGGGTCTTGGATTATGTTTTCCAATTGAGAGCAACTCTTTATCTTCAAAG
1 TATGTATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAG
*
55269595 TATGCAATTGTCCAAGACAATTAGCAACAGATAGTAGAAAGAGATACTTTAAATTATCGCATTTT
66 TATGCAATTGTCCAAGACAATTAGCAACAGATAGTAGAAAGAGATACTTTAAATTATCACATTTT
* * *
55269660 TTAACATTTACTTCCCATAAACTTCGGAGGCT
131 TCAACATTTACTTCCCTTAAACTTTGGAGGCT
* ** * *
55269692 TACGTATGGCACTTGTAGACCTAGGATTATGTCTTCCAATTGCGAGCAACTCTTTATC-TCCAAG
1 TATGTATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAG
* * * * * *
55269756 TATGC---TGTCTAAGACCATTATCAATAGACAG-ACGAAAAAGATACTTTAAATTATCACATTT
66 TATGCAATTGTCCAAGACAATTAGCAACAGATAGTA-GAAAGAGATACTTTAAATTATCACATTT
* *
55269817 TTCAACTTTTACTTCCTTTAAACTTTGGAG
130 TTCAACATTTACTTCCCTTAAACTTTGGAG
55269847 TCTCATGTTC
Statistics
Matches: 271, Mismatches: 45, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
157 1 0.00
158 72 0.27
161 10 0.04
162 188 0.69
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (162 bp):
TATGTATGGCACTTGTAGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAG
TATGCAATTGTCCAAGACAATTAGCAACAGATAGTAGAAAGAGATACTTTAAATTATCACATTTT
TCAACATTTACTTCCCTTAAACTTTGGAGGCT
Found at i:55270676 original size:21 final size:21
Alignment explanation
Indices: 55270652--55270699 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
55270642 CAGCAACTTA
* * *
55270652 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
*
55270673 AAGCAGATGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
55270694 AAGCAG
1 AAGCAG
55270700 CGATAGAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:55271181 original size:42 final size:42
Alignment explanation
Indices: 55271109--55271201 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
55271099 TCAAAATAGT
* * *
55271109 GGCGTTTGTGAAATAAGCGCTGCTAAAGAACACTACTTTTAGC
1 GGCGTTT-TGAAACAAGCGCCGCTAAAGAACACTACTTTTAGA
* * *
55271152 GGCGTTTTTAAACAAGCGCCGCTATAGAACATTACTTTTAGA
1 GGCGTTTTGAAACAAGCGCCGCTAAAGAACACTACTTTTAGA
55271194 GGCGTTTT
1 GGCGTTTT
55271202 CTTCCAAAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 37 0.84
43 7 0.16
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
GGCGTTTTGAAACAAGCGCCGCTAAAGAACACTACTTTTAGA
Found at i:55271375 original size:43 final size:43
Alignment explanation
Indices: 55271122--55271393 Score: 266
Period size: 43 Copynumber: 6.3 Consensus size: 43
55271112 GTTTGTGAAA
* ***
55271122 TAAGCGCTGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTAAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTTC
* * * * *
55271165 -AAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTTC
* ** * *
55271207 AAAGCGCCGCTAAAGAATGTGATCTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
* *
55271250 AAAGCGCCTCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
*
55271293 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-CTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
* * ** *
55271335 TAAGCGACGCTAAAGAGCATGATCTTTAGCGGTATTTTTTTATG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-TC
*
55271379 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
55271394 TTAGCGACGT
Statistics
Matches: 196, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 70 0.36
43 110 0.56
44 15 0.08
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTC
Found at i:55271490 original size:21 final size:21
Alignment explanation
Indices: 55271464--55271507 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55271454 TTAGTGGCGT
* *
55271464 TAAAAAGCGCCGCTAAAGACC
1 TAAAAAACGCCGCTAAAAACC
*
55271485 TAAAAAATGCCGCTAAAAACC
1 TAAAAAACGCCGCTAAAAACC
55271506 TA
1 TA
55271508 TTCTGCTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.14
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAACC
Found at i:55274027 original size:17 final size:17
Alignment explanation
Indices: 55274005--55274038 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55273995 ATCCACTAAT
*
55274005 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
55274022 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
55274039 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:55278666 original size:17 final size:17
Alignment explanation
Indices: 55278644--55278677 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55278634 ATCCACTAAT
*
55278644 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
55278661 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
55278678 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:55279167 original size:41 final size:41
Alignment explanation
Indices: 55279119--55279201 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
55279109 GAAATTCATC
55279119 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
1 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
*
55279160 TAAGAAATGAGATTCAATTGAAGTTAAGAATGAAGAATGCT
1 TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
55279201 T
1 T
55279202 TCAATGTGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (41 bp):
TAAGAAATGAGATTCAATTGAAGTTAACAATGAAGAATGCT
Found at i:55280978 original size:19 final size:17
Alignment explanation
Indices: 55280946--55280980 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
55280936 CAATCATCAT
55280946 TTTAAAATTTTTAAATA
1 TTTAAAATTTTTAAATA
55280963 TTTAATAATATTTTAAAT
1 TTTAA-AAT-TTTTAAAT
55280981 GATGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAAATTTTTAAATA
Found at i:55285044 original size:19 final size:20
Alignment explanation
Indices: 55285014--55285053 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
55285004 ACAAAAAGAA
55285014 TTAAAATAATTT-TCAAAAAT
1 TTAAAATAATTTAT-AAAAAT
55285034 TTAAAAT-ATTTATAAAAAT
1 TTAAAATAATTTATAAAAAT
55285053 T
1 T
55285054 CTAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATAATTTATAAAAAT
Found at i:55288371 original size:162 final size:162
Alignment explanation
Indices: 55288202--55288710 Score: 919
Period size: 162 Copynumber: 3.1 Consensus size: 162
55288192 TTGGGAACAA
* *
55288202 CTCTCTATCCTCGGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGAAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
55288267 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
55288332 AGTATTGGATTATTTCTTCCATTCTAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCTAAAGCAC
* * *
55288364 CTCTCTATCTTCAGAGTTTGCAATTGCCCAAGATTATTAGCAACACCCATTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
55288429 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
55288494 AGGCTTGGATTATTTCTTCCATTCTAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCTAAAGCAC
*
55288526 CTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
*
55288591 CAACTTATTGCATTTTGTGACCTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
55288656 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCTAAAGCAC
*
55288688 CTCTCTATCCTCAAAGTTTGCAA
1 CTCTCTATCCTCAGAGTTTGCAA
55288711 ATTGGGCGCA
Statistics
Matches: 333, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 333 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (162 bp):
CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
AGTCTTGGATTATTTCTTCCATTCTAAAGCAC
Found at i:55291308 original size:27 final size:27
Alignment explanation
Indices: 55291270--55291330 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
55291260 CTCATCATTC
55291270 TTCTTCATTATCACCGGTACAACAAAG
1 TTCTTCATTATCACCGGTACAACAAAG
*
55291297 TTCTTCATTATCACCGGTTCAACAAAG
1 TTCTTCATTATCACCGGTACAACAAAG
55291324 TTCTTCA
1 TTCTTCA
55291331 CCAGATGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (27 bp):
TTCTTCATTATCACCGGTACAACAAAG
Found at i:55294793 original size:19 final size:17
Alignment explanation
Indices: 55294749--55294796 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
55294739 TTTTTAAGAT
55294749 ATAAATAAAAAAAATAA
1 ATAAATAAAAAAAATAA
*
55294766 ATAGTAATAAACAAATTATAA
1 ATA--AATAAA-AAA-AATAA
55294787 ATAAATAAAA
1 ATAAATAAAA
55294797 GAAACTCGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 12 0.46
20 3 0.12
21 7 0.27
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
ATAAATAAAAAAAATAA
Found at i:55295777 original size:20 final size:18
Alignment explanation
Indices: 55295729--55295779 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
55295719 AGCTCAATTC
55295729 GGTATCGATACTATGAAA
1 GGTATCGATACTATGAAA
* *
55295747 GAGTTTCGATACTTTGGTAAA
1 G-GTATCGATACTAT-G-AAA
55295768 GGTATCGATACT
1 GGTATCGATACT
55295780 CTTTTATTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 11 0.41
21 4 0.15
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (18 bp):
GGTATCGATACTATGAAA
Found at i:55296082 original size:17 final size:18
Alignment explanation
Indices: 55296049--55296085 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55296039 TCAAATTTAT
*
55296049 CAAGTTTTATTTCAAAAA
1 CAAGTTTTATCTCAAAAA
55296067 CAAGTTTTA-CTCAAAAA
1 CAAGTTTTATCTCAAAAA
55296084 CA
1 CA
55296086 TTATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (18 bp):
CAAGTTTTATCTCAAAAA
Found at i:55299928 original size:25 final size:23
Alignment explanation
Indices: 55299877--55299927 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
55299867 CCCATCGGTT
55299877 AAAACTAGTTATTTTTCCTTTTAA
1 AAAACTAGTTATTTTT-CTTTTAA
55299901 AAAATCTAGTTATTTTT-TTTTAA
1 AAAA-CTAGTTATTTTTCTTTTAA
55299924 AAAA
1 AAAA
55299928 AGTAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 10 0.38
24 4 0.15
25 12 0.46
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAACTAGTTATTTTTCTTTTAA
Found at i:55299959 original size:9 final size:9
Alignment explanation
Indices: 55299932--55299969 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
55299922 AAAAAAAGTA
*
55299932 ATATTTTAT
1 ATATTTAAT
*
55299941 -TATTTTAT
1 ATATTTAAT
55299949 ATATTTAAT
1 ATATTTAAT
55299958 ATATTTAAT
1 ATATTTAAT
55299967 ATA
1 ATA
55299970 AAATTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATATTTAAT
Found at i:55300209 original size:28 final size:28
Alignment explanation
Indices: 55300165--55300228 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
55300155 TGTTTTATTG
*
55300165 TTTTTAAAAAATTAATAATATTAATATA
1 TTTTTTAAAAATTAATAATATTAATATA
* * *
55300193 TTATTTTAAAAA-TAATAATTTTATTTTA
1 TT-TTTTAAAAATTAATAATATTAATATA
55300221 TTTTTTAA
1 TTTTTTAA
55300229 TATTTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 6 0.19
28 17 0.55
29 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTTTAAAAATTAATAATATTAATATA
Found at i:55300218 original size:107 final size:109
Alignment explanation
Indices: 55300075--55300272 Score: 246
Period size: 107 Copynumber: 1.8 Consensus size: 109
55300065 TTTAATATTT
* * * *
55300075 ATATTAATATATTAATTTAATATAAAAACATATATTTTAATTTTTT-TTA-TTTATATACATT-A
1 ATATTAATATATTAATTTAAAATAAAAACATATATTTT-ATTTTTTAATATTTTATAAAAATTAA
55300137 AT-TTATAAATATTTTTATTGTT-TTATTGTTTTTAAAAAATTAATA
65 ATGTTAT-AATATTTTTATT-TTGTTATTGTTTTTAAAAAATTAATA
* * * *
55300182 ATATTAATATATTATTTTAAAAATAATAA-TTTTATTTTATTTTTTAATATTTTATAAAAATTAA
1 ATATTAATATATTAATTT-AAAATAAAAACATATATTTTATTTTTTAATATTTTATAAAAATTAA
55300246 ATGTTATAATATTTTTATTTTGTTATT
65 ATGTTATAATATTTTTATTTTGTTATT
55300273 TTATTATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
106 7 0.09
107 26 0.34
108 20 0.26
109 20 0.26
110 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (109 bp):
ATATTAATATATTAATTTAAAATAAAAACATATATTTTATTTTTTAATATTTTATAAAAATTAAA
TGTTATAATATTTTTATTTTGTTATTGTTTTTAAAAAATTAATA
Done.