Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 325 of 328
Found at i:96230128 original size:42 final size:42
Alignment explanation
Indices: 96230080--96230161 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
96230070 TATTTAAATG
* *
96230080 TTTTATATTATTAAAAATAATATTTAACA-TTTAAAAAATATA
1 TTTTATATT-TAAAAAATAATATTTAAAATTTTAAAAAATATA
96230122 TTTTATATTTAAAAAATAATATTTAAAATTTTAAAAAATA
1 TTTTATATTTAAAAAATAATATTTAAAATTTTAAAAAATA
96230162 AATTCAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 17 0.46
42 20 0.54
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (42 bp):
TTTTATATTTAAAAAATAATATTTAAAATTTTAAAAAATATA
Found at i:96230170 original size:21 final size:22
Alignment explanation
Indices: 96230092--96230172 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 22
96230082 TTATATTATT
* *
96230092 AAAAATAATATTTAACA-TTTA
1 AAAAATAATATTCAAAATTTTA
** *
96230113 AAAAAT-ATATTTTATA-TTTA
1 AAAAATAATATTCAAAATTTTA
*
96230133 AAAAATAATATTTAAAATTTTA
1 AAAAATAATATTCAAAATTTTA
96230155 AAAAATAA-ATTCAAAATT
1 AAAAATAATATTCAAAATT
96230173 ATATATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
20 18 0.34
21 23 0.43
22 12 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAATATTCAAAATTTTA
Found at i:96231510 original size:59 final size:59
Alignment explanation
Indices: 96231418--96231537 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
96231408 ACATAAAAAC
*
96231418 ACCATGGATAAAGTTTAAGGTTTGCCAAGCAAGGATTCATGCATGTAAGTGAATTTCTA
1 ACCATGGATAAAGCTTAAGGTTTGCCAAGCAAGGATTCATGCATGTAAGTGAATTTCTA
*
96231477 ACCATGGATAAAGCTTAAGGTTTGCCAAGCAAGGGTTCATGCATGTAAGTGAATTTCTA
1 ACCATGGATAAAGCTTAAGGTTTGCCAAGCAAGGATTCATGCATGTAAGTGAATTTCTA
96231536 AC
1 AC
96231538 ACGTTTTTCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (59 bp):
ACCATGGATAAAGCTTAAGGTTTGCCAAGCAAGGATTCATGCATGTAAGTGAATTTCTA
Found at i:96232272 original size:30 final size:29
Alignment explanation
Indices: 96232238--96232307 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
96232228 AATATGTGCT
*
96232238 AGTGATTATATTGATCAGGTACTATGTATC
1 AGTGATTATATT-ATCAGGTACTATGTACC
** * *
96232268 AGTGACCATATTATTAGGTACTTTGTACC
1 AGTGATTATATTATCAGGTACTATGTACC
*
96232297 GGTG-TTATATT
1 AGTGATTATATT
96232308 TATGGTTCAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 5 0.16
29 17 0.53
30 10 0.31
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (29 bp):
AGTGATTATATTATCAGGTACTATGTACC
Found at i:96236460 original size:17 final size:16
Alignment explanation
Indices: 96236432--96236473 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
96236422 GATTAATAAG
96236432 ATAAATTAAATAAGGAAA
1 ATAAA-TAAATAA-GAAA
96236450 ATAAATAAATAAGAAA
1 ATAAATAAATAAGAAA
96236466 A-AAATAAA
1 ATAAATAAA
96236474 AAATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 7 0.29
18 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
ATAAATAAATAAGAAA
Found at i:96242205 original size:153 final size:152
Alignment explanation
Indices: 96241926--96242240 Score: 515
Period size: 153 Copynumber: 2.1 Consensus size: 152
96241916 GTAAAAGAAT
96241926 CAAAATGAAAATTTGGTTCAAATACTTAGAAAGGTTATTATGTTGTCTCCAAATCCAATTGGAGA
1 CAAAATGAAAATTTGGTTCAAATACTTAGAAAGGTTATTATGTTGTCTCCAAATCCAATTGGAGA
* * * *
96241991 GATGACTAGTCTTGGCTATTGGAGCAGTTGACTCCATGAGTAGATATATAGATGTATTCATTGGA
66 GATAACTAGTCTTGGCTATCGGAGCAGTTGACTCCACGAGTAGAGATATAGATGTATTCATTGGA
96242056 AGAATTATACTTTGGACTGGAC
131 AGAATTATACTTTGGACTGGAC
* *
96242078 CTAAAATGAACATTTGGTTCAAATACTTAGAAAGGTTATTATGTCT-TCTCCAAATCCAATTGGG
1 C-AAAATGAAAATTTGGTTCAAATACTTAGAAAGGTTATTATGT-TGTCTCCAAATCCAATTGGA
* * *
96242142 GAGATAACTAGTCTTGGTTATCGGAGCAGTTGACTTCACGGGTAGAGATATAGATGTATTCATTG
64 GAGATAACTAGTCTTGGCTATCGGAGCAGTTGACTCCACGAGTAGAGATATAGATGTATTCATTG
96242207 GAAGAATTATACTTTGGACTGGAC
129 GAAGAATTATACTTTGGACTGGAC
96242231 CAAAGATGAA
1 CAAA-ATGAA
96242241 TTAATTCTTA
Statistics
Matches: 151, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
152 4 0.03
153 146 0.97
154 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (152 bp):
CAAAATGAAAATTTGGTTCAAATACTTAGAAAGGTTATTATGTTGTCTCCAAATCCAATTGGAGA
GATAACTAGTCTTGGCTATCGGAGCAGTTGACTCCACGAGTAGAGATATAGATGTATTCATTGGA
AGAATTATACTTTGGACTGGAC
Found at i:96244333 original size:21 final size:21
Alignment explanation
Indices: 96244303--96244343 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
96244293 TAACGGGAGT
96244303 GCTGACGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
* *
96244324 GCTGATGTGGCCAGTTAACT
1 GCTGACGTGGCAAGTTAACT
96244344 TGCCATGTTG
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:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:96245506 original size:30 final size:30
Alignment explanation
Indices: 96245471--96245529 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
96245461 ATATATCACT
*
96245471 CTCCTTTCATTTTC-TCTTATTCTTCTTCTC
1 CTCC-TTCATTTTCTTATTATTCTTCTTCTC
*
96245501 CTCCTTCTTTTTCTTATTATTCTTCTTCT
1 CTCCTTCATTTTCTTATTATTCTTCTTCT
96245530 TCTCTGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.63
Consensus pattern (30 bp):
CTCCTTCATTTTCTTATTATTCTTCTTCTC
Found at i:96245515 original size:27 final size:30
Alignment explanation
Indices: 96245471--96245526 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
96245461 ATATATCACT
*
96245471 CTCCTTTCATTTTCTCTTATTCTTCTTCTC
1 CTCCTTTCATTTTCTCTTATTATTCTTCTC
96245501 CTCC-TTC-TTTT-TCTTATTATTCTTCT
1 CTCCTTTCATTTTCTCTTATTATTCTTCT
96245527 TCTTCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 14 0.56
28 4 0.16
29 3 0.12
30 4 0.16
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.62
Consensus pattern (30 bp):
CTCCTTTCATTTTCTCTTATTATTCTTCTC
Found at i:96245571 original size:31 final size:31
Alignment explanation
Indices: 96245487--96245560 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 31
96245477 TCATTTTCTC
*
96245487 TTATTCTTCTTCTCCTCCT-TCTT-TT-TCTTA
1 TTATTCTTCTTCTTCT-CTGT-TTCTTCTCTTA
96245517 TTATTCTTCTTCTTCTCTGTTTCTTCTCTTA
1 TTATTCTTCTTCTTCTCTGTTTCTTCTCTTA
* *
96245548 TTTTTCTTTTTCT
1 TTATTCTTCTTCT
96245561 CTTCTTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 4 0.11
30 18 0.47
31 16 0.42
ACGTcount: A:0.05, C:0.26, G:0.01, T:0.68
Consensus pattern (31 bp):
TTATTCTTCTTCTTCTCTGTTTCTTCTCTTA
Found at i:96250251 original size:2 final size:2
Alignment explanation
Indices: 96250244--96250283 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
96250234 CAAAACACAA
96250244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96250284 TAACCAAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96250761 original size:19 final size:20
Alignment explanation
Indices: 96250721--96250762 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
96250711 GTTTTATTGC
96250721 ATAAATTTAGAAATCAAACA
1 ATAAATTTAGAAATCAAACA
96250741 ATAAATTTAGAAATC-AACA
1 ATAAATTTAGAAATCAAACA
96250760 ATA
1 ATA
96250763 GAATCCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAAATTTAGAAATCAAACA
Found at i:96251458 original size:31 final size:30
Alignment explanation
Indices: 96251389--96251458 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
96251379 ACTTGACAAC
*
96251389 TCATTGACTTAAAAAAAACTTTGAAATAAT
1 TCATTGACTTAAAAAAAACTTTCAAATAAT
* * * *
96251419 ACAGTGACTTAAATGAAAACTTTCAAATAGT
1 TCATTGACTTAAA-AAAAACTTTCAAATAAT
96251450 TCATTGACT
1 TCATTGACT
96251459 ATTTTATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
TCATTGACTTAAAAAAAACTTTCAAATAAT
Found at i:96254961 original size:12 final size:12
Alignment explanation
Indices: 96254944--96254968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
96254934 TAATTATGTA
96254944 TAATTTTTTATT
1 TAATTTTTTATT
96254956 TAATTTTTTATT
1 TAATTTTTTATT
96254968 T
1 T
96254969 TGATGATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TAATTTTTTATT
Found at i:96264971 original size:18 final size:20
Alignment explanation
Indices: 96264950--96264992 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
96264940 ACATAAATAC
96264950 ATAAAAG-TAGATA-AAATT
1 ATAAAAGATAGATACAAATT
96264968 ATAAAAAGATAGATACAAATT
1 AT-AAAAGATAGATACAAATT
96264989 -TAAA
1 ATAAA
96264993 TATAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 8 0.36
20 7 0.32
21 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (20 bp):
ATAAAAGATAGATACAAATT
Found at i:96264982 original size:20 final size:19
Alignment explanation
Indices: 96264952--96264992 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
96264942 ATAAATACAT
96264952 AAAAGTAGATA-AAATTATA
1 AAAAGTAGATACAAATT-TA
96264971 AAAAGATAGATACAAATTTA
1 AAAAG-TAGATACAAATTTA
96264991 AA
1 AA
96264993 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAAGTAGATACAAATTTA
Found at i:96265174 original size:31 final size:31
Alignment explanation
Indices: 96265139--96265197 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
96265129 GAAAACCCTA
*
96265139 AAGTTCAAG-TCTCAATATAAAAATAATTGCT
1 AAGTTCAAGTTCT-AATACAAAAATAATTGCT
*
96265170 AAGTTCAAGTTCTAATACAAGAATAATT
1 AAGTTCAAGTTCTAATACAAAAATAATT
96265198 TGACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (31 bp):
AAGTTCAAGTTCTAATACAAAAATAATTGCT
Found at i:96266583 original size:18 final size:18
Alignment explanation
Indices: 96266562--96266618 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
96266552 AAAATACAAA
96266562 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
96266580 AAAAATTCCAAA-ATTTAT
1 -AAAATTCAAAATATTTAT
* * *
96266598 -AATTTTAAAATAATTAT
1 AAAATTCAAAATATTTAT
96266615 AAAA
1 AAAA
96266619 ATTTAAGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 8 0.27
19 10 0.33
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:96268175 original size:16 final size:16
Alignment explanation
Indices: 96268154--96268184 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96268144 ATTTGAATAG
*
96268154 AAAAGAAAGAAGAAAT
1 AAAAGAAAAAAGAAAT
96268170 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
96268185 CAGATTCGGG
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:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAT
Found at i:96270028 original size:18 final size:19
Alignment explanation
Indices: 96270007--96270042 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
96269997 AACTTTTGAA
*
96270007 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
96270025 AATTTTAAAAATTATTTT
1 AATTTTAAAAATTATTTT
96270043 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:96270056 original size:19 final size:19
Alignment explanation
Indices: 96270009--96270056 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
96269999 CTTTTGAAAA
*
96270009 TTTTATAAATATTTTGAAT
1 TTTTATAATTATTTTGAAT
* * * *
96270028 TTTAAAAATTATTTTTATT
1 TTTTATAATTATTTTGAAT
96270047 TTTTATAATT
1 TTTTATAATT
96270057 TTTATTGAGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAATTATTTTGAAT
Found at i:96270140 original size:9 final size:9
Alignment explanation
Indices: 96270126--96270164 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
96270116 ACACTAATCT
96270126 ATTATTCGA
1 ATTATTCGA
*
96270135 ATTATTTGA
1 ATTATTCGA
96270144 ATTATTCGA
1 ATTATTCGA
* *
96270153 GTTATTTGA
1 ATTATTCGA
96270162 ATT
1 ATT
96270165 GTGAAATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (9 bp):
ATTATTCGA
Found at i:96270149 original size:18 final size:18
Alignment explanation
Indices: 96270126--96270164 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
96270116 ACACTAATCT
96270126 ATTATTCGAATTATTTGA
1 ATTATTCGAATTATTTGA
*
96270144 ATTATTCGAGTTATTTGA
1 ATTATTCGAATTATTTGA
96270162 ATT
1 ATT
96270165 GTGAAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
ATTATTCGAATTATTTGA
Found at i:96272960 original size:21 final size:21
Alignment explanation
Indices: 96272936--96273004 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
96272926 TTAGAATTTT
96272936 TTAAGTTGAAAAATAATTGGA
1 TTAAGTTGAAAAATAATTGGA
* * **
96272957 TTAAATGCTT-AAACTAGAATT-TT
1 TT-AA-G-TTGAAA-AATAATTGGA
96272980 TTAAGTTGAAAAATAATTGGA
1 TTAAGTTGAAAAATAATTGGA
96273001 TTAA
1 TTAA
96273005 ACTTTTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 4 0.12
23 6 0.18
24 7 0.21
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (21 bp):
TTAAGTTGAAAAATAATTGGA
Found at i:96272964 original size:44 final size:44
Alignment explanation
Indices: 96272916--96273005 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
96272906 CAACAACAGT
*
96272916 AATGCTTAAATTAGAATTTTTTAAGTTGAAAAATAATTGGATTA
1 AATGCTTAAACTAGAATTTTTTAAGTTGAAAAATAATTGGATTA
96272960 AATGCTTAAACTAGAATTTTTTAAGTTGAAAAATAATTGGATTA
1 AATGCTTAAACTAGAATTTTTTAAGTTGAAAAATAATTGGATTA
96273004 AA
1 AA
96273006 CTTTTTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (44 bp):
AATGCTTAAACTAGAATTTTTTAAGTTGAAAAATAATTGGATTA
Found at i:96273613 original size:16 final size:16
Alignment explanation
Indices: 96273570--96273622 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
96273560 CATAATGTGA
96273570 AATTT-ATTTTTTATT
1 AATTTAATTTTTTATT
*
96273585 -ATTTACATATTTTATT
1 AATTTA-ATTTTTTATT
96273601 AATTTAATTTTTTAGTT
1 AATTTAATTTTTTA-TT
96273618 AATTT
1 AATTT
96273623 GATGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
16 16 0.50
17 12 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
AATTTAATTTTTTATT
Found at i:96273952 original size:16 final size:18
Alignment explanation
Indices: 96273922--96273983 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 18
96273912 TTTCATTAAA
96273922 AATAATAATTTAATTTTTT
1 AATAA-AATTTAATTTTTT
96273941 AA-AAAA-TTAA-TTTTT
1 AATAAAATTTAATTTTTT
96273956 AATAAAATTTAATTGTTTTT
1 AATAAAATTTAA-T-TTTTT
96273976 AATAAAAT
1 AATAAAAT
96273984 ACAGTTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.18
16 8 0.21
17 6 0.16
18 2 0.05
19 2 0.05
20 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATAAAATTTAATTTTTT
Found at i:96276030 original size:2 final size:2
Alignment explanation
Indices: 96276023--96276049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96276013 TATTCATTAC
96276023 AT 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 AT A
96276050 AAATTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96277353 original size:2 final size:2
Alignment explanation
Indices: 96277346--96277375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96277336 ATAATCTCAG
96277346 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
96277376 TCGTCTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:96278618 original size:176 final size:184
Alignment explanation
Indices: 96278313--96278819 Score: 638
Period size: 194 Copynumber: 2.7 Consensus size: 184
96278303 AATCAGTAAT
* *
96278313 GTTTTATGTCATACTTAAGCCGAAATAGGTTGATATTGTCTATGACTATCTGTGAAATCGGAAAG
1 GTTTTATGTCATACTTAAGCCGAAATAGGTTGATATTGTCTATGAATATCTGCGAAATCGGAAAG
** * *
96278378 TTTTAGGTCATATTAAGCGGCAATAGGCGTCTGTCTTAGCATTTGGCATGCCGGTTTTTTGGATC
66 TTTTAGGTCATATTAAGCGGCAATAGGCGTCTGTCTTAGCATTTGGTGTGCAGGTTTGTTGGATC
* * *
96278443 ATTATAT-TT-TTT-GG-T-T-TC-C-GTCTATTGACATCCTCGAATCCACATA
131 ATTATATGTTGTTTCGGTTATATCACTGTCGATTGACATCCGCAAATCCACATA
*
96278489 GTTTTATGTCATACTTAAGCCGAAATAGGTTAATATTGTCTATGAATATCTGCGAAATCGGAAAG
1 GTTTTATGTCATACTTAAGCCGAAATAGGTTGATATTGTCTATGAATATCTGCGAAATCGGAAAG
*
96278554 TTTTAGGTCATATTAAGTGGCAATAGGCGTCTGTCTTAGCATTTGGTGTGCAGGTTTGTTGGATC
66 TTTTAGGTCATATTAAGCGGCAATAGGCGTCTGTCTTAGCATTTGGTGTGCAGGTTTGTTGGATC
*
96278619 ATTATATGTGTTGGTTTCGGTTTATAATCAATACATTGTCGATTGATATCCGCAAATCCACATA
131 ATTATA--TGTT-GTTTCGG-TTAT-ATC---AC--TGTCGATTGACATCCGCAAATCCACATA
* * * *
96278683 GTTTTACGGCATACTTAAGCTGAAATAGGTTGATATTGTGTATGAATATCTGCCG-AATC-GAGA
1 GTTTTATGTCATACTTAAGCCGAAATAGGTTGATATTGTCTATGAATATCTG-CGAAATCGGA-A
* * * * *
96278746 AGTTTTAGGTGATGTTAAGCGGCAATAGGCTTCTGTCTTAGCATATGGTGTGAAGGTTTGTTGGA
64 AGTTTTAGGTCATATTAAGCGGCAATAGGCGTCTGTCTTAGCATTTGGTGTGCAGGTTTGTTGGA
*
96278811 TCACTATAT
129 TCATTATAT
96278820 CTGATGTCTC
Statistics
Matches: 287, Mismatches: 24, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
176 128 0.45
178 1 0.00
179 2 0.01
181 3 0.01
182 2 0.01
184 1 0.00
185 1 0.00
187 2 0.01
191 1 0.00
192 1 0.00
193 2 0.01
194 141 0.49
195 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (184 bp):
GTTTTATGTCATACTTAAGCCGAAATAGGTTGATATTGTCTATGAATATCTGCGAAATCGGAAAG
TTTTAGGTCATATTAAGCGGCAATAGGCGTCTGTCTTAGCATTTGGTGTGCAGGTTTGTTGGATC
ATTATATGTTGTTTCGGTTATATCACTGTCGATTGACATCCGCAAATCCACATA
Found at i:96281354 original size:26 final size:26
Alignment explanation
Indices: 96281302--96281356 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
96281292 TACCTAATTT
** * * *
96281302 TTTTTTTGTCTTTTTTGGTACCTAAA
1 TTTTTTTGTCTAATTAGGCACCCAAA
96281328 TTTTTTTGTCTAATTAGGCACCCAAA
1 TTTTTTTGTCTAATTAGGCACCCAAA
96281354 TTT
1 TTT
96281357 GACATTTTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.55
Consensus pattern (26 bp):
TTTTTTTGTCTAATTAGGCACCCAAA
Found at i:96284295 original size:25 final size:25
Alignment explanation
Indices: 96284267--96284320 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
96284257 TACAAAGGGT
96284267 AAGTCCTAATAGAATTCCTAATTTA
1 AAGTCCTAATAGAATTCCTAATTTA
*
96284292 AAGTGCTAATAGAATTCCTAATTTA
1 AAGTCCTAATAGAATTCCTAATTTA
96284317 AAGT
1 AAGT
96284321 TTATAAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (25 bp):
AAGTCCTAATAGAATTCCTAATTTA
Found at i:96286968 original size:52 final size:52
Alignment explanation
Indices: 96286841--96287003 Score: 202
Period size: 52 Copynumber: 3.1 Consensus size: 52
96286831 ACACGGATCA
* * * *
96286841 CACATCATATCGATGCCATATCCCAGATATGGTCTTATAC-AGAAACACATTAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGA-AAACACA-TAT
*
96286894 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATGCGAAAACACATAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAACACATAT
** * * * *
96286946 CACATTGCACCGATGCCATAGCCTAGCTATGGTCTTATATGGAAGCACATAT
1 CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAACACATAT
96286998 CACATC
1 CACATC
96287004 TTTTCCTTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
52 53 0.55
53 42 0.44
54 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (52 bp):
CACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAACACATAT
Found at i:96287093 original size:35 final size:35
Alignment explanation
Indices: 96287047--96287117 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
96287037 AAGCACTCAA
96287047 AACCATTGTTCCATCTAATTTGTACTTTTAGTTAC
1 AACCATTGTTCCATCTAATTTGTACTTTTAGTTAC
96287082 AACCATTGTTCCATCTAATTTGTACTTTTAGTTAC
1 AACCATTGTTCCATCTAATTTGTACTTTTAGTTAC
96287117 A
1 A
96287118 CATTATTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (35 bp):
AACCATTGTTCCATCTAATTTGTACTTTTAGTTAC
Found at i:96297758 original size:2 final size:2
Alignment explanation
Indices: 96297751--96297786 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
96297741 TAAGCCCATA
96297751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96297787 GGCATTGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96300793 original size:20 final size:20
Alignment explanation
Indices: 96300768--96300817 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
96300758 CCCCAAAATT
96300768 TTCAAACATCGAAATTAATA
1 TTCAAACATCGAAATTAATA
96300788 TTCAAACATCGAAATTAATA
1 TTCAAACATCGAAATTAATA
96300808 TTCAAACATC
1 TTCAAACATC
96300818 ATCTCTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (20 bp):
TTCAAACATCGAAATTAATA
Found at i:96301483 original size:19 final size:19
Alignment explanation
Indices: 96301459--96301496 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
96301449 TGAGGGGATG
96301459 ACCATGTTGGAGGTTCCTT
1 ACCATGTTGGAGGTTCCTT
96301478 ACCATGTTGGAGGTTCCTT
1 ACCATGTTGGAGGTTCCTT
96301497 CTTAAGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (19 bp):
ACCATGTTGGAGGTTCCTT
Found at i:96306094 original size:2 final size:2
Alignment explanation
Indices: 96306087--96306114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96306077 AATTATTTTA
96306087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96306115 TTGTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96307346 original size:21 final size:21
Alignment explanation
Indices: 96307299--96307352 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
96307289 TAATTTCTCC
**
96307299 CTTTTCTTTCTTTTCCTTTGT
1 CTTTTCTTTCTTTTCCCCTGT
*
96307320 CCTTTCTTTCTTTCTCCCCTGT
1 CTTTTCTTTCTTT-TCCCCTGT
96307342 -TTTTCGTTTCT
1 CTTTTC-TTTCT
96307353 ATCGTGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.00, C:0.30, G:0.06, T:0.65
Consensus pattern (21 bp):
CTTTTCTTTCTTTTCCCCTGT
Found at i:96322028 original size:51 final size:51
Alignment explanation
Indices: 96321961--96322061 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
96321951 ATTTATCCTT
96321961 TGCACATTTGTATTTCAGATGGGATTCATCGCAGGCTTTGTCAATTTTCTC
1 TGCACATTTGTATTTCAGATGGGATTCATCGCAGGCTTTGTCAATTTTCTC
*
96322012 TGCACATTTGTATTTCAGATGGGATTCATCGTAGGCTTTGTCAATTTTCT
1 TGCACATTTGTATTTCAGATGGGATTCATCGCAGGCTTTGTCAATTTTCT
96322062 TATCACCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (51 bp):
TGCACATTTGTATTTCAGATGGGATTCATCGCAGGCTTTGTCAATTTTCTC
Found at i:96331220 original size:29 final size:29
Alignment explanation
Indices: 96331178--96331235 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
96331168 GCGTGTATGT
96331178 GTGTGTGAGAGAGGGAGAGAGAGAACTGG
1 GTGTGTGAGAGAGGGAGAGAGAGAACTGG
96331207 GTGTGTGAGAGAGGGAGAGAGAGAACTGG
1 GTGTGTGAGAGAGGGAGAGAGAGAACTGG
96331236 CCTTTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.52, T:0.14
Consensus pattern (29 bp):
GTGTGTGAGAGAGGGAGAGAGAGAACTGG
Found at i:96333745 original size:14 final size:15
Alignment explanation
Indices: 96333726--96333762 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
96333716 GAATATTTTA
96333726 TATTTATTTTAAT-T
1 TATTTATTTTAATGT
96333740 TATTTATTTTAATGT
1 TATTTATTTTAATGT
96333755 TATATTAT
1 TAT-TTAT
96333763 CCTATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 4 0.19
16 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTATTTTAATGT
Found at i:96335425 original size:6 final size:6
Alignment explanation
Indices: 96335416--96335453 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
96335406 CAATTGGAAT
96335416 ATGTTA ATGTTA ATGTTA ATGTTA ATGTTA ATGTTA AT
1 ATGTTA ATGTTA ATGTTA ATGTTA ATGTTA ATGTTA AT
96335454 TGAGGATGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATGTTA
Found at i:96336916 original size:21 final size:21
Alignment explanation
Indices: 96336892--96336931 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
96336882 ATAGAGTTAA
*
96336892 CATTTATTATTTAAAAAATAT
1 CATTTACTATTTAAAAAATAT
*
96336913 CATTTACTATTTAACAAAT
1 CATTTACTATTTAAAAAAT
96336932 TTACTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
CATTTACTATTTAAAAAATAT
Found at i:96350861 original size:2 final size:2
Alignment explanation
Indices: 96350854--96350889 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
96350844 TACCTTACTC
96350854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96350890 TTCAGTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96351747 original size:41 final size:41
Alignment explanation
Indices: 96351690--96351772 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
96351680 TTGAGAAGAA
96351690 TGCATTTGGAGGAAGGTATAACTTATAGTAAAGTATGACTT
1 TGCATTTGGAGGAAGGTATAACTTATAGTAAAGTATGACTT
96351731 TGCATTTGGAGGAAGGTATAACTTATAGTAAAGTATGACTT
1 TGCATTTGGAGGAAGGTATAACTTATAGTAAAGTATGACTT
96351772 T
1 T
96351773 ACTAAATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (41 bp):
TGCATTTGGAGGAAGGTATAACTTATAGTAAAGTATGACTT
Found at i:96351991 original size:18 final size:19
Alignment explanation
Indices: 96351968--96352004 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
96351958 AATAAGTTTT
96351968 GAATTT-TCATATTTTTAA
1 GAATTTGTCATATTTTTAA
*
96351986 GAATTTGTGATATTTTTAA
1 GAATTTGTCATATTTTTAA
96352005 ATTTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (19 bp):
GAATTTGTCATATTTTTAA
Found at i:96353354 original size:9 final size:9
Alignment explanation
Indices: 96353295--96353362 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
96353285 GTTATAATAA
*
96353295 AAAAGTATT
1 AAAATTATT
96353304 AAAATT-TT
1 AAAATTATT
**
96353312 AAAAGCATT
1 AAAATTATT
*
96353321 AAATATTACAAT
1 AAA-ATT--ATT
96353333 AAAATTA-T
1 AAAATTATT
*
96353341 AAAATTCTT
1 AAAATTATT
96353350 AAAATTATT
1 AAAATTATT
96353359 AAAA
1 AAAA
96353363 ATTTAATAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
8 13 0.28
9 24 0.52
10 1 0.02
11 3 0.07
12 5 0.11
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAATTATT
Found at i:96353368 original size:17 final size:17
Alignment explanation
Indices: 96353332--96353390 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
96353322 AATATTACAA
*
96353332 TAAAATTA-TAAAATTCT
1 TAAAATTATTAAAAAT-T
96353349 TAAAATTATTAAAAATT
1 TAAAATTATTAAAAATT
*
96353366 TAATAGTTATTAAGAAATT
1 TAA-AATTATTAA-AAATT
96353385 ATAAAA
1 -TAAAA
96353391 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 12 0.34
18 14 0.40
19 6 0.17
20 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAATTATTAAAAATT
Found at i:96353598 original size:18 final size:19
Alignment explanation
Indices: 96353568--96353611 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
96353558 TTTTTTCAAT
*
96353568 TTTTTTATAATTTTAT-TA
1 TTTTTTATAATTTAATATA
96353586 CTTTTTTAT-ATTTAATATA
1 -TTTTTTATAATTTAATATA
96353605 TTTTTTA
1 TTTTTTA
96353612 CCATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTAATATA
Found at i:96353609 original size:19 final size:19
Alignment explanation
Indices: 96353566--96353610 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
96353556 CATTTTTTCA
*
96353566 ATTTTTTTATAATTTTATT
1 ATTTTTTTATAATTTAATT
*
96353585 ACTTTTTTAT-ATTTAATAT
1 ATTTTTTTATAATTTAAT-T
96353604 ATTTTTT
1 ATTTTTT
96353611 ACCATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTTATAATTTAATT
Found at i:96353638 original size:15 final size:15
Alignment explanation
Indices: 96353614--96353643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96353604 ATTTTTTACC
*
96353614 ATTTTTAATATTTTT
1 ATTTTAAATATTTTT
96353629 ATTTTAAATATTTTT
1 ATTTTAAATATTTTT
96353644 TTTACAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTAAATATTTTT
Found at i:96364179 original size:15 final size:16
Alignment explanation
Indices: 96364154--96364196 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
96364144 ATTACATAAT
96364154 ATATAAAAATAACATA
1 ATATAAAAATAACATA
*
96364170 ATAT-AAAATATCATAA
1 ATATAAAAATAACAT-A
*
96364186 ATTTAAAAATA
1 ATATAAAAATA
96364197 GGTCGGGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAAAATAACATA
Found at i:96369379 original size:43 final size:43
Alignment explanation
Indices: 96369313--96369400 Score: 160
Period size: 43 Copynumber: 2.0 Consensus size: 43
96369303 AATTATTGTA
96369313 ATTAAATTGAATTTAACAAAAAAATAGTAGTGTTAACAATTGG
1 ATTAAATTGAATTTAACAAAAAAATAGTAGTGTTAACAATTGG
96369356 ATTAATATTGAATTTAAC-AAAAAATAGTAGTGTTAACAATTGG
1 ATTAA-ATTGAATTTAACAAAAAAATAGTAGTGTTAACAATTGG
96369399 AT
1 AT
96369401 CTGAATTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 32 0.73
44 12 0.27
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (43 bp):
ATTAAATTGAATTTAACAAAAAAATAGTAGTGTTAACAATTGG
Found at i:96369425 original size:43 final size:41
Alignment explanation
Indices: 96369313--96369422 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 41
96369303 AATTATTGTA
96369313 ATTAA-ATTGAATTTAACAAAAAAATAGTAGTGTTAACAATTGG
1 ATTAATATTGAATTT---AAAAAAATAGTAGTGTTAACAATTGG
96369356 ATTAATATTGAATTTAACAAAAAATAGTAGTGTTAACAATTGG
1 ATTAATATTGAATTT-A-AAAAAATAGTAGTGTTAACAATTGG
96369399 ATCTGAAT-TTAGAATTCTAAAAAA
1 AT-T-AATATT-GAATT-TAAAAAA
96369423 TAGAGGGCTT
Statistics
Matches: 60, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
42 1 0.02
43 32 0.53
44 17 0.28
45 9 0.15
46 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (41 bp):
ATTAATATTGAATTTAAAAAAATAGTAGTGTTAACAATTGG
Found at i:96373497 original size:19 final size:19
Alignment explanation
Indices: 96373473--96373516 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
96373463 TTGGTAAACA
96373473 TTTATCAAAACAACGTAAT
1 TTTATCAAAACAACGTAAT
*
96373492 TTTATCAAAACGACGTAAT
1 TTTATCAAAACAACGTAAT
96373511 TTTATC
1 TTTATC
96373517 TTTTCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (19 bp):
TTTATCAAAACAACGTAAT
Found at i:96379320 original size:96 final size:96
Alignment explanation
Indices: 96379167--96379345 Score: 288
Period size: 96 Copynumber: 1.9 Consensus size: 96
96379157 TGTCATGGAT
* * *
96379167 GGGAACGATGGAACAGATACGGAGCCCAATAAGCTTGGTTCGAGCAAGGTAAAAGCCGAAGCCAA
1 GGGAACGATGGAACAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGTAAAAGCCGAAGCCAA
96379232 GAGGGCAAACAGGAGCAAGCCTGTCATCAAA
66 GAGGGCAAACAGGAGCAAGCCTGTCATCAAA
*
96379263 GGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGGT-AAAGCCGAAGCCA
1 GGGAACGATGGAACAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAA-GGTAAAAGCCGAAGCCA
* *
96379327 AGAGGGCTAAGAGGAGCAA
65 AGAGGGCAAACAGGAGCAA
96379346 AAAGAAGTGA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
96 73 0.96
97 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.34, T:0.10
Consensus pattern (96 bp):
GGGAACGATGGAACAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGTAAAAGCCGAAGCCAA
GAGGGCAAACAGGAGCAAGCCTGTCATCAAA
Found at i:96383049 original size:58 final size:58
Alignment explanation
Indices: 96382974--96383107 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 58
96382964 TTATTTGATT
*
96382974 AGTGACAAGTGACAAGTGATAAATGGTAGCCTCAGCTACACTTATCTG---A-T--C-
1 AGTGACAAGTGACAAGTGATAAATGGTAGCCTCAGCTACACTTATATGATCAGTGACA
* * * *
96383025 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATTAGTGACA
1 AGTGACAAGTGACAAGTGATAAATGGTAGCCTCAGCTACACTTATATGATCAGTGACA
*
96383083 AGTGACAAGTTACAAGTGATAAATG
1 AGTGACAAGTGACAAGTGATAAATG
96383108 TGATCTGTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
51 44 0.63
54 1 0.01
55 1 0.01
57 1 0.01
58 23 0.33
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (58 bp):
AGTGACAAGTGACAAGTGATAAATGGTAGCCTCAGCTACACTTATATGATCAGTGACA
Found at i:96383100 original size:51 final size:51
Alignment explanation
Indices: 96382930--96383092 Score: 263
Period size: 51 Copynumber: 3.2 Consensus size: 51
96382920 ACTTCTTATC
* *
96382930 AGTGACAAGTGATAAGTGGTAACCTCAGCTACACTTATTTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATATGATTAGTGACA
* * *
96382981 AGTGACAAGTGATAAATGGTAGCCTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATATGATTAGTGACA
* *
96383032 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATATGATTAGTGACA
96383083 AGTGACAAGT
1 AGTGACAAGT
96383093 TACAAGTGAT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATATGATTAGTGACA
Found at i:96384798 original size:37 final size:37
Alignment explanation
Indices: 96384757--96384869 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 37
96384747 TGGAGGCCCA
96384757 TTTAAAGGACGTTTAAATACTATTCAATTCACTTTCT
1 TTTAAAGGACGTTTAAATACTATTCAATTCACTTTCT
* ** ** *
96384794 TTTAAAGTGA--ATTAAATAGCT-TTGGAGGC-C---CA
1 TTTAAAG-GACGTTTAAATA-CTATTCAATTCACTTTCT
96384826 TTTAAAGGACGTTTAAATACTATTCAATTCACTTTCT
1 TTTAAAGGACGTTTAAATACTATTCAATTCACTTTCT
96384863 TTTAAAG
1 TTTAAAG
96384870 TGAATTAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
31 2 0.04
32 10 0.18
33 11 0.20
34 1 0.02
35 1 0.02
36 11 0.20
37 17 0.31
38 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTAAAGGACGTTTAAATACTATTCAATTCACTTTCT
Found at i:96384832 original size:32 final size:32
Alignment explanation
Indices: 96384794--96384901 Score: 85
Period size: 32 Copynumber: 3.2 Consensus size: 32
96384784 TTCACTTTCT
96384794 TTTAAAGTGAATTAAATAGCTTTGGAGGCCCA
1 TTTAAAGTGAATTAAATAGCTTTGGAGGCCCA
* ** ** *
96384826 TTTAAAG-GACGTTTAAATA-CTATTCAATTCACTTTCT
1 TTTAAAGTGA--ATTAAATAGCT-TTGGAGGC-C---CA
96384863 TTTAAAGTGAATTAAATAGCTTTGGAGGCCCA
1 TTTAAAGTGAATTAAATAGCTTTGGAGGCCCA
96384895 TTTAAAG
1 TTTAAAG
96384902 GACGTCATGA
Statistics
Matches: 55, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
31 2 0.04
32 17 0.31
33 11 0.20
34 1 0.02
35 1 0.02
36 11 0.20
37 10 0.18
38 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TTTAAAGTGAATTAAATAGCTTTGGAGGCCCA
Found at i:96384857 original size:69 final size:69
Alignment explanation
Indices: 96384737--96384906 Score: 322
Period size: 69 Copynumber: 2.4 Consensus size: 69
96384727 CGTCCAGCCC
*
96384737 AAATAGACCTTGGAGGCCCATTTAAAGGACGTTTAAATACTATTCAATTCACTTTCTTTTAAAGT
1 AAATAG-CTTTGGAGGCCCATTTAAAGGACGTTTAAATACTATTCAATTCACTTTCTTTTAAAGT
96384802 GAATT
65 GAATT
96384807 AAATAGCTTTGGAGGCCCATTTAAAGGACGTTTAAATACTATTCAATTCACTTTCTTTTAAAGTG
1 AAATAGCTTTGGAGGCCCATTTAAAGGACGTTTAAATACTATTCAATTCACTTTCTTTTAAAGTG
96384872 AATT
66 AATT
96384876 AAATAGCTTTGGAGGCCCATTTAAAGGACGT
1 AAATAGCTTTGGAGGCCCATTTAAAGGACGT
96384907 CATGACATGT
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
69 93 0.94
70 6 0.06
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (69 bp):
AAATAGCTTTGGAGGCCCATTTAAAGGACGTTTAAATACTATTCAATTCACTTTCTTTTAAAGTG
AATT
Found at i:96389123 original size:25 final size:25
Alignment explanation
Indices: 96389094--96389145 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
96389084 GATTAACTAT
*
96389094 TTTAAAAATAATATT-ATTTTAATAG
1 TTTAAAAATAA-ATTAAATTTAATAG
* *
96389119 TTTAATATTAAATTAAATTTAATAG
1 TTTAAAAATAAATTAAATTTAATAG
96389144 TT
1 TT
96389146 ATCTTAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTAAAAATAAATTAAATTTAATAG
Found at i:96389165 original size:37 final size:38
Alignment explanation
Indices: 96389102--96389214 Score: 96
Period size: 37 Copynumber: 3.1 Consensus size: 38
96389092 ATTTTAAAAA
*
96389102 TAATA-TTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATAGTTATCTTAATAGTTTAATATTAAATTAATATT
* *
96389138 TAATAGTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATAGTTATCTTAATAGT-TTAATATTAAATTAATATT
* *
96389176 AAAGT-GATTATCTTAATA--TTAA-ATTAAATTTAATGTT
1 TAA-TAG-TTATCTTAATAGTTTAATATTAAA-TTAATATT
96389213 TA
1 TA
96389215 TCTTGTAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
36 12 0.19
37 30 0.48
38 8 0.13
39 12 0.19
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (38 bp):
TAATAGTTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:96389196 original size:31 final size:29
Alignment explanation
Indices: 96389161--96389218 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
96389151 AATAGTATTT
*
96389161 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
96389192 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
96389219 GTAGATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:96389289 original size:18 final size:17
Alignment explanation
Indices: 96389262--96389295 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
96389252 TGCAGATAAG
96389262 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
*
96389279 ATTTAAATATTATATTT
1 ATTT-AATATTAAATTT
96389296 TACACATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:96422188 original size:20 final size:20
Alignment explanation
Indices: 96422165--96422202 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96422155 CACATCCAAA
*
96422165 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
96422185 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
96422203 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:96430158 original size:20 final size:20
Alignment explanation
Indices: 96430121--96430158 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
96430111 CACATCCAAA
*
96430121 TACAAAATTTTAAGAATCTT
1 TACAAAATTTGAAGAATCTT
96430141 TACAAAATATTGAA-AATC
1 TACAAAAT-TTGAAGAATC
96430159 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
TACAAAATTTGAAGAATCTT
Found at i:96451943 original size:9 final size:10
Alignment explanation
Indices: 96451916--96451940 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
96451906 ATTTCATTAA
96451916 AATTTTAATT
1 AATTTTAATT
96451926 AATTTTAATT
1 AATTTTAATT
96451936 AATTT
1 AATTT
96451941 AATAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:96453024 original size:37 final size:37
Alignment explanation
Indices: 96452974--96453049 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
96452964 AAGAGAGAAT
*
96452974 AAATTAATTAATTAAAAGTAGGATTCATTATCGTTCC
1 AAATTAATTAATTAAAAGTAGGATTCATCATCGTTCC
96453011 AAATTAATTAATTAAAAGTAGGATTCATCATCGTTCC
1 AAATTAATTAATTAAAAGTAGGATTCATCATCGTTCC
96453048 AA
1 AA
96453050 GAAAATAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (37 bp):
AAATTAATTAATTAAAAGTAGGATTCATCATCGTTCC
Found at i:96464153 original size:16 final size:17
Alignment explanation
Indices: 96464130--96464168 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
96464120 ATATATAATA
*
96464130 ATAAAATTGAAAATTAT
1 ATAAAATTAAAAATTAT
96464147 A-AAAATTAAAAATTAT
1 ATAAAATTAAAAATTAT
96464163 ATAAAA
1 ATAAAA
96464169 GTAGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAATTAAAAATTAT
Found at i:96467550 original size:51 final size:51
Alignment explanation
Indices: 96467492--96467593 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
96467482 AAAGATGAAT
96467492 GTTTCTCTTTCCTTCAACAATTTCAACTATTTATACATGTATTAATCTTTG
1 GTTTCTCTTTCCTTCAACAATTTCAACTATTTATACATGTATTAATCTTTG
* *
96467543 GTTTCTCTTTCCTTCCACTATTTCAACTATTTATACATGTATTAATCTTTG
1 GTTTCTCTTTCCTTCAACAATTTCAACTATTTATACATGTATTAATCTTTG
96467594 ATTAACCTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (51 bp):
GTTTCTCTTTCCTTCAACAATTTCAACTATTTATACATGTATTAATCTTTG
Found at i:96468207 original size:14 final size:14
Alignment explanation
Indices: 96468149--96468207 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
96468139 CTTATCTATT
*
96468149 TTATTATTATGATA
1 TTATTATTATAATA
*
96468163 TGATTATTAATAATA
1 TTATTATT-ATAATA
* *
96468178 TTATTATTACATTA
1 TTATTATTATAATA
* *
96468192 TTGTTATTATAGTA
1 TTATTATTATAATA
96468206 TT
1 TT
96468208 CTTTTATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (14 bp):
TTATTATTATAATA
Found at i:96473554 original size:13 final size:13
Alignment explanation
Indices: 96473516--96473554 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
96473506 TCAAAAAAAA
*
96473516 TTTATAATTTATTT
1 TTTATAATTT-TTG
*
96473530 TTTATAAATTTTG
1 TTTATAATTTTTG
96473543 TTTATAATTTTT
1 TTTATAATTTTT
96473555 ATGTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTATAATTTTTG
Found at i:96473561 original size:20 final size:20
Alignment explanation
Indices: 96473538--96473575 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
96473528 TTTTTATAAA
96473538 TTTTGTTTA-TAATTTTTATG
1 TTTT-TTTACTAATTTTTATG
96473558 TTTTTTTACTAATTTTTA
1 TTTTTTTACTAATTTTTA
96473576 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTTTACTAATTTTTATG
Found at i:96488937 original size:2 final size:2
Alignment explanation
Indices: 96488930--96488954 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96488920 TTTAACCTAT
96488930 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
96488955 TAGTACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96489172 original size:17 final size:17
Alignment explanation
Indices: 96489134--96489172 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
96489124 TTTTCATTTT
96489134 TTTTTGAATTTTTCTAA
1 TTTTTGAATTTTTCTAA
*
96489151 CTTTTGAATTTTTCTAA
1 TTTTTGAATTTTTCTAA
96489168 TTTTT
1 TTTTT
96489173 TTTTAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTTGAATTTTTCTAA
Found at i:96490116 original size:46 final size:46
Alignment explanation
Indices: 96490049--96490146 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
96490039 TAGGTGAAGG
96490049 TGTTGTAGTTTCAAGGTTAACTTTTCGTATTGATGAGTAATGTTTT
1 TGTTGTAGTTTCAAGGTTAACTTTTCGTATTGATGAGTAATGTTTT
96490095 TGTTGTAGTTTCAAGGTTAACTTTTCGTATTGATGAGTAATGTTTT
1 TGTTGTAGTTTCAAGGTTAACTTTTCGTATTGATGAGTAATGTTTT
96490141 TGTTGT
1 TGTTGT
96490147 GTGCGCACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.51
Consensus pattern (46 bp):
TGTTGTAGTTTCAAGGTTAACTTTTCGTATTGATGAGTAATGTTTT
Found at i:96490895 original size:27 final size:27
Alignment explanation
Indices: 96490865--96490919 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
96490855 ACATCAAGAA
96490865 AGAACAACCATGTTTAAAACTAGGTCT
1 AGAACAACCATGTTTAAAACTAGGTCT
96490892 AGAACAACCATGTTTAAAACTAGGTCT
1 AGAACAACCATGTTTAAAACTAGGTCT
96490919 A
1 A
96490920 AATATCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (27 bp):
AGAACAACCATGTTTAAAACTAGGTCT
Found at i:96492680 original size:13 final size:13
Alignment explanation
Indices: 96492662--96492687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96492652 GCTTGATTTA
96492662 TCTTCTTTTTTTT
1 TCTTCTTTTTTTT
96492675 TCTTCTTTTTTTT
1 TCTTCTTTTTTTT
96492688 AGTGAAGGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTCTTTTTTTT
Found at i:96496278 original size:21 final size:21
Alignment explanation
Indices: 96496252--96496292 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
96496242 AGACAAGCGA
* *
96496252 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
96496273 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
96496293 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:96500612 original size:14 final size:14
Alignment explanation
Indices: 96500593--96500620 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
96500583 TAAAAACAAA
96500593 GTCAATGTTTATGT
1 GTCAATGTTTATGT
96500607 GTCAATGTTTATGT
1 GTCAATGTTTATGT
96500621 ATCAGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
GTCAATGTTTATGT
Found at i:96501152 original size:16 final size:18
Alignment explanation
Indices: 96501113--96501146 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96501103 TAAGTTTATA
96501113 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
96501130 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
96501147 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:96501318 original size:33 final size:33
Alignment explanation
Indices: 96501234--96501321 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
96501224 AATGCCTATA
96501234 TAAAAAAATTTAATAAATAA-A-AATATATAATTT
1 TAAAAAAA-TTAA-AAATAATATAATATATAATTT
* * *
96501267 TATTAAATATT-AATATAATATAATATA-AATATT
1 TA-AAAAAATTAAAAATAATATAATATATAAT-TT
96501300 TAAAAAAATTAAAAATAATATA
1 TAAAAAAATTAAAAATAATATA
96501322 GGTAGGCCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.11
32 11 0.25
33 24 0.55
34 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATTAAAAATAATATAATATATAATTT
Found at i:96502695 original size:27 final size:26
Alignment explanation
Indices: 96502662--96502716 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
96502652 GAATTTTGTC
96502662 AAATTTAAATACTAAATTGAACAAAAA
1 AAATTTAAATACTAAATT-AACAAAAA
*
96502689 AAATTTAAATACTAAATTAAGAAAAA
1 AAATTTAAATACTAAATTAACAAAAA
96502715 AA
1 AA
96502717 TGTCGAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (26 bp):
AAATTTAAATACTAAATTAACAAAAA
Found at i:96503041 original size:16 final size:16
Alignment explanation
Indices: 96503022--96503054 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96503012 TTAATTAAAT
96503022 AAAT-TATTAAAAATTA
1 AAATATATT-AAAATTA
96503038 AAATATATTAAAATTA
1 AAATATATTAAAATTA
96503054 A
1 A
96503055 TTTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATATTAAAATTA
Found at i:96515476 original size:146 final size:146
Alignment explanation
Indices: 96515212--96515510 Score: 517
Period size: 146 Copynumber: 2.0 Consensus size: 146
96515202 TACAAGTAGC
96515212 ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
1 ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
* * * *
96515277 TCTACCAATCATCGAATCAAGCATAAAAATTACCCACATTGCATCTACTAAAACTGAACGAATTT
66 TCTAACAATCATCAAATCAAGCATAAAAATTACCCACATTGCATCTACTAAAACCGAACAAATTT
*
96515342 AAGCTTAAAAATTCAA
131 AAGCTTAAAAACTCAA
96515358 ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
1 ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
* * **
96515423 TCTAACGATCATCAAATCAAGCATAAAAGTTACTTACATTGCATCTACTAAAACCGAACAAATTT
66 TCTAACAATCATCAAATCAAGCATAAAAATTACCCACATTGCATCTACTAAAACCGAACAAATTT
96515488 AAGCTTAAAAACTCAA
131 AAGCTTAAAAACTCAA
96515504 ATTTCCC
1 ATTTCCC
96515511 AGATCAAATT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
146 144 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (146 bp):
ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
TCTAACAATCATCAAATCAAGCATAAAAATTACCCACATTGCATCTACTAAAACCGAACAAATTT
AAGCTTAAAAACTCAA
Found at i:96522309 original size:176 final size:175
Alignment explanation
Indices: 96522014--96522504 Score: 734
Period size: 176 Copynumber: 2.8 Consensus size: 175
96522004 ATATAGATAT
* * ** * *
96522014 GTGTGTGTGTTGAAAATATCTGACATACACAAAACCAACCCAGTCTAGAGTACATCGAACTATAA
1 GTGTGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATAA
* *
96522079 AAAAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCACCTTCTTTTCTCCGCTTTAGGG
66 AAAAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGG
*
96522144 GCAAAGCATGCAGCAGATTATATATATATATGTATATGTATATAATC
131 GCAAAGCATGCAGCAGAATATATATATATATG--TATGTATATAATC
*
96522191 -TGTGTGTGTTGAAAATATCTAACACACGCAAAACCAGGCCAATCTAGA-TAACATCCAACTATA
1 GTGTGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGT-ACATCCAACTATA
* * *
96522254 ACAAAAGCCTCAATTAATATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGG
65 AAAAAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGG
* * *
96522319 GGCAAAGCATGCAGCATAATATATATATGTATGTATGTATATTATC
130 GGCAAAGCATGCAGCAGAATATATATATATATGTATGTATATAATC
* * *
96522365 TGTGTGTGTGTTGAAAATATGTAACACACACAAAATCAGGCCAATCTAGAGTACATCCAACCATA
1 -GTGTGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATA
* *
96522430 AAAAAAGCCCCAATTAGTGTAACTACTAATCTCATTTGAGTTCATCTTCTTTTCTCCACTTTAGG
65 AAAAAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGG
*
96522495 GGCCAAGCAT
130 GGCAAAGCAT
96522505 ACCTAATAGT
Statistics
Matches: 284, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
174 12 0.04
175 1 0.00
176 270 0.95
177 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (175 bp):
GTGTGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATAA
AAAAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGG
GCAAAGCATGCAGCAGAATATATATATATATGTATGTATATAATC
Found at i:96522938 original size:6 final size:6
Alignment explanation
Indices: 96522929--96522955 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
96522919 AAGGAAAAAA
96522929 AATTAG AATTAG AATTAG AATTAG AAT
1 AATTAG AATTAG AATTAG AATTAG AAT
96522956 GAATCCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
AATTAG
Found at i:96524661 original size:15 final size:16
Alignment explanation
Indices: 96524623--96524662 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
96524613 CCATCAATTC
*
96524623 TTAATTTATAGTTAAT
1 TTAATTAATAGTTAAT
96524639 TTAA-TAATAGTTAA-
1 TTAATTAATAGTTAAT
96524653 TTAATTAATA
1 TTAATTAATA
96524663 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAATTAATAGTTAAT
Found at i:96524673 original size:19 final size:18
Alignment explanation
Indices: 96524651--96524689 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
96524641 AATAATAGTT
*
96524651 AATTAATTAATAAATTAAA
1 AATTAA-TAAAAAATTAAA
*
96524670 AATTTATAAAAAATTAAA
1 AATTAATAAAAAATTAAA
96524688 AA
1 AA
96524690 ATTGATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAATAAAAAATTAAA
Found at i:96524690 original size:19 final size:19
Alignment explanation
Indices: 96524651--96524702 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
96524641 AATAATAGTT
* *
96524651 AATTAATTAATAAATTAAA
1 AATTGATTAAAAAATTAAA
*
96524670 AATTTA-TAAAAAATTAAAA
1 AATTGATTAAAAAATT-AAA
96524689 AATTGATTAAAAAA
1 AATTGATTAAAAAA
96524703 AAACCAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.29
19 13 0.46
20 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AATTGATTAAAAAATTAAA
Found at i:96525677 original size:20 final size:20
Alignment explanation
Indices: 96525636--96525677 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
96525626 ATTTTAAACA
*
96525636 TAAACAATATAAAATATATC
1 TAAACAATATAAAAAATATC
*
96525656 TAAAGAATACTAAAAAAT-TC
1 TAAACAATA-TAAAAAATATC
96525676 TA
1 TA
96525678 TATCTAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAACAATATAAAAAATATC
Found at i:96533137 original size:2 final size:2
Alignment explanation
Indices: 96533130--96533159 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
96533120 ATAGAAACAT
*
96533130 TA TA TA TA TC 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
96533160 GCTTTGCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96534047 original size:18 final size:18
Alignment explanation
Indices: 96534024--96534059 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
96534014 TTATATTCTA
96534024 AAAACCGTAATTTTATAT
1 AAAACCGTAATTTTATAT
96534042 AAAACCGTAATTTTATAT
1 AAAACCGTAATTTTATAT
96534060 GTGATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAACCGTAATTTTATAT
Found at i:96534605 original size:31 final size:31
Alignment explanation
Indices: 96534570--96534632 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
96534560 GAAACCTACC
* *
96534570 AATTCATTTACTTAAATAAAAACTTTTGAAT
1 AATTCAGTGACTTAAATAAAAACTTTTGAAT
**
96534601 AATTCAGTGACTTAAATAAAATTTTTTGAAT
1 AATTCAGTGACTTAAATAAAAACTTTTGAAT
96534632 A
1 A
96534633 GTTTAATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (31 bp):
AATTCAGTGACTTAAATAAAAACTTTTGAAT
Found at i:96538126 original size:55 final size:54
Alignment explanation
Indices: 96538037--96538167 Score: 199
Period size: 55 Copynumber: 2.4 Consensus size: 54
96538027 TTTTTTTTCA
* * * *
96538037 AAGCAAGGTTTTGGGTTCAAGTATTTGTGCGATGGTGAGGAGTTTGGTACCTTT
1 AAGCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTGAGGAGTTTGATACCTTT
* *
96538091 AAGGCAAGGTTCCGGGTTCATGTAATTGTGAGATGGTGAGGAGTTTGATACCTTT
1 AA-GCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTGAGGAGTTTGATACCTTT
96538146 AAGCAAGGTTTCGGGTTCAAGT
1 AAGCAAGGTTTCGGGTTCAAGT
96538168 GTTCTATTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 20 0.29
55 48 0.71
ACGTcount: A:0.23, C:0.11, G:0.33, T:0.34
Consensus pattern (54 bp):
AAGCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTGAGGAGTTTGATACCTTT
Found at i:96540199 original size:26 final size:26
Alignment explanation
Indices: 96540162--96540323 Score: 288
Period size: 26 Copynumber: 6.2 Consensus size: 26
96540152 TGATACAGAT
*
96540162 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
96540188 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
96540214 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
96540240 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
96540266 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
96540292 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
96540318 TGATAA
1 TGATAA
96540324 GAATATCATG
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 132 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:96547531 original size:22 final size:22
Alignment explanation
Indices: 96547489--96547531 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
96547479 TTGATTTAAT
*
96547489 TATTTAAAAATTATATTTTTAC
1 TATTTAAAAATTATATATTTAC
96547511 TATTATAAAAATTATA-ATTTA
1 TATT-TAAAAATTATATATTTA
96547532 ATTTCGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTAAAAATTATATATTTAC
Found at i:96552683 original size:13 final size:13
Alignment explanation
Indices: 96552667--96552692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96552657 TTTATTTGAA
96552667 AATTTTAAAAAAT
1 AATTTTAAAAAAT
96552680 AATTTTAAAAAAT
1 AATTTTAAAAAAT
96552693 GAAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTTTAAAAAAT
Found at i:96565721 original size:3 final size:3
Alignment explanation
Indices: 96565713--96565743 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
96565703 TTTTTAATTA
96565713 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
96565744 AAATAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:96569605 original size:2 final size:2
Alignment explanation
Indices: 96569598--96569626 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96569588 TTTTGAAATT
96569598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96569627 GTCAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96576567 original size:18 final size:18
Alignment explanation
Indices: 96576544--96576580 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
96576534 ACTATTGAAG
96576544 TAAAGTTTGATAGTAGTT
1 TAAAGTTTGATAGTAGTT
96576562 TAAAGTTTGATAGTAGTT
1 TAAAGTTTGATAGTAGTT
96576580 T
1 T
96576581 CGAGCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (18 bp):
TAAAGTTTGATAGTAGTT
Found at i:96578242 original size:6 final size:6
Alignment explanation
Indices: 96578231--96578272 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
96578221 ATCTACTTTG
96578231 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
96578273 TATCATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:96594693 original size:18 final size:17
Alignment explanation
Indices: 96594665--96594705 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
96594655 CGTTCTTCAA
*
96594665 AATTGTTATTTAATTTTTT
1 AATT-TTATTTAA-TATTT
96594684 AATTTTATTTAATATTT
1 AATTTTATTTAATATTT
96594701 AATTT
1 AATTT
96594706 AATGTCACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
AATTTTATTTAATATTT
Found at i:96594954 original size:21 final size:21
Alignment explanation
Indices: 96594904--96594954 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 21
96594894 CTCAATTTTT
96594904 ATAATTTTTTTAATATCTCTTTA
1 ATAATTTTTTTAATA--TCTTTA
* *
96594927 TTTATTTTTTATAATA-CTTTA
1 ATAATTTTTT-TAATATCTTTA
96594948 ATAATTT
1 ATAATTT
96594955 GTATTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
ATAATTTTTTTAATATCTTTA
Found at i:96595009 original size:18 final size:17
Alignment explanation
Indices: 96594986--96595034 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
96594976 TGCAATTTCT
96594986 TTTTTACAATATTTATAA
1 TTTTTACAATATTTA-AA
*
96595004 TTTTTACAACATTTAAA
1 TTTTTACAATATTTAAA
* *
96595021 ATTTTAAAATATTT
1 TTTTTACAATATTT
96595035 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTACAATATTTAAA
Found at i:96597451 original size:25 final size:27
Alignment explanation
Indices: 96597403--96597454 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
96597393 ATTAAAATTT
* *
96597403 ATAAAAATATTAAATAAAAGTAAAAAC
1 ATAAAAATATTAAAAAAAAATAAAAAC
96597430 ATAAAAA-A-TAAAAAAAAATAAAAAC
1 ATAAAAATATTAAAAAAAAATAAAAAC
96597455 CATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 1 0.04
27 7 0.30
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (27 bp):
ATAAAAATATTAAAAAAAAATAAAAAC
Found at i:96599838 original size:2 final size:2
Alignment explanation
Indices: 96599833--96599858 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
96599823 GAGAGTAGCA
96599833 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
96599859 TGATAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96614759 original size:14 final size:14
Alignment explanation
Indices: 96614736--96614769 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
96614726 TGATGTTGTG
96614736 ATAT-TACATATAT
1 ATATATACATATAT
*
96614749 TTATATACATATAT
1 ATATATACATATAT
96614763 ATATATA
1 ATATATA
96614770 TAACAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:96615262 original size:8 final size:8
Alignment explanation
Indices: 96615249--96615289 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
96615239 AAAAATTAAT
96615249 ATTTGAAA
1 ATTTGAAA
96615257 ATTTGAAA
1 ATTTGAAA
96615265 ATTTGAAA
1 ATTTGAAA
96615273 ATTTGAAA
1 ATTTGAAA
96615281 ATTTGAAA
1 ATTTGAAA
96615289 A
1 A
96615290 AGAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (8 bp):
ATTTGAAA
Found at i:96615297 original size:24 final size:24
Alignment explanation
Indices: 96615249--96615297 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
96615239 AAAAATTAAT
****
96615249 ATTTGAAAATTTGAAAATTTGAAA
1 ATTTGAAAATTTGAAAAAGAAAAA
96615273 ATTTGAAAATTTGAAAAAGAAAAA
1 ATTTGAAAATTTGAAAAAGAAAAA
96615297 A
1 A
96615298 AAACAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (24 bp):
ATTTGAAAATTTGAAAAAGAAAAA
Found at i:96618178 original size:2 final size:2
Alignment explanation
Indices: 96618171--96618199 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96618161 GATTTCCCTC
96618171 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
96618200 TTTTGGTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:96622932 original size:39 final size:39
Alignment explanation
Indices: 96622873--96622979 Score: 169
Period size: 39 Copynumber: 2.7 Consensus size: 39
96622863 ATCGTGATCT
** *
96622873 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
96622912 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
96622951 GAAGCCTGGAGGCTAACTGAAGCACATAA
1 GAAGCCCGAAGGCTAACTGAAGCACATAA
96622980 TAGCTGAACT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:96622955 original size:21 final size:21
Alignment explanation
Indices: 96622891--96622955 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
96622881 AAATCTAGCT
96622891 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** *
96622912 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
96622930 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
96622951 GAAGC
1 GAAGC
96622956 CTGGAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:96627502 original size:36 final size:36
Alignment explanation
Indices: 96627454--96627532 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
96627444 TATAATACCA
* * *
96627454 GACATAATCATATACGTCAATCATAATCTCAAGCTT
1 GACATAAGCATATACATAAATCATAATCTCAAGCTT
96627490 GACATAAGCATATACATAAATCATAATCTCAAGCTT
1 GACATAAGCATATACATAAATCATAATCTCAAGCTT
*
96627526 AACATAA
1 GACATAA
96627533 CTCATTTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (36 bp):
GACATAAGCATATACATAAATCATAATCTCAAGCTT
Found at i:96627886 original size:34 final size:34
Alignment explanation
Indices: 96627843--96627914 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
96627833 ATTCCAACCA
96627843 AACACACCAGACGCTCACACGAGTCAATCCCTCC
1 AACACACCAGACGCTCACACGAGTCAATCCCTCC
* * * *
96627877 AACACACCAGATGCTCACATGAGTTATTCCCTCC
1 AACACACCAGACGCTCACACGAGTCAATCCCTCC
96627911 AACA
1 AACA
96627915 TATCAATGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.39, G:0.11, T:0.17
Consensus pattern (34 bp):
AACACACCAGACGCTCACACGAGTCAATCCCTCC
Found at i:96627934 original size:33 final size:33
Alignment explanation
Indices: 96627843--96627983 Score: 120
Period size: 33 Copynumber: 4.2 Consensus size: 33
96627833 ATTCCAACCA
* * * *
96627843 AACACACCAGACGCTCACACGAGTCAATCCCTCC
1 AACACACCA-ATGCTCATAAGAGTTAATCCCTCC
* * *
96627877 AACACACCAGATGCTCACATGAGTTATTCCCTCC
1 AACACACCA-ATGCTCATAAGAGTTAATCCCTCC
* * **
96627911 AACATATCAATGCTCATAAGAGTTAATCCAACC
1 AACACACCAATGCTCATAAGAGTTAATCCCTCC
* * * **
96627944 AACACACCAATGTTCATAAAAGCTAATCCAACC
1 AACACACCAATGCTCATAAGAGTTAATCCCTCC
96627977 AACACAC
1 AACACAC
96627984 TAAACAGAGT
Statistics
Matches: 91, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 54 0.59
34 37 0.41
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.18
Consensus pattern (33 bp):
AACACACCAATGCTCATAAGAGTTAATCCCTCC
Found at i:96629957 original size:13 final size:13
Alignment explanation
Indices: 96629939--96629969 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
96629929 CACTACTTTA
96629939 GTTTCCAATTCAT
1 GTTTCCAATTCAT
96629952 GTTTCCAATTCAT
1 GTTTCCAATTCAT
*
96629965 ATTTC
1 GTTTC
96629970 ATTCTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (13 bp):
GTTTCCAATTCAT
Found at i:96630922 original size:3 final size:3
Alignment explanation
Indices: 96630914--96630980 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
96630904 CTCATTTCAT
*
96630914 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
96630962 TTA TTA TTA TTG TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
96630981 AACACAATTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Done.